@phdthesis{AbdAllahSalem2018,
  author    = {Abd Allah Salem, Mohamed},
  title     = {Comparative and systemic metabolomic analysis of the model plant Arabidopsis thaliana after perturbing the essential Target of Rapamycin (TOR) pathway},
  school      = {Universit{\"a}t Potsdam},
  pages     = {113},
  year      = {2018},
  language  = {en}
}
@article{AdemKueteMbavengetal.2018,
  author    = {Adem, Fozia A. and Kuete, Victor and Mbaveng, Armelle T. and Heydenreich, Matthias and Ndakala, Albert and Irungu, Beatrice and Efferth, Thomas and Yenesew, Abiy},
  title     = {Cytotoxic benzylbenzofuran derivatives from Dorstenia kameruniana},
  series = {Fitoterapia},
  volume    = {128},
  journal   = {Fitoterapia},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0367-326X},
  doi       = {10.1016/j.fitote.2018.04.019},
  pages     = {26 -- 30},
  year      = {2018},
  abstract  = {Chromatographic separation of the extract of the roots of Dorstenia kameruniana (family Moraceae) led to the isolation of three new benzylbenzofuran derivatives, 2-(p-hydroxybenzyl)benzofuran-6-ol (1), 2-(p-hydroxybenzyl)-7-methoxybenzofuran-6-ol (2) and 2-(p-hydroxy)-3-(3-methylbut-2-en-1-yl)benzyl)benzofuran-6-ol (3) (named dorsmerunin A, B and C, respectively), along with the known furanocoumarin, bergapten (4). The twigs of Dorstenia kameruniana also produced compounds 1-4 as well as the known chalcone licoagrochalcone A (5). The structures were elucidated by NMR spectroscopy and mass spectrometry. The isolated compounds displayed cytotoxicity against the sensitive CCRF-CEM and multidrug-resistant CEM/ADR5000 leukemia cells, where compounds 4 and 5 had the highest activities (IC50 values of 7.17 mu M and 5.16 mu M, respectively) against CCRF-CEM leukemia cells. Compound 5 also showed cytotoxicity against 7 sensitive or drug-resistant solid tumor cell lines (breast carcinoma, colon carcinoma, glioblastoma), with IC50 below 50 mu M, whilst 4 showed selective activity.},
  language  = {en}
}
@phdthesis{Agrawal2018,
  author    = {Agrawal, Shreya},
  title     = {Engineering the isoprenoid pathway for molecular farming and effect of tRNA(Glu) manipulation on tetrapyrrole biosynthesis},
  school      = {Universit{\"a}t Potsdam},
  pages     = {viii, 131},
  year      = {2018},
  language  = {en}
}
@phdthesis{AlFadel2018,
  author    = {Al Fadel, Frdoos},
  title     = {Influence of sphingosine 1-phosphate and its receptor modulators on the development of liver fibrosis},
  school      = {Universit{\"a}t Potsdam},
  pages     = {156},
  year      = {2018},
  language  = {en}
}
@phdthesis{Albers2018,
  author    = {Albers, Philip},
  title     = {Funktionelle Charakterisierung des bakteriellen Typ-III Effektorproteins HopZ1a in Nicotiana benthamiana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {viii, 134},
  year      = {2018},
  abstract  = {Um das Immunsystem der Pflanze zu manipulieren translozieren gram-negative pathogene Bakterien Typ-III Effektorproteine (T3E) {\"u}ber ein Typ-III Sekretionssystem (T3SS) in die pflanzliche Wirtszelle. Dort lokalisieren T3Es in verschiedenen subzellul{\"a}ren Kompartimenten, wo sie Zielproteine modifizieren und so die Infektion beg{\"u}nstigen. HopZ1a, ein T3E des Pflanzenpathogens Pseudomonas syringae pv. syringae, ist eine Acetyltransferase und lokalisiert {\"u}ber ein Myristolierungsmotiv an der Plasmamembran der Wirtszelle. Obwohl gezeigt wurde, dass HopZ1a die fr{\"u}he Signalweiterleitung an der Plasmamembran st{\"o}rt, wurde bisher kein mit der Plasmamembran assoziiertes Zielprotein f{\"u}r diesen T3E identifiziert. Um bisher unbekannte HopZ1a-Zieleproteine zu identifizieren wurde im Vorfeld dieser Arbeit eine Hefe-Zwei-Hybrid-Durchmusterung mit einer cDNA-Bibliothek aus Tabak durchgef{\"u}hrt, wobei ein nicht n{\"a}her charakterisiertes Remorin als Interaktor gefunden wurde. Bei dem Remorin handelt es sich um einen Vertreter der Gruppe 4 der Remorin-Familie, weshalb es in NbREM4 umbenannt wurde. Durch den Einsatz verschiedener Interaktionsstudien konnte demonstriert werden, dass HopZ1a mit NbREM4 in Hefe, in vitro und in planta wechselwirkt. Es wurde ferner deutlich, dass HopZ1a auf spezifische Weise mit dem konservierten C-Terminus von NbREM4 interagiert, das Remorin jedoch in vitro nicht acetyliert. Analysen mittels BiFC haben zudem ergeben, dass NbREM4 in Homodimeren an der Plasmamembran lokalisiert, wo auch die Interaktion mit HopZ1a stattfindet. Eine funktionelle Charakterisierung von NbREM4 ergab, dass das Remorin eine spezifische Rolle im Immunsystem der Pflanze einnimmt. Die transiente Expression in N. benthamiana induziert die Expression von Abwehrgenen sowie einen ver{\"a}nderten Blattph{\"a}notyp. In A. thaliana wird HopZ1a {\"u}ber das Decoy ZED1 und das R-Protein ZAR1 erkannt, was zur Ausl{\"o}sung einer starken Hypersensitiven Antwort (HR von hypersensitive response) f{\"u}hrt. Es konnte im Rahmen dieser Arbeit gezeigt werden, dass ZAR1 in N. benthamiana konserviert ist, NbREM4 jedoch nicht in der ETI als Decoy fungiert. Mit Hilfe einer Hefe-Zwei-Hybrid-Durchmusterung mit NbZAR1 als K{\"o}der konnten zwei Proteine, die Catalase CAT1 und der Protonenpumpeninteraktor PPI1, als Interaktoren von NbZAR1 identifiziert werden, welche m{\"o}glicherweise in der Regulation der HR eine Rolle spielen. Aus Voruntersuchungen war bekannt, dass NbREM4 mit weiteren, nicht n{\"a}her charakterisierten Proteinen aus Tabak interagieren k{\"o}nnte. Eine phylogenetische Einordnung hat gezeigt, dass es sich um die bekannte Immun-Kinase PBS1 sowie zwei E3-Ubiquitin-Ligasen, NbSINA1 und NbSINAL3, handelt. PBS1 interagiert mit NbREM4 an der Plasmamembran und phosphoryliert das Remorin innerhalb des intrinsisch ungeordneten N-Terminus. Mittels Massenspektrometrie konnten die Serine an Position 64 und 65 innerhalb der Aminos{\"a}uresequenz von NbREM4 als PBS1-abh{\"a}ngige Phosphorylierungsstellen identifiziert wurden. NbSINA1 und NbSINAL3 besitzen in vitro Ubiquitinierungsaktivit{\"a}t, bilden Homo- und Heterodimere und interagieren ebenfalls mit dem N-terminalen Teil von NbREM4, wobei sie das Remorin in vitro nicht ubiquitinieren. Aus den in dieser Arbeit gewonnenen Ergebnissen l{\"a}sst sich ableiten, dass der bakterielle T3E HopZ1a gezielt mit dem Tabak-Remorin NbREM4 an der Plasmamembran interagiert und {\"u}ber einen noch unbekannten Mechanismus mit dem Immunsystem der Pflanze interferiert, wobei NbREM4 m{\"o}glicherweise eine Rolle als Adapter- oder Ankerprotein zukommt, {\"u}ber welches HopZ1a mit weiteren Immunkomponenten interagiert. NbREM4 ist Teil eines gr{\"o}ßeren Immunnetzwerkes, zu welchem die bekannte Immun-Kinase PBS1 und zwei E3-Ubiquitin-Ligasen geh{\"o}ren. Mit NbREM4 konnte damit erstmalig ein membranst{\"a}ndiges Protein mit einer Funktion im Immunsystem der Pflanze als Zielprotein von HopZ1a identifiziert werden.},
  language  = {de}
}
@misc{AlbersUestuenWitzeletal.2018,
  author    = {Albers, Philip and Uestuen, Suayib and Witzel, Katja and Bornke, Frederik},
  title     = {Identification of a novel target of the bacterial effector HopZ1a},
  series = {Phytopathology},
  volume    = {108},
  journal   = {Phytopathology},
  number    = {10},
  publisher = {American Phytopathological Society},
  address   = {Saint Paul},
  issn      = {0031-949X},
  pages     = {1},
  year      = {2018},
  abstract  = {The plant pathogen Pseudomonas syringae is a gram-negative bacterium which infects a wide range of plant species including important crops plants. To suppress plant immunity and cause disease P.syringae injects type-III effector proteins (T3Es) into the plant cell cytosol. In this study, we identified a novel target of the well characterized bacterial T3E HopZ1a. HopZ1a is an acetyltransferase that was shown to disrupt vesicle transport during innate immunity by acetylating tubulin. Using a yeast-two-hybrid screen approach, we identified a REMORIN (REM) protein from tobacco as a novel HopZ1a target. HopZ1a interacts with REM at the plasma membrane (PM) as shown by split-YFP experiments. Interestingly, we found that PBS1, a well-known kinase involved in plant immunity also interacts with REM in pull-down assays, and at the PM as shown by BiFC. Furthermore, we confirmed that REM is phosphorylated by PBS1 in vitro. Overexpression of REM provokes the upregulation of defense genes and leads to disease-like phenotypes pointing to a role of REM in plant immune signaling. Further protein-protein interaction studies reveal novel REM binding partners with a possible role in plant immune signaling. Thus, REM might act as an assembly hub for an immune signaling complex targeted by HopZ1a. Taken together, this is the first report describing that a REM protein is targeted by a bacterial effector. How HopZ1a might mechanistically manipulate the plant immune system through interfering with REM function will be discussed.},
  language  = {en}
}
@article{AlbertiGonzalezPaijmansetal.2018,
  author    = {Alberti, Federica and Gonzalez, Javier and Paijmans, Johanna L. A. and Basler, Nikolas and Preick, Michaela and Henneberger, Kirstin and Trinks, Alexandra and Rabeder, Gernot and Conard, Nicholas J. and Muenzel, Susanne C. and Joger, Ulrich and Fritsch, Guido and Hildebrandt, Thomas and Hofreiter, Michael and Barlow, Axel},
  title     = {Optimized DNA sampling of ancient bones using Computed Tomography scans},
  series = {Molecular ecology resources},
  volume    = {18},
  journal   = {Molecular ecology resources},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12911},
  pages     = {1196 -- 1208},
  year      = {2018},
  abstract  = {The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99\% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.},
  language  = {en}
}
@article{AmbarliMenguellueoğluFickeletal.2018,
  author    = {Ambarli, H{\"u}seyin and Meng{\"u}ll{\"u}oğlu, Deniz and Fickel, J{\"o}rns and F{\"o}rster, Daniel W.},
