@article{SchimkaSanterMujkicNinnemannetal.2016,
  author    = {Schimka, Selina and Santer, Svetlana and Mujkic-Ninnemann, Nina M. and Bleger, David and Hartmann, Laura and Wehle, Marko and Lipowsky, Reinhard and Santer, Mark},
  title     = {Photosensitive Peptidomimetic for Light-Controlled, Reversible DNA Compaction},
  series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  volume    = {17},
  journal   = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1525-7797},
  doi       = {10.1021/acs.biomac.6b00052},
  pages     = {1959 -- 1968},
  year      = {2016},
  abstract  = {Light-induced DNA compaction as part of nonviral gene delivery was investigated intensively in the past years, although the bridging between the artificial light switchable compacting.agents and biodompatible light insensitive compacting agents was not achieved until now. In this paper, we report on light-induced compaction and decompaction of DNA molecules in the presence of a new typeof agent, a multivalent cationic peptidomimetic molecule containing a photosensitive Azo-group as a branch (Azo-PM). Az-o-PM is synthesized using a solid-phase procedure during Which anrazoberizene unit is attached as a side chain to an Oligo(arnidoamine) backbone. We shoW, that within a-certain Tange,of concentrations and under illumination with light of appropriate-wavelengths, these cationic Molecules induce reversible DNA compaction/decompaction by photo-isomerization of the incorporated azobenzene unit between a hydrophobic trans- and 4 hydrophilic cis-conformation, as characterized by dynamic light scattering and AFM measurements. In contrast to other molecular Species used for invasive DNA compaction, such as-widely used azobenzene containing cationic surfactant (Azo-TAR, C-4-Azo-OCX-TMAB), the presented peptidomimetic agent appears to lead to different compleication/compaction mechanisms., An investigation of Ato-PM in close proximity to a DNA segment by means of a molecular dynamics simulation sustains a picture in which Azo-PM acts as a multivalent counterion, with its rather large cationic oligo(amidoamine) backbone dominating the interaction with the double helix, fine-tuned or assisted by the presence" andisomerization state of the Azo-moiety. However, due to its peptidomimetic backbone, Azo-PM should be far less toxic than photosensitive surfactants and might represent a starting point for a conscious design of photoswitchable, biocompatible vectors for gene delivery.},
  language  = {en}
}
@article{HegerBernardVerdierGessleretal.2019,
  author    = {Heger, Tina and Bernard-Verdier, Maud and Gessler, Arthur and Greenwood, Alex D. and Grossart, Hans-Peter and Hilker, Monika and Keinath, Silvia and Kowarik, Ingo and K{\"u}ffer, Christoph and Marquard, Elisabeth and Mueller, Johannes and Niemeier, Stephanie and Onandia, Gabriela and Petermann, Jana S. and Rillig, Matthias C. and Rodel, Mark-Oliver and Saul, Wolf-Christian and Schittko, Conrad and Tockner, Klement and Joshi, Jasmin Radha and Jeschke, Jonathan M.},
  title     = {Towards an Integrative, Eco-Evolutionary Understanding of Ecological Novelty: Studying and Communicating Interlinked Effects of Global Change},
  series = {Bioscience},
  volume    = {69},
  journal   = {Bioscience},
  number    = {11},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0006-3568},
  doi       = {10.1093/biosci/biz095},
  pages     = {888 -- 899},
  year      = {2019},
  abstract  = {Global change has complex eco-evolutionary consequences for organisms and ecosystems, but related concepts (e.g., novel ecosystems) do not cover their full range. Here we propose an umbrella concept of "ecological novelty" comprising (1) a site-specific and (2) an organism-centered, eco-evolutionary perspective. Under this umbrella, complementary options for studying and communicating effects of global change on organisms, ecosystems, and landscapes can be included in a toolbox. This allows researchers to address ecological novelty from different perspectives, e.g., by defining it based on (a) categorical or continuous measures, (b) reference conditions related to sites or organisms, and (c) types of human activities. We suggest striving for a descriptive, non-normative usage of the term "ecological novelty" in science. Normative evaluations and decisions about conservation policies or management are important, but require additional societal processes and engagement with multiple stakeholders.},