  title     = {Hotel AMANO Grand Central of brown bears in southwest Asia},
  series = {PeerJ},
  volume    = {6},
  journal   = {PeerJ},
  publisher = {PeerJ Inc.},
  address   = {London},
  issn      = {2167-8359},
  doi       = {10.7717/peerj.5660},
  pages     = {18},
  year      = {2018},
  abstract  = {Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kackar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroduction in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus.},
  language  = {en}
}
@misc{AntoniettiLopezSalasPrimo2018,
  author    = {Antonietti, Markus and Lopez-Salas, Nieves and Primo, Ana},
  title     = {Adjusting the Structure and Electronic Properties of Carbons for Metal-Free Carbocatalysis of Organic Transformations},
  series = {Advanced materials},
  volume    = {31},
  journal   = {Advanced materials},
  number    = {13},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {0935-9648},
  doi       = {10.1002/adma.201805719},
  pages     = {15},
  year      = {2018},
  abstract  = {Carbon nanomaterials doped with some other lightweight elements were recently described as powerful, heterogeneous, metal-free organocatalysts, adding to their high performance in electrocatalysis. Here, recent observations in traditional catalysis are reviewed, and the underlying reaction mechanisms of the catalyzed organic transformations are explored. In some cases, these are due to specific active functional sites, but more generally the catalytic activity relates to collective properties of the conjugated nanocarbon frameworks and the electron transfer from and to the catalytic centers and substrates. It is shown that the !earnings are tightly related to those of electrocatalysis; i.e., the search for better electrocatalysts also improves chemocatalysis, and vice versa. Carbon-carbon heterojunction effects and some perspectives on future possibilities are discussed at the end.},
  language  = {en}
}
@article{AriasAndresKettnerMikietal.2018,
  author    = {Arias Andr{\´e}s, Mar{\´i}a de Jes{\´u}s and Kettner, Marie Therese and Miki, Takeshi and Grossart, Hans-Peter},
  title     = {Microplastics: New substrates for heterotrophic activity contribute to altering organic matter cycles in aquatic ecosystems},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {635},
  journal   = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0048-9697},
  doi       = {10.1016/j.scitotenv.2018.04.199},
  pages     = {1152 -- 1159},
  year      = {2018},
  abstract  = {Heterotrophic microbes with the capability to process considerable amounts of organic matter can colonize microplastic particles (MP) in aquatic ecosystems. Weather colonization of microorganisms on MP will alter ecological niche and functioning of microbial communities remains still unanswered. Therefore, we compared the functional diversity of biofilms on microplastics when incubated in three lakes in northeastern Germany differing in trophy and limnological features. For all lakes, we compared heterotrophic activities of MP biofilms with those of microorganisms in the surrounding water by using Biolog (R) EcoPlates and assessed their oxygen consumption in microcosm assays with and without MP. The present study found that the total biofilm biomass was higher in the oligo-mesotrophic and dystrophic lakes than in the eutrophic lake. In all lakes, functional diversity profiles of MP biofilms consistently differed from those in the surrounding water. However, solely in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. These results demonstrate that the functionality and hence the ecological role of MP-associated microbial communities are context-dependent, i.e. different environments lead to substantial changes in biomass build up and heterotrophic activities of MP biofilms. We propose that MP surfaces act as new niches for aquatic microorganisms and that the constantly increasing MP pollution has the potential to globally impact carbon dynamics of pelagic environments by altering heterotrophic activities. (C) 2018 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@article{AriasAndresKluemperRojasJimenezetal.2018,
  author    = {Arias-Andres, Maria and Kluemper, Uli and Rojas-Jimenez, Keilor and Grossart, Hans-Peter},
  title     = {Microplastic pollution increases gene exchange in aquatic ecosystems},
  series = {Environmental pollution},
  volume    = {237},
  journal   = {Environmental pollution},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0269-7491},
  doi       = {10.1016/j.envpol.2018.02.058},
  pages     = {253 -- 261},
  year      = {2018},
  abstract  = {Pollution by microplastics in aquatic ecosystems is accumulating at an unprecedented scale, emerging as a new surface for biofilm formation and gene exchange. In this study, we determined the permissiveness of aquatic bacteria towards a model antibiotic resistance plasmid, comparing communities that form biofilms on microplastics vs. those that are free-living. We used an exogenous and red-fluorescent E. coli donor strain to introduce the green-fluorescent broad-host-range plasmid pKJKS which encodes for trimethoprim resistance. We demonstrate an increased frequency of plasmid transfer in bacteria associated with microplastics compared to bacteria that are free-living or in natural aggregates. Moreover, comparison of communities grown on polycarbonate filters showed that increased gene exchange occurs in a broad range of phylogenetically-diverse bacteria. Our results indicate horizontal gene transfer in this habitat could distinctly affect the ecology of aquatic microbial communities on a global scale. The spread of antibiotic resistance through microplastics could also have profound consequences for the evolution of aquatic bacteria and poses a neglected hazard for human health.},
  language  = {en}
}
@misc{AriasAndresRojasJimenezGrossart2018,
  author    = {Arias-Andres, Maria and Rojas-Jimenez, Keilor and Grossart, Hans-Peter},
  title     = {Collateral effects of microplastic pollution on aquatic microorganisms},
  series = {Trends in Analytical Chemistry},
  volume    = {112},
  journal   = {Trends in Analytical Chemistry},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0165-9936},
  doi       = {10.1016/j.trac.2018.11.041},
  pages     = {234 -- 240},
  year      = {2018},
  abstract  = {Microplastics (MP) provide a unique and extensive surface for microbial colonization in aquatic ecosystems. The formation of microorganism-microplastic complexes, such as biofilms, maximizes the degradation of organic matter and horizontal gene transfer. In this context, MP affect the structure and function of microbial communities, which in turn render the physical and chemical fate of MP. This new paradigm generates challenges for microbiology, ecology, and ecotoxicology. Dispersal of MP is concomitant with that of their associated microorganisms and their mobile genetic elements, including antibiotic resistance genes, islands of pathogenicity, and diverse metabolic pathways. Functional changes in aquatic microbiomes can alter carbon metabolism and food webs, with unknown consequences on higher organisms or human microbiomes and hence health. Here, we examine a variety of effects of MP pollution from the microbial ecology perspective, whose repercussions on aquatic ecosystems begin to be unraveled. (C) 2018 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@misc{AutenriethErnstDeavilleetal.2018,
  author    = {Autenrieth, Marijke and Ernst, Anja and Deaville, Rob and Demaret, Fabien and Ijsseldijk, Lonneke L. and Siebert, Ursula and Tiedemann, Ralph},
  title     = {Putative origin and maternal relatedness of male sperm whales (Physeter macrocephalus) recently stranded in the North Sea},
  series = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde},
  volume    = {88},
  journal   = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde},
  publisher = {Elsevier},
  address   = {M{\"u}nchen},
  issn      = {1616-5047},
  doi       = {10.1016/j.mambio.2017.09.003},
  pages     = {156 -- 160},
  year      = {2018},
  abstract  = {The globally distributed sperm whale (Physeter macrocephalus) has a partly matrilineal social structure with predominant male dispersal. At the beginning of 2016, a total of 30 male sperm whales stranded in five different countries bordering the southern North Sea. It has been postulated that these individuals were on a migration route from the north to warmer temperate and tropical waters where females live in social groups. By including samples from four countries (n = 27), this event provided a unique chance to genetically investigate the maternal relatedness and the putative origin of these temporally and spatially co-occuring male sperm whales. To utilize existing genetic resources, we sequenced 422 bp of the mitochondrial control region, a molecular marker for which sperm whale data are readily available from the entire distribution range. Based on four single nucleotide polymorphisms (SNPs) within the mitochondrial control region, five matrilines could be distinguished within the stranded specimens, four of which matched published haplotypes previously described in the Atlantic. Among these male sperm whales, multiple matrilineal lineages co-occur. We analyzed the population differentiation and could show that the genetic diversity of these male sperm whales is comparable to the genetic diversity in sperm whales from the entire Atlantic Ocean. We confirm that within this stranding event, males do not comprise maternally related individuals and apparently include assemblages of individuals from different geographic regions. (c) 2017 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.},
  language  = {en}
}
@article{AutenriethHartmannLahetal.2018,
  author    = {Autenrieth, Marijke and Hartmann, Stefanie and Lah, Ljerka and Roos, Anna and Dennis, Alice B. and Tiedemann, Ralph},
  title     = {High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)},
  series = {Molecular ecology resources},
  volume    = {18},
  journal   = {Molecular ecology resources},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12932},
  pages     = {1469 -- 1481},
  year      = {2018},
  abstract  = {The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50\% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.},
  language  = {en}
}
@misc{AyllonGrimmAttingeretal.2018,
  author    = {Ayllon, Daniel and Grimm, Volker and Attinger, Sabine and Hauhs, Michael and Simmer, Clemens and Vereecken, Harry and Lischeid, Gunnar},
  title     = {Cross-disciplinary links in environmental systems science},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {622},
  journal   = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0048-9697},
  doi       = {10.1016/j.scitotenv.2017.12.007},
  pages     = {954 -- 973},
  year      = {2018},
  abstract  = {Terrestrial environmental systems are characterised by numerous feedback links between their different compartments. However, scientific research is organized into disciplines that focus on processes within the respective compartments rather than on interdisciplinary links. Major feedback mechanisms between compartments might therefore have been systematically overlooked so far. Without identifying these gaps, initiatives on future comprehensive environmental monitoring schemes and experimental platforms might fail. We performed a comprehensive overview of feedbacks between compartments currently represented in environmental sciences and explores to what degree missing links have already been acknowledged in the literature. We focused on process models as they can be regarded as repositories of scientific knowledge that compile findings of numerous single studies. In total, 118 simulation models from 23 model types were analysed. Missing processes linking different environmental compartments were identified based on a meta-review of 346 published reviews, model inter-comparison studies, and model descriptions. Eight disciplines of environmental sciences were considered and 396 linking processes were identified and ascribed to the physical, chemical or biological domain. There were significant differences between model types and scientific disciplines regarding implemented interdisciplinary links. The most wide-spread interdisciplinary links were between physical processes in meteorology, hydrology and soil science that drive or set the boundary conditions for other processes (e.g., ecological processes). In contrast, most chemical and biological processes were restricted to links within the same compartment. Integration of multiple environmental compartments and interdisciplinary knowledge was scarce in most model types. There was a strong bias of suggested future research foci and model extensions towards reinforcing existing interdisciplinary knowledge rather than to open up new interdisciplinary pathways. No clear pattern across disciplines exists with respect to suggested future research efforts. There is no evidence that environmental research would clearly converge towards more integrated approaches or towards an overarching environmental systems theory. (c) 2017 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@article{BachmannHeimbachHassenruecketal.2018,
  author    = {Bachmann, Jennifer and Heimbach, Tabea and Hassenr{\"u}ck, Christiane and Kopprio, German A. and Iversen, Morten Hvitfeldt and Grossart, Hans-Peter and G{\"a}rdes, Astrid},
  title     = {Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System},
  series = {Frontiers in microbiology},
  volume    = {9},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2018.02836},
  pages     = {13},
  year      = {2018},
  abstract  = {Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; > 3.0 mu m) and free-living (FL; 0.2-3.0 mu m) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.},
  language  = {en}
}
@misc{BalazadehMuellerRoeber2018,
  author    = {Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {A balance to death},
  series = {Nature plants},
  volume    = {4},
  journal   = {Nature plants},
  number    = {11},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2055-026X},
  doi       = {10.1038/s41477-018-0279-6},
  pages     = {863 -- 864},
  year      = {2018},
  abstract  = {Leaf senescence plays a crucial role in nutrient recovery in late-stage plant development and requires vast transcriptional reprogramming by transcription factors such as ORESARA1 (ORE1). A proteolytic mechanism is now found to control ORE1 degradation, and thus senescence, during nitrogen starvation.},
  language  = {en}
}
@article{BalintMartonSchatzetal.2018,
  author    = {Balint, Miklos and Marton, Orsolya and Schatz, Marlene and D{\"u}ring, Rolf-Alexander and Grossart, Hans-Peter},
  title     = {Proper experimental design requires randomization/balancing of molecular ecology experiments},
  series = {Ecology and evolution},
  volume    = {8},
  journal   = {Ecology and evolution},
  number    = {3},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.3687},
  pages     = {1786 -- 1793},
  year      = {2018},
  abstract  = {Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.},
  language  = {en}
}
@article{BarlowCahillHartmannetal.2018,
  author    = {Barlow, Axel and Cahill, James A. and Hartmann, Stefanie and Theunert, Christoph and Xenikoudakis, Georgios and Gonzalez-Fortes, Gloria M. and Paijmans, Johanna L. A. and Rabeder, Gernot and Frischauf, Christine and Garcia-Vazquez, Ana and Murtskhvaladze, Marine and Saarma, Urmas and Anijalg, Peeter and Skrbinsek, Tomaz and Bertorelle, Giorgio and Gasparian, Boris and Bar-Oz, Guy and Pinhasi, Ron and Slatkin, Montgomery and Dalen, Love and Shapiro, Beth and Hofreiter, Michael},
  title     = {Partial genomic survival of cave bears in living brown bears},
  series = {Nature Ecology \& Evolution},
  volume    = {2},
  journal   = {Nature Ecology \& Evolution},
  number    = {10},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2397-334X},
  doi       = {10.1038/s41559-018-0654-8},
  pages     = {1563 -- 1570},
  year      = {2018},
  abstract  = {Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4\% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.},
  language  = {en}
}
@misc{BarlowShengLaietal.2018,
  author    = {Barlow, Axel and Sheng, Gui-Lian and Lai, Xu-Long and Hofreiter, Michael and Paijmans, Johanna L. A.},
  title     = {Once lost, twice found: Combined analysis of ancient giant panda sequences characterises extinct clade},
  series = {Journal of biogeography},
  volume    = {46},
  journal   = {Journal of biogeography},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0305-0270},
  doi       = {10.1111/jbi.13486},
  pages     = {251 -- 253},
  year      = {2018},
  language  = {en}
}
@misc{BaslerFernieNikoloski2018,
  author    = {Basler, Georg and Fernie, Alisdair R. and Nikoloski, Zoran},
  title     = {Advances in metabolic flux analysis toward genome-scale profiling of higher organisms},
  series = {Bioscience reports : communications and reviews in molecular and cellular biology},
  volume    = {38},
  journal   = {Bioscience reports : communications and reviews in molecular and cellular biology},
  publisher = {Portland Press (London)},
  address   = {London},
  issn      = {0144-8463},
  doi       = {10.1042/BSR20170224},
  pages     = {11},
  year      = {2018},
  abstract  = {Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison with omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies.},
  language  = {en}
}
@article{BatistaWoodhouseGrossartetal.2018,
  author    = {Batista, A. M. M. and Woodhouse, Jason Nicholas and Grossart, Hans-Peter and Giani, A.},
  title     = {Methanogenic archaea associated to Microcystis sp. in field samples and in culture},
  series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica},
  volume    = {831},
  journal   = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica},
  number    = {1},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0018-8158},
  doi       = {10.1007/s10750-018-3655-3},
  pages     = {163 -- 172},
  year      = {2018},
  abstract  = {Cyanobacterial mass developments impact the community composition of heterotrophic microorganisms with far-reaching consequences for biogeochemical and energy cycles of freshwater ecosystems including reservoirs. Here we sought to evaluate the temporal stability of methanogenic archaea in the water column and further scrutinize their associations with cyanobacteria. Monthly samples were collected from October 2009 to December 2010 in hypereutrophic Pampulha reservoir with permanently blooming cyanobacteria, and from January to December 2011 in oligotrophic Volta Grande reservoir with only sporadic cyanobacteria incidence. The presence of archaea in cyanobacterial cultures was investigated by screening numerous strains of Microcystis spp. from these reservoirs as well as from lakes in Europe, Asia, and North-America. We consistently determined the occurrence of archaea, in particular methanogenic archaea, in both reservoirs throughout the year. However, archaea were only associated with two strains (Microcystis sp. UFMG 165 and UFMG 175) recently isolated from these reservoirs. These findings do not implicate archaea in the occurrence of methane in the epilimnion of inland waters, but rather serve to highlight the potential of microhabitats associated with particles, including phytoplankton, to shelter unique microbial communities.},
  language  = {en}
}
@article{BayerlKrausNowaketal.2018,
  author    = {Bayerl, Helmut and Kraus, Robert H. S. and Nowak, Carsten and Foerster, Daniel W. and Fickel, J{\"o}rns and K{\"u}hn, Ralph},