  language  = {en}
}
@article{KuekenSommerYanevaRoderetal.2018,
  author    = {K{\"u}ken, Anika and Sommer, Frederik and Yaneva-Roder, Liliya and Mackinder, Luke C. M. and Hoehne, Melanie and Geimer, Stefan and Jonikas, Martin C. and Schroda, Michael and Stitt, Mark and Nikoloski, Zoran and Mettler-Altmann, Tabea},
  title     = {Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts},
  series = {eLife},
  volume    = {7},
  journal   = {eLife},
  publisher = {eLife Sciences Publications},
  address   = {Cambridge},
  issn      = {2050-084X},
  doi       = {10.7554/eLife.37960},
  pages     = {23},
  year      = {2018},
  abstract  = {Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms.},
  language  = {en}
}
@article{AlshareefOtterbachAlluetal.2022,
  author    = {Alshareef, Nouf Owdah and Otterbach, Sophie L. and Allu, Annapurna Devi and Woo, Yong H. and de Werk, Tobias and Kamranfar, Iman and M{\"u}ller-R{\"o}ber, Bernd and Tester, Mark and Balazadeh, Salma and Schm{\"o}ckel, Sandra M.},
  title     = {NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis},
  series = {Scientific reports},
  volume    = {12},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Nature Research},
  address   = {Berlin},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-022-14429-x},
  pages     = {15},
  year      = {2022},
  abstract  = {Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. 'Thermomemory' is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/ CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Ara bidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like atafl, anac055 mutants show improved thermomemory, revealing a potential co-control of both NACTFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.},
  language  = {en}
}
@unpublished{AsendorpfConnerDeFruytetal.2013,
  author    = {Asendorpf, Jens B. and Conner, Mark and De Fruyt, Filip and De Houwer, Jan and Denissen, Jaap J. A. and Fiedler, Klaus and Fiedler, Susann and Funder, David C. and Kliegl, Reinhold and Nosek, Brian A. and Perugini, Marco and Roberts, Brent W. and Schmitt, Manfred and Van Aken, Marcel A. G. and Weber, Hannelore and Wicherts, Jelte M.},
  title     = {Replication is more than hitting the lottery twice},
  series = {European journal of personality},
  volume    = {27},
  journal   = {European journal of personality},
  number    = {2},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0890-2070},
  pages     = {138 -- 144},
  year      = {2013},
  abstract  = {The main goal of our target article was to provide concrete recommendations for improving the replicability of research findings. Most of the comments focus on this point. In addition, a few comments were concerned with the distinction between replicability and generalizability and the role of theory in replication. We address all comments within the conceptual structure of the target article and hope to convince readers that replication in psychological science amounts to much more than hitting the lottery twice.},
  language  = {en}
}
@article{AsendorpfConnerDeFruytetal.2013,
  author    = {Asendorpf, Jens B. and Conner, Mark and De Fruyt, Filip and De Houwer, Jan and Denissen, Jaap J. A. and Fiedler, Klaus and Fiedler, Susann and Funder, David C. and Kliegl, Reinhold and Nosek, Brian A. and Perugini, Marco and Roberts, Brent W. and Schmitt, Manfred and vanAken, Marcel A. G. and Weber, Hannelore and Wicherts, Jelte M.},
  title     = {Recommendations for increasing replicability in psychology},
  series = {European journal of personality},
  volume    = {27},
  journal   = {European journal of personality},
  number    = {2},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0890-2070},
  doi       = {10.1002/per.1919},
  pages     = {108 -- 119},
  year      = {2013},
  abstract  = {Replicability of findings is at the heart of any empirical science. The aim of this article is to move the current replicability debate in psychology towards concrete recommendations for improvement. We focus on research practices but also offer guidelines for reviewers, editors, journal management, teachers, granting institutions, and university promotion committees, highlighting some of the emerging and existing practical solutions that can facilitate implementation of these recommendations. The challenges for improving replicability in psychological science are systemic. Improvement can occur only if changes are made at many levels of practice, evaluation, and reward.},