  title     = {Fast and cost-effective single nucleotide polymorphism (SNP) detection in the absence of a reference genome using semideep next-generation Random Amplicon Sequencing (RAMseq)},
  series = {Molecular ecology resources},
  volume    = {18},
  journal   = {Molecular ecology resources},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12717},
  pages     = {107 -- 117},
  year      = {2018},
  abstract  = {Biodiversity has suffered a dramatic global decline during the past decades, and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and on a genetic level. However, in wild species, the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article, we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in nonmodel species by semideep sequencing of random amplicons. By applying RAMseq to the Eurasian otter (Lutra lutra), we identified 238 putative SNPs after quality filtering of all candidate loci and were able to validate 32 of 77 loci tested. In a second step, we evaluated the genotyping performance of these SNP loci in noninvasive samples, one of the most challenging genotyping applications, by comparing it with genotyping results of the same faecal samples at microsatellite markers. We compared (i) polymerase chain reaction (PCR) success rate, (ii) genotyping errors and (iii) Mendelian inheritance (population parameters). SNPs produced a significantly higher PCR success rate (75.5\% vs. 65.1\%) and lower mean allelic error rate (8.8\% vs. 13.3\%) than microsatellites, but showed a higher allelic dropout rate (29.7\% vs. 19.8\%). Genotyping results showed no deviations from Mendelian inheritance in any of the SNP loci. Hence, RAMseq appears to be a valuable tool for the detection of genetic markers in nonmodel species, which is a common challenge in conservation genetic studies.},
  language  = {en}
}
@article{BeaumontWarringtonCavadinoetal.2018,
  author    = {Beaumont, Robin N. and Warrington, Nicole M. and Cavadino, Alana and Tyrrell, Jessica and Nodzenski, Michael and Horikoshi, Momoko and Geller, Frank and Myhre, Ronny and Richmond, Rebecca C. and Paternoster, Lavinia and Bradfield, Jonathan P. and Kreiner-Moller, Eskil and Huikari, Ville and Metrustry, Sarah and Lunetta, Kathryn L. and Painter, Jodie N. and Hottenga, Jouke-Jan and Allard, Catherine and Barton, Sheila J. and Espinosa, Ana and Marsh, Julie A. and Potter, Catherine and Zhang, Ge and Ang, Wei and Berry, Diane J. and Bouchard, Luigi and Das, Shikta and Hakonarson, Hakon and Heikkinen, Jani and Helgeland, Oyvind and Hocher, Berthold and Hofman, Albert and Inskip, Hazel M. and Jones, Samuel E. and Kogevinas, Manolis and Lind, Penelope A. and Marullo, Letizia and Medland, Sarah E. and Murray, Anna and Murray, Jeffrey C. and Njolstad, Pal R. and Nohr, Ellen A. and Reichetzeder, Christoph and Ring, Susan M. and Ruth, Katherine S. and Santa-Marina, Loreto and Scholtens, Denise M. and Sebert, Sylvain and Sengpiel, Verena and Tuke, Marcus A. and Vaudel, Marc and Weedon, Michael N. and Willemsen, Gonneke and Wood, Andrew R. and Yaghootkar, Hanieh and Muglia, Louis J. and Bartels, Meike and Relton, Caroline L. and Pennell, Craig E. and Chatzi, Leda and Estivill, Xavier and Holloway, John W. and Boomsma, Dorret I. and Montgomery, Grant W. and Murabito, Joanne M. and Spector, Tim D. and Power, Christine and Jarvelin, Marjo-Ritta and Bisgaard, Hans and Grant, Struan F. A. and Sorensen, Thorkild I. A. and Jaddoe, Vincent W. and Jacobsson, Bo and Melbye, Mads and McCarthy, Mark I. and Hattersley, Andrew T. and Hayes, M. Geoffrey and Frayling, Timothy M. and Hivert, Marie-France and Felix, Janine F. and Hypponen, Elina and Lowe, William L. and Evans, David M. and Lawlor, Debbie A. and Feenstra, Bjarke and Freathy, Rachel M.},
  title     = {Genome-wide association study of offspring birth weight in 86 577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics},
  series = {Human molecular genetics},
  volume    = {27},
  journal   = {Human molecular genetics},
  number    = {4},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  organization    = {Early Growth Genetics EGG},
  issn      = {0964-6906},
  doi       = {10.1093/hmg/ddx429},
  pages     = {742 -- 756},
  year      = {2018},
  abstract  = {Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86 577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother-child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B, HMGA2, SH2B3, KCNAB1, L3MBTL3, GCK, EBF1, TCF7L2, ACTL9, CYP3A7) were associated with offspring birth weight at P< 5 x 10(-8). In SEM analyses, at least 7 of the 10 associations were consistent with effects of the maternal genotype acting via the intrauterine environment, rather than via effects of shared alleles with the fetus. Variants, or correlated proxies, at many of the loci had been previously associated with adult traits, including fasting glucose (MTNR1B, GCK and TCF7L2) and sex hormone levels (CYP3A7), and one (EBF1) with gestational duration. The identified associations indicate that genetic effects on maternal glucose, cytochrome P450 activity and gestational duration, and potentially on maternal blood pressure and immune function, are relevant for fetal growth. Further characterization of these associations in mechanistic and causal analyses will enhance understanding of the potentially modifiable maternal determinants of fetal growth, with the goal of reducing the morbidity and mortality associated with low and high birth weights.},
  language  = {en}
}
@article{BeckmannKadowSchumacheretal.2018,
  author    = {Beckmann, Nadine and Kadow, Stephanie and Schumacher, Fabian and Goethert, Joachim R. and Kesper, Stefanie and Draeger, Annette and Schulz-Schaeffer, Walter J. and Wang, Jiang and Becker, Jan U. and Kramer, Melanie and Kuehn, Claudine and Kleuser, Burkhard and Becker, Katrin Anne and Gulbins, Erich and Carpinteiro, Alexander},
  title     = {Pathological manifestations of Farber disease in a new mouse model},
  series = {Biological chemistry},
  volume    = {399},
  journal   = {Biological chemistry},
  number    = {10},
  publisher = {De Gruyter},
  address   = {Berlin},
  issn      = {1431-6730},
  doi       = {10.1515/hsz-2018-0170},
  pages     = {1183 -- 1202},
  year      = {2018},
  abstract  = {Farber disease (FD) is a rare lysosomal storage disorder resulting from acid ceramidase deficiency and subsequent ceramide accumulation. No treatments are clinically available and affected patients have a severely shortened lifespan. Due to the low incidence, the pathogenesis of FD is still poorly understood. Here, we report a novel acid ceramidase mutant mouse model that enables the study of pathogenic mechanisms of FD and ceramide accumulation. Asah1(tmEx1) mice were generated by deletion of the acid ceramidase signal peptide sequence. The effects on lysosomal targeting and activity of the enzyme were assessed. Ceramide and sphingomyelin levels were quantified by liquid chromatography tandem-mass spectrometry (LC-MS/MS) and disease manifestations in several organ systems were analyzed by histology and biochemistry. We show that deletion of the signal peptide sequence disrupts lysosomal targeting and enzyme activity, resulting in ceramide and sphingomyelin accumulation. The affected mice fail to thrive and die early. Histiocytic infiltrations were observed in many tissues, as well as lung inflammation, liver fibrosis, muscular disease manifestations and mild kidney injury. Our new mouse model mirrors human FD and thus offers further insights into the pathogenesis of this disease. In the future, it may also facilitate the development of urgently needed therapies.},
  language  = {en}
}
@article{BeermannWestburyHofreiteretal.2018,
  author    = {Beermann, Jan and Westbury, Michael V. and Hofreiter, Michael and Hilgers, Leon and Deister, Fabian and Neumann, Hermann and Raupach, Michael J.},
  title     = {Cryptic species in a well-known habitat},
  series = {Scientific reports},
  volume    = {8},
  journal   = {Scientific reports},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-018-25225-x},
  pages     = {26},
  year      = {2018},
  abstract  = {Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.},
  language  = {en}
}
@article{BentsGrothSatake2018,
  author    = {Bents, Dominik and Groth, Detlef and Satake, Takashi},
  title     = {The secular trend and network effects on height of male Japanese students from 1955 to 2015},
  series = {Journal of biological and clinical anthropology},
  volume    = {74},
  journal   = {Journal of biological and clinical anthropology},
  number    = {5},
  publisher = {Schweizerbart},
  address   = {Stuttgart},
  issn      = {0003-5548},
  doi       = {10.1127/anthranz/2018/0838},
  pages     = {423 -- 429},
  year      = {2018},
  abstract  = {Introduction: Body height is influenced by biological factors such as genetics, nutrition and health, but also by the social network, and environmental and economical factors. During centuries, the Japanese society has developed on islands. This setting provides ideal natural conditions for studying the influence of social networks on human height. Material and methods: We investigated body height of male Japanese students aged 17.5 years obtained in 47 prefectures, from the Japanese school health survey of the years 1955, 1975, 1995, and 2015. Results: Japanese students increased in height from 163.23 cm in 1955 to 170.84 cm in 1995, with no further increase thereafter (170.63 cm in 2015). Students living in neighboring prefectures were similar in height. The correlation of height between neighboring prefectures ranged between r = 0.79 and r = 0.49 among first degree neighbors, between r = 0.49 and r = 0.21 among second degree neighbors and dropped to insignificance among third degree neighbors indicating psychosocial effects of the community on body height. Tall stature and short stature prefectures did not remain tall or short throughout history. Autocorrelations of height within the same prefectures decreased from the 20 years periods of 1955-1975, 1975-1995 and 1995-2015 (r = 0.52, r = 0.61, r = 0.63, respectively) to the 40 years periods of 1955-1995 and 1975-2015 (r = 0.49, r = 0.52), down to the 60 years period of 1955-2015 (r = 0.27), indicating significant volatility of height. Conclusion: Body height of 17.5 years old Japanese students increased since 1955. Body height depended on height of the neighboring prefecture, but was volatile with decreasing autocorrelation during a period of 60 years.},
  language  = {en}
}
@misc{BestZhengBorgiaetal.2018,
  author    = {Best, Robert B. and Zheng, Wenwei and Borgia, Alessandro and Buholzer, Karin and Borgia, Madeleine B. and Hofmann, Hagen and Soranno, Andrea and Nettels, Daniel and Gast, Klaus and Grishaev, Alexander and Schuler, Benjamin},
  title     = {Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water"},
  series = {Science},
  volume    = {361},
  journal   = {Science},
  number    = {6405},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {0036-8075},
  doi       = {10.1126/science.aar7101},
  pages     = {2},
  year      = {2018},
  abstract  = {Riback et al. (Reports, 13 October 2017, p. 238) used small-angle x-ray scattering (SAXS) experiments to infer a degree of compaction for unfolded proteins in water versus chemical denaturant that is highly consistent with the results from Forster resonance energy transfer (FRET) experiments. There is thus no "contradiction" between the two methods, nor evidence to support their claim that commonly used FRET fluorophores cause protein compaction.},
  language  = {en}
}
@phdthesis{Bibi2018,
  author    = {Bibi, Faysal},
  title     = {Paleoecology and evolution in the Afro-Arabian neogene},
  school      = {Universit{\"a}t Potsdam},
  year      = {2018},
  abstract  = {This cumulative habilitation thesis presents new work on the systematics, paleoecology, and evolution of antelopes and other large mammals, focusing mainly on the late Miocene to Pleistocene terrestrial fossil record of Africa and Arabia. The studies included here range from descriptions of new species to broad-scale analyses of diversification and community evolution in large mammals over millions of years. A uniting theme is the evolution, across both temporal and spatial scales, of the environments and faunas that characterize modern African savannas today. One conclusion of this work is that macroevolutionary changes in large mammals are best characterized at regional (subcontinental to continental) and long-term temporal scales. General views of evolution developed on records that are too restricted in spatial and temporal extent are likely to ascribe too much influence to local or short-lived events. While this distinction in the scale of analysis and interpretation may seem trivial, it is challenging to implement given the geographically and temporally uneven nature of the fossil record, and the difficulties of synthesizing spatially and temporally dispersed datasets. This work attempts to do just that, bringing together primary fossil discoveries from eastern Africa to Arabia, from the Miocene to the Pleistocene, and across a wide range of (mainly large mammal) taxa. The end result is support for hypotheses stressing the impact of both climatic and biotic factors on long-term faunal change, and a more geographically integrated view of evolution in the African fossil record.},
  language  = {en}
}
@article{BiterovaEsmaeeliMoghaddamTabalvandaniAlanenetal.2018,
  author    = {Biterova, Ekaterina and Esmaeeli Moghaddam Tabalvandani, Mariam and Alanen, Heli I. and Saaranen, Mirva and Ruddock, Lloyd W.},
  title     = {Structures of Angptl3 and Angptl4, modulators of triglyceride levels and coronary artery disease},
  series = {Scientific reports},
  volume    = {8},
  journal   = {Scientific reports},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-018-25237-7},
  pages     = {12},
  year      = {2018},
  abstract  = {Coronary artery disease is the most common cause of death globally and is linked to a number of risk factors including serum low density lipoprotein, high density lipoprotein, triglycerides and lipoprotein(a). Recently two proteins, angiopoietin-like protein 3 and 4, have emerged from genetic studies as being factors that significantly modulate plasma triglyceride levels and coronary artery disease. The exact function and mechanism of action of both proteins remains to be elucidated, however, mutations in these proteins results in up to 34\% reduction in coronary artery disease and inhibition of function results in reduced plasma triglyceride levels. Here we report the crystal structures of the fibrinogen-like domains of both proteins. These structures offer new insights into the reported loss of function mutations, the mechanisms of action of the proteins and open up the possibility for the rational design of low molecular weight inhibitors for intervention in coronary artery disease.},
  language  = {en}
}
@article{BizicIonescuIonescuGrossart2018,
  author    = {Bizic-Ionescu, Mina and Ionescu, Danny and Grossart, Hans-Peter},
  title     = {Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems},
  series = {Frontiers in microbiology},
  volume    = {9},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2018.02569},
  pages     = {15},
  year      = {2018},
  abstract  = {The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3-4 particles of identical source and age and further evaluated the consequences of averaging 10-1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as "the bottle-effect." In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn't change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems.},
  language  = {en}
}
@article{BochMuellerPratietal.2018,
  author    = {Boch, Steffen and M{\"u}ller, J{\"o}rg and Prati, Daniel and Fischer, Markus},
  title     = {Low-intensity management promotes bryophyte diversity in grasslands},
  series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft},
  journal   = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft},
  number    = {38},
  publisher = {Floristisch-Soziologische Arbeitsgemeinschaft},
  address   = {G{\"o}ttingen},
  issn      = {0722-494X},
  doi       = {10.14471/2018.38.014},
  pages     = {311 -- 328},
  year      = {2018},
  abstract  = {Bryophytes constitute an important and permanent component of the grassland flora and diversity in Europe. As most bryophyte species are sensitive to habitat change, their diversity is likely to decline following land-use intensification. Most previous studies on bryophyte diversity focused on specific habitats of high bryophyte diversity, such as bogs, montane grasslands, or calcareous dry grasslands. In contrast, mesic grasslands are rarely studied, although they are the most common grassland habitat in Europe. They are secondary vegetation, maintained by agricultural use and thus, are influenced by different forms of land use. We studied bryophyte species richness in three regions in Germany, in 707 plots of 16 m(2) representing different land-use types and environmental conditions. Our study is one of the few to inspect the relationships between bryophyte richness and land use across contrasting regions and using a high number of replicates. Among the managed grasslands, pastures harboured 2.5 times more bryophyte species than meadows and mown pastures. Similarly, bryophyte cover was about twice as high in fallows and pastures than in meadows and mown pastures. Among the pastures, bryophyte species richness was about three times higher in sheep grazed plots than in the ones grazed by cattle or horses. In general, bryophyte species richness and cover was more than 50\% lower in fertilized than in unfertilized plots. Moreover, the amount of suitable substrates was linked to bryophyte diversity. Species richness of bryophytes growing on stones increased with stone cover, and the one of bryophytes growing on bark and deadwood increased with larger values of woody plant species and deadwood cover. Our findings highlight the importance of low-intensity land use and high structural heterogeneity for bryophyte conservation. They also caution against an intensification of traditionally managed pastures. In the light of our results, we recommend to maintain low-intensity sheep grazing on sites with low productivity, such as slopes on shallow soils.},
  language  = {en}
}
@article{BoginHermanussenScheffler2018,
  author    = {Bogin, Barry and Hermanussen, Michael and Scheffler, Christiane},
  title     = {As tall as my peers},
  series = {Journal of biological and clinical anthropology},
  volume    = {74},
  journal   = {Journal of biological and clinical anthropology},
  number    = {5},
  publisher = {Schweizerbart},
  address   = {Stuttgart},
  issn      = {0003-5548},
  doi       = {10.1127/anthranz/2018/0828},
  pages     = {365 -- 376},
  year      = {2018},