  language  = {en}
}
@article{VencesKoehlerCrottinietal.2022,
  author    = {Vences, Miguel and K{\"o}hler, J{\"o}rn and Crottini, Angelica and Hofreiter, Michael and Hutter, Carl R. and du Preez, Louis and Preick, Michaela and Rakotoarison, Andolalao and Rancilhac, Lo{\"i}s and Raselimanana, Achille P. and Rosa, Gon{\c{c}}alo M. and Scherz, Mark D. and Glaw, Frank},
  title     = {An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar},
  series = {Vertebrate zoology},
  volume    = {72},
  journal   = {Vertebrate zoology},
  publisher = {Senckenberg Gesellschaft f{\"u}r Naturforschung},
  address   = {Frankfurt am Main},
  issn      = {1864-5755},
  doi       = {10.3897/vz.72.e78830},
  pages     = {271 -- 309},
  year      = {2022},
  abstract  = {The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4\% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar's eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar's North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d'Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy.},
  language  = {en}
}
@article{OwenMuiruriLowensteinetal.2018,
  author    = {Owen, Richard Bernhart and Muiruri, Veronica M. and Lowenstein, Tim K. and Renaut, Robin W. and Rabideaux, Nathan and Luo, Shangde and Deino, Alan L. and Sier, Mark J. and Dupont-Nivet, Guillaume and McNulty, Emma P. and Leet, Kennie and Cohen, Andrew and Campisano, Christopher and Deocampo, Daniel and Shen, Chuan-Chou and Billingsley, Anne and Mbuthia, Anthony},
  title     = {Progressive aridification in East Africa over the last half million years and implications for human evolution},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {115},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  number    = {44},
  publisher = {National Academy of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1801357115},
  pages     = {11174 -- 11179},
  year      = {2018},
  abstract  = {Evidence for Quaternary climate change in East Africa has been derived from outcrops on land and lake cores and from marine dust, leaf wax, and pollen records. These data have previously been used to evaluate the impact of climate change on hominin evolution, but correlations have proved to be difficult, given poor data continuity and the great distances between marine cores and terrestrial basins where fossil evidence is located. Here, we present continental coring evidence for progressive aridification since about 575 thousand years before present (ka), based on Lake Magadi (Kenya) sediments. This long-term drying trend was interrupted by many wet-dry cycles, with the greatest variability developing during times of high eccentricity-modulated precession. Intense aridification apparent in the Magadi record took place between 525 and 400 ka, with relatively persistent arid conditions after 350 ka and through to the present. Arid conditions in the Magadi Basin coincide with the Mid-Brunhes Event and overlap with mammalian extinctions in the South Kenya Rift between 500 and 400 ka. The 525 to 400 ka arid phase developed in the South Kenya Rift between the period when the last Acheulean tools are reported (at about 500 ka) and before the appearance of Middle Stone Age artifacts (by about 320 ka). Our data suggest that increasing Middle- to Late-Pleistocene aridification and environmental variability may have been drivers in the physical and cultural evolution of Homo sapiens in East Africa.},
  language  = {en}
}
@misc{KuekenSommerYanevaRoderetal.2018,
  author    = {K{\"u}ken, Anika and Sommer, Frederik and Yaneva-Roder, Liliya and Mackinder, Luke C.M. and H{\"o}hne, Melanie and Geimer, Stefan and Jonikas, Martin C. and Schroda, Michael and Stitt, Mark and Nikoloski, Zoran and Mettler-Altmann, Tabea},
  title     = {Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1122},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44635},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-446358},
  pages     = {25},
  year      = {2018},
  abstract  = {Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms.},
  language  = {en}
}