  abstract  = {Background: We define migrants as people who move from their place of birth to a new place of residence. Migration usually is directed by "Push-Pull" factors, for example to escape from poor living conditions or to find more prosperous socio-economic conditions. Migrant children tend to assimilate quickly, and soon perceive themselves as peers within their new social networks. Differences exist between growth of first generation and second generation migrants. Methods: We review body heights and height distributions of historic and modern migrant populations to test two hypotheses: 1) that migrant and adopted children coming from lower social status localities to higher status localities adjust their height growth toward the mean of the dominant recipient social network, and 2) social dominant colonial and military migrants display growth that significantly surpasses the median height of both the conquered population and the population of origin. Our analytical framework also considered social networks. Recent publications indicate that spatial connectedness (community effects) and social competitiveness can affect human growth. Results: Migrant children and adolescents of lower social status rapidly adjust in height towards average height of their hosts, but tend to mature earlier, and are prone to overweight. The mean height of colonial/military migrants does surpass that of the conquered and origin population. Conclusion: Observations on human social networks, non-human animal strategic growth adjustments, and competitive growth processes strengthen the concept of social connectedness being involved in the regulation of human migrant growth.},
  language  = {en}
}
@article{BoginVareaHermanussenetal.2018,
  author    = {Bogin, Barry and Varea, Carlos and Hermanussen, Michael and Scheffler, Christiane},
  title     = {Human life course biology},
  series = {American journal of physical anthropology},
  volume    = {165},
  journal   = {American journal of physical anthropology},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0002-9483},
  doi       = {10.1002/ajpa.23357},
  pages     = {834 -- 854},
  year      = {2018},
  language  = {en}
}
@phdthesis{Bolius2018,
  author    = {Bolius, Sarah},
  title     = {Microbial invasions in aquatic systems - strain identity, genetic diversity and timing},
  school      = {Universit{\"a}t Potsdam},
  pages     = {154},
  year      = {2018},
  abstract  = {Biological invasions are the dispersal and following establishment of species outside their native habitat. Due to globalisation, connectivity of regions and climate changes the number of invasive species and their successful establishment is rising. The impact of these species is mostly negative, can induce community and habitat alterations, and is one main cause for biodiversity loss. This impact is particularly high and less researched in aquatic systems and microbial organisms and despite the high impact, the knowledge about overall mechanisms and specific factors affecting invasions are not fully understood. In general, the characteristics of the habitat, native community and invader determine the invasiveness. In this thesis, I aimed to provide a better understanding of aquatic invasions focusing on the invader and its traits and identity. This thesis used a set of 12 strains of the invasive cyanobacterium <i>Cylindrospermopsis raciborskii</i> to examine the effect and impact of the invaders' identity and genetic diversity. Further, the effect of timing on the invasion potential and success was determined, because aquatic systems in particular undergo seasonal fluctuations. Most studies revealed a higher invasion success with increasing genetic diversity. Here, the increase of the genetic diversity, by either strain richness or phylogenetic dissimilarity, is not firstly driving the invasion, but the strain-identity. The high variability among the strains in traits important for invasions led to the highly varying strain-specific invasion success. This success was most dependent on nitrogen uptake and efficient resource use. The lower invasion success into communities comprising further N-fixing species indicates <i>C. raciborskii</i> can use this advantage only without the presence of competitive species. The relief of grazing pressure, which is suggested to be more important in aquatic invasions, was only promoting the invasion when unselective and larger consumers were present. High abundances of unselective consumers hampered the invasion success. This indicates a more complex and temporal interplay of competitive and consumptive resistance mechanisms during the invasion process. Further, the fluctuation abundance and presence of competitors (= primary producers) and consumers (= zooplankton) in lakes can open certain 'invasion windows'. Remarkably, the composition of the resident community was also strain-specific affected and altered, independent of a high or low invasion success. Prior, this was only documented on the species level. Further, investigations on the population of invasive strains can reveal more about the invasion patterns and how multiple strain invasions change resident communities. The present dissertation emphasises the importance of invader-addition experiments with a community context and the importance of the strain-level for microbial invasions and in general, e.g. for community assemblies and the outcome of experiments. The strain-specific community changes, also after days, may explain some sudden changes in communities, which have not been explained yet. This and further knowledge may also facilitate earlier and less cost-intensive management to step in, because these species are rarely tracked until they reach a high abundance or bloom, because of their small size. Concluded for <i>C. raciborskii</i>, it shows that this species is no 'generalistic' invader and its invasion success depends more on the competitor presence than grazing pressure. This may explain its, still unknown, invasion pattern, as <i>C. raciborskii</i> is not found in all lakes of a region.},
  language  = {en}
}
@article{BollierSicardLeblondetal.2018,
  author    = {Bollier, Norbert and Sicard, Adrien and Leblond, Julie and Latrasse, David and Gonzalez, Nathalie and Gevaudant, Frederic and Benhamed, Moussa and Raynaud, Cecile and Lenhard, Michael and Chevalier, Christian and Hernould, Michel and Delmas, Frederic},
  title     = {At-MINI ZINC FINGER2 and Sl-INHIBITOR OF MERISTEM ACTIVITY, a Conserved Missing Link in the Regulation of Floral Meristem Termination in Arabidopsis and Tomato},
  series = {The plant cell},
  volume    = {30},
  journal   = {The plant cell},
  number    = {1},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {1040-4651},
  doi       = {10.1105/tpc.17.00653},
  pages     = {83 -- 100},
  year      = {2018},
  abstract  = {In angiosperms, the gynoecium is the last structure to develop within the flower due to the determinate fate of floral meristem (FM) stem cells. The maintenance of stem cell activity before its arrest at the stage called FM termination affects the number of carpels that develop. The necessary inhibition at this stage of WUSCHEL (WUS), which is responsible for stem cell maintenance, involves a two-step mechanism. Direct repression mediated by the MADS domain transcription factor AGAMOUS (AG), followed by indirect repression requiring the C2H2 zinc-finger protein KNUCKLES (KNU), allow for the complete termination of floral stem cell activity. Here, we show that Arabidopsis thaliana MINI ZINC FINGER2 (AtMIF2) and its homolog in tomato (Solanum lycopersicum), INHIBITOR OF MERISTEM ACTIVITY (SlIMA), participate in the FM termination process by functioning as adaptor proteins. AtMIF2 and SlIMA recruit AtKNU and SlKNU, respectively, to form a transcriptional repressor complex together with TOPLESS and HISTONE DEACETYLASE19. AtMIF2 and SlIMA bind to the WUS and SIWUS loci in the respective plants, leading to their repression. These results provide important insights into the molecular mechanisms governing (FM) termination and highlight the essential role of AtMIF2/SlIMA during this developmental step, which determines carpel number and therefore fruit size.},
  language  = {en}
}
@article{BragaGomezAparicioHegeretal.2018,
  author    = {Braga, Raul Renno and Gomez-Aparicio, Lorena and Heger, Tina and Simoes Vitule, Jean Ricardo and Jeschke, Jonathan M.},
  title     = {Structuring evidence for invasional meltdown},
  series = {Biological invasions : unique international journal uniting scientists in the broad field of biological invasions},
  volume    = {20},
  journal   = {Biological invasions : unique international journal uniting scientists in the broad field of biological invasions},
  number    = {4},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1387-3547},
  doi       = {10.1007/s10530-017-1582-2},
  pages     = {923 -- 936},
  year      = {2018},
  abstract  = {Negative interactions have been suggested as a major barrier for species arriving in a new habitat. More recently, positive interactions drew attention from community assembly theory and invasion science. The invasional meltdown hypothesis (IMH) introduced the idea that positive interactions among non-native species could facilitate one another's invasion, even increasing their impact upon the native community. Many studies have addressed IMH, but with contrasting results, reflecting various types of evidence on a multitude of scales. Here we use the hierarchy-of-hypotheses (HoH) approach to differentiate key aspects of IMH, organizing and linking empirical studies to sub-hypotheses of IMH. We also assess the level of empirical support for each sub-hypothesis based on the evidence reported in the studies. We identified 150 studies addressing IMH. The majority of studies support IMH, but the evidence comes from studies with different aims and questions. Supporting studies at the community or ecosystem level are currently rare. Evidence is scarce for marine habitats and vertebrates. Few sub-hypotheses are questioned by more than 50\% of the evaluated studies, indicating that non-native species do not affect each other's survival, growth, reproduction, abundance, density or biomass in reciprocal A ↔ B interactions. With the HoH for IMH presented here, we can monitor progress in empirical tests and evidences of IMH. For instance, more tests at the community and ecosystem level are needed, as these are necessary to address the core of this hypothesis.},
  language  = {en}
}
@article{BrechunArndtWoolley2018,
  author    = {Brechun, Katherine Emily and Arndt, Katja Maren and Woolley, G. Andrew},
  title     = {Selection of protein-protein interactions of desired affinities with a bandpass circuit},
  series = {Journal of molecular biology : JMB},
  volume    = {431},
  journal   = {Journal of molecular biology : JMB},
  number    = {2},
  publisher = {Elsevier},
  address   = {London},
  issn      = {0022-2836},
  doi       = {10.1016/j.jmb.2018.11.011},
  pages     = {391 -- 400},
  year      = {2018},
  abstract  = {We have developed a genetic circuit in Escherichia coli that can be used to select for protein-protein interactions of different strengths by changing antibiotic concentrations in the media. The genetic circuit links protein-protein interaction strength to beta-lactamase activity while simultaneously imposing tuneable positive and negative selection pressure for beta-lactamase activity. Cells only survive if they express interacting proteins with affinities that fall within set high- and low-pass thresholds; i.e. the circuit therefore acts as a bandpass filter for protein-protein interactions. We show that the circuit can be used to recover protein-protein interactions of desired affinity from a mixed population with a range of affinities. The circuit can also be used to select for inhibitors of protein-protein interactions of defined strength. (C) 2018 Elsevier Ltd. All rights reserved.},
  language  = {en}
}
@article{BroekerKieleCasjensetal.2018,
  author    = {Broeker, Nina K. and Kiele, Franziska and Casjens, Sherwood R. and Gilcrease, Eddie B. and Thalhammer, Anja and Koetz, Joachim},
  title     = {In Vitro Studies of Lipopolysaccharide-Mediated DNA Release of Podovirus HK620},
  series = {Viruses},
  volume    = {10},
  journal   = {Viruses},
  number    = {6},
  publisher = {Molecular Diversity Preservation International (MDPI)},
  address   = {Basel},
  issn      = {1999-4915},
  doi       = {10.3390/v10060289},
  pages     = {1 -- 15},
  year      = {2018},
  abstract  = {Gram-negative bacteria protect themselves with an outermost layer containing lipopolysaccharide (LPS). O-antigen-specific bacteriophages use tailspike proteins (TSP) to recognize and cleave the O-polysaccharide part of LPS. However, O-antigen composition and structure can be highly variable depending on the environmental conditions. It is important to understand how these changes may influence the early steps of the bacteriophage infection cycle because they can be linked to changes in host range or the occurrence of phage resistance. In this work, we have analyzed how LPS preparations in vitro trigger particle opening and DNA ejection from the E. coli podovirus HK620. Fluorescence-based monitoring of DNA release showed that HK620 phage particles in vitro ejected their genome at velocities comparable to those found for other podoviruses. Moreover, we found that HK620 irreversibly adsorbed to the LPS receptor via its TSP at restrictive low temperatures, without opening the particle but could eject its DNA at permissive temperatures. DNA ejection was solely stimulated by LPS, however, the composition of the O-antigen dictated whether the LPS receptor could start the DNA release from E. coli phage HK620 in vitro. This finding can be significant when optimizing bacteriophage mixtures for therapy, where in natural environments O-antigen structures may rapidly change.},
  language  = {en}
}
@article{BukowskiSchittkoPetermann2018,
  author    = {Bukowski, Alexandra R. and Schittko, Conrad and Petermann, Jana S.},
  title     = {The strength of negative plant-soil feedback increases from the intraspecific to the interspecific and the functional group level},
  series = {Ecology and evolution},
  volume    = {8},
  journal   = {Ecology and evolution},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.3755},
  pages     = {2280 -- 2289},
  year      = {2018},
  abstract  = {One of the processes that may play a key role in plant species coexistence and ecosystem functioning is plant-soil feedback, the effect of plants on associated soil communities and the resulting feedback on plant performance. Plant-soil feedback at the interspecific level (comparing growth on own soil with growth on soil from different species) has been studied extensively, while plant-soil feedback at the intraspecific level (comparing growth on own soil with growth on soil from different accessions within a species) has only recently gained attention. Very few studies have investigated the direction and strength of feedback among different taxonomic levels, and initial results have been inconclusive, discussing phylogeny, and morphology as possible determinants. To test our hypotheses that the strength of negative feedback on plant performance increases with increasing taxonomic level and that this relationship is explained by morphological similarities, we conducted a greenhouse experiment using species assigned to three taxonomic levels (intraspecific, interspecific, and functional group level). We measured certain fitness-related aboveground traits and used them along literature-derived traits to determine the influence of morphological similarities on the strength and direction of the feedback. We found that the average strength of negative feedback increased from the intraspecific over the interspecific to the functional group level. However, individual accessions and species differed in the direction and strength of the feedback. None of our results could be explained by morphological dissimilarities or individual traits. Synthesis. Our results indicate that negative plant-soil feedback is stronger if the involved plants belong to more distantly related species. We conclude that the taxonomic level is an important factor in the maintenance of plant coexistence with plant-soil feedback as a potential stabilizing mechanism and should be addressed explicitly in coexistence research, while the traits considered here seem to play a minor role.},
  language  = {en}
}
@article{BurschelDecovicNuberetal.2018,
  author    = {Burschel, Sabrina and Decovic, Doris Kreuzer and Nuber, Franziska and Stiller, Marie and Hofmann, Maud and Zupok, Arkadiusz and Siemiatkowska, Beata and Gorka, Michal Jakub and Leimk{\"u}hler, Silke and Friedrich, Thorsten},
  title     = {Iron-sulfur cluster carrier proteins involved in the assembly of Escherichia coli NADH},
  series = {Molecular microbiology},
  volume    = {111},
  journal   = {Molecular microbiology},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0950-382X},
  doi       = {10.1111/mmi.14137},
  pages     = {31 -- 45},
  year      = {2018},
  abstract  = {The NADH:ubiquinone oxidoreductase (respiratory complex I) is the main entry point for electrons into the Escherichia coli aerobic respiratory chain. With its sophisticated setup of 13 different subunits and 10 cofactors, it is anticipated that various chaperones are needed for its proper maturation. However, very little is known about the assembly of E. coli complex I, especially concerning the incorporation of the iron-sulfur clusters. To identify iron-sulfur cluster carrier proteins possibly involved in the process, we generated knockout strains of NfuA, BolA, YajL, Mrp, GrxD and IbaG that have been reported either to be involved in the maturation of mitochondrial complex I or to exert influence on the clusters of bacterial complex. We determined the NADH and succinate oxidase activities of membranes from the mutant strains to monitor the specificity of the individual mutations for complex I. The deletion of NfuA, BolA and Mrp led to a decreased stability and partially disturbed assembly of the complex as determined by sucrose gradient centrifugation and native PAGE. EPR spectroscopy of cytoplasmic membranes revealed that the BolA deletion results in the loss of the binuclear Fe/S cluster N1b.},
  language  = {en}
}
@misc{BalintPfenningerGrossartetal.2018,
  author    = {B{\´a}lint, Mikl{\´o}s and Pfenninger, Markus and Grossart, Hans-Peter and Taberlet, Pierre and Vellend, Mark and Leibold, Mathew A. and Englund, Goran and Bowler, Diana},
  title     = {Environmental DNA time series in ecology},
  series = {Trends in ecology \& evolution},
  volume    = {33},
  journal   = {Trends in ecology \& evolution},
  number    = {12},
  publisher = {Elsevier},
  address   = {London},
  issn      = {0169-5347},
  doi       = {10.1016/j.tree.2018.09.003},
  pages     = {945 -- 957},
  year      = {2018},
  abstract  = {Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent examples and new perspectives to highlight how environmental DNA (eDNA) is starting to provide a powerful new source of temporal data for research questions that have so far been overlooked, by helping to resolve the ecological dynamics of populations, communities, and ecosystems over hundreds to thousands of years. We give examples of hypotheses that may be addressed by temporal eDNA biodiversity data, discuss possible research directions, and outline related challenges.},
  language  = {en}
}
@article{BaerFegerFajoletal.2018,
  author    = {B{\"a}r, Ludmilla and Feger, Martina and Fajol, Abul and Klotz, Lars-Oliver and Zeng, Shufei and Lang, Florian and Hocher, Berthold and F{\"o}ller, Michael},
  title     = {Insulin suppresses the production of fibroblast growth factor 23 (FGF23)},
  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    = {22},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1800160115},
  pages     = {5804 -- 5809},
  year      = {2018},
  abstract  = {Fibroblast growth factor 23 (FGF23) is produced by bone cells and regulates renal phosphate and vitamin D metabolism, as well as causing left ventricular hypertrophy. FGF23 deficiency results in rapid aging, whereas high plasma FGF23 levels are found in several disorders, including kidney or cardiovascular diseases. Regulators of FGF23 production include parathyroid hormone (PTH), calcitriol, dietary phosphate, and inflammation. We report that insulin and insulin-like growth factor 1 (IGF1) are negative regulators of FGF23 production. In UMR106 osteoblast-like cells, insulin and IGF1 down-regulated FGF23 production by inhibiting the transcription factor forkhead box protein O1 (FOXO1) through phosphoinositide 3-kinase (PI3K)/protein kinase B (PKB)/Akt signaling. Insulin deficiency caused a surge in the serum FGF23 concentration in mice, which was reversed by administration of insulin. In women, a highly significant negative correlation between FGF23 plasma concentration and increase in plasma insulin level following an oral glucose load was found. Our results provide strong evidence that insulin/IGF1dependent PI3K/PKB/Akt/FOXO1 signaling is a powerful suppressor of FGF23 production in vitro as well as in mice and in humans.},
  language  = {en}
}
@article{BaeurleBrzezinkaAltmann2018,
  author    = {B{\"a}urle, Isabel and Brzezinka, Krzysztof and Altmann, Simone},
  title     = {BRUSHY1/TONSOKU/MGOUN3 is required for heat stress memory},
  series = {Plant Cell \& Environment},
  volume    = {42},
  journal   = {Plant Cell \& Environment},
  doi       = {10.1111/pce.13365},
  pages     = {771 -- 781},
  year      = {2018},
  abstract  = {Plants encounter biotic and abiotic stresses many times during their life cycle and this limits their productivity. Moderate heat stress (HS) primes a plant to survive higher temperatures that are lethal in the na{\"i}ve state. Once temperature stress subsides, the memory of the priming event is actively retained for several days preparing the plant to better cope with recurring HS. Recently, chromatin regulation at different levels has been implicated in HS memory. Here, we report that the chromatin protein BRUSHY1 (BRU1)/TONSOKU/MGOUN3 plays a role in the HS memory in Arabidopsis thaliana. BRU1 is also involved in transcriptional gene silencing and DNA damage repair. This corresponds with the functions of its mammalian orthologue TONSOKU-LIKE/NFΚBIL2. During HS memory, BRU1 is required to maintain sustained induction of HS memory-associated genes, whereas it is dispensable for the acquisition of thermotolerance. In summary, we report that BRU1 is required for HS memory in A. thaliana, and propose a model where BRU1 mediates the epigenetic inheritance of chromatin states across DNA replication and cell division.},
  language  = {en}
}
@article{BoernkeRocksch2018,
  author    = {B{\"o}rnke, Frederik and Rocksch, Thorsten},
  title     = {Thigmomorphogenesis},
  series = {Scientia horticulturae : an international journal sponsored by the International Society for Horticultural Science},
  volume    = {234},
  journal   = {Scientia horticulturae : an international journal sponsored by the International Society for Horticultural Science},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-4238},
  doi       = {10.1016/j.scienta.2018.02.059},
  pages     = {344 -- 353},
  year      = {2018},
  abstract  = {Controlled regulation of plant growth is a general prerequisite for the production of marketable ornamental plants. Consumers as well as retailers prefer stronger, more compact plants with greener leaves as these not only better meet a certain desired visual quality but also allow for a maximization of production per unit area as well as facilitation of packaging and transport. The same applies for the production of young vegetable plants. Special attention is paid to solid, compact and resilient plants that survive transport and planting without any problems. During the last decades plant growth control has mainly been achieved through the application of chemical plant growth regulators that generally interfere with the function of growth regulating hormones. However, there is an increasing demand to replace chemical treatments by other means such as the modulation of growth conditions, including temperature, light and fertilization. Alternatively, the application of mechanical stimulation has been shown to induce plant responses that yield some of the commercially relevant phenotypes including increased compactness, higher girth, darker leaves and a delay in flowering. The ability of plants to sense and respond to mechanical stimuli is an adaptive trait associated with increased fitness in many environmental settings. Mechanical stimulation in nature occurs e.g. through wind, rain, neighboring plants or predatory animals and induces a range of morphogenic responses that have been summarized under the term thigmomorphogenesis. We are only just about to begin to understand the molecular mechanisms underlying mechanosensing and the associated morphogenic changes in plants. However, a number of examples suggest that mechanical stimulation applied in a greenhouse setting can be used to alter plant growth in order to produce marketable plants. In this review will briefly summarize the current knowledge concerning the biological principles of thigmomorphogenesis and discuss the potential of mechanical growth regulation in commercial plant production especially with respect to organic horticulture.},
  language  = {en}
}
@phdthesis{Buehning2018,
  author    = {B{\"u}hning, Martin},
  title     = {Charakterisierung des Zusammenspiels von FeS-Cluster-Assemblierung, Molybd{\"a}nkofaktor-Biosynthese und tRNA-Thiolierung in Escherichia coli},
  school      = {Universit{\"a}t Potsdam},
  pages     = {167},
  year      = {2018},
  language  = {de}
}
@article{CardenasMolinerHontoriaetal.2018,
  author    = {Cardenas, Aura and Moliner, Ana and Hontoria, Chiquinquira and Schernthanner, Harald},
  title     = {Analysis of land-use/land-cover changes in a livestock landscape dominated by traditional silvopastoral systems},
  series = {International Journal of Remote Sensing},
  volume    = {39},
  journal   = {International Journal of Remote Sensing},
  number    = {14},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Abingdon},
  issn      = {0143-1161},
  doi       = {10.1080/01431161.2018.1463116},
  pages     = {4684 -- 4698},
  year      = {2018},
  abstract  = {Remote sensing, which is a common method to examine land-use/land-cover (LULC) changes, could be useful in the analysis of livestock ecosystem transformations. In the last two decades, before Landsat images were free, developing countries could not afford monitoring through remote sensing because of the high cost of acquiring satellite imagery and commercial software. However, Landsat time series nowadays allows the characterization of changes in vegetation across large areas over time. The aim of this study is to analyse the LULC changes affecting forest frontiers and traditional silvopastoral systems (TSPS) in a representative livestock area of Nicaragua. Nearly cloud-free Landsat scenes - a Landsat 5 Thematic Mapper (TM) scene from 1986 and a Landsat 8 Operational Land Imager (OLI) scene from 2015 - have been the data sets used in the study. A process chain following a four-step definition of the remote-sensing process was conceptually developed and implemented based onfree open source software components and by applying the random forest (RF) algorithm. A conceptual LULC classification scheme representing TSPS was developed. Although the imagery shows a heterogeneous surface cover and mixed pixels, it is possible to achieve promising classification results with the RF algorithm with out-of-the-bag (OOB) errors below 13\% for both images along with an overall accuracy level of 85.9\% for the 2015 subset and 85.2\% for the 1986 subset. The classification shows that from 1986 to 2015 (29years) the intervened secondary forest (ISF) increased 2.6 times, whereas the degraded pastures decreased by 34.5\%. The livestock landscape in Matiguas is in a state of constant transformation, but the main changes head towards the positive direction of tree-cover recovery and an increased number of areas of natural regeneration.},
  language  = {en}
}
@article{ChenPerssonGrebeetal.2018,
  author    = {Chen, Hsiang-Wen and Persson, Staffan and Grebe, Markus and McFarlane, Heather E.},
  title     = {Cellulose synthesis during cell plate assembly},
  series = {Physiologia plantarum},
  volume    = {164},
  journal   = {Physiologia plantarum},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0031-9317},
  doi       = {10.1111/ppl.12703},
  pages     = {17 -- 26},
  year      = {2018},
  abstract  = {The plant cell wall surrounds and protects the cells. To divide, plant cells must synthesize a new cell wall to separate the two daughter cells. The cell plate is a transient polysaccharide-based compartment that grows between daughter cells and gives rise to the new cell wall. Cellulose constitutes a key component of the cell wall, and mutants with defects in cellulose synthesis commonly share phenotypes with cytokinesis-defective mutants. However, despite the importance of cellulose in the cell plate and the daughter cell wall, many open questions remain regarding the timing and regulation of cellulose synthesis during cell division. These questions represent a critical gap in our knowledge of cell plate assembly, cell division and growth. Here, we review what is known about cellulose synthesis at the cell plate and in the newly formed cross-wall and pose key questions about the molecular mechanisms that govern these processes. We further provide an outlook discussing outstanding questions and possible future directions for this field of research.},
  language  = {en}
}
@article{ChenBornhorstAschner2018,
  author    = {Chen, Pan and Bornhorst, Julia and Aschner, Michael},
  title     = {Manganese metabolism in humans},
  series = {Frontiers in Bioscience-Landmark},
  volume    = {23},
  journal   = {Frontiers in Bioscience-Landmark},
  number    = {9},
  publisher = {Frontiers in Bioscience INC},
  address   = {Irvine},
  issn      = {1093-9946},
  doi       = {10.2741/4665},
  pages     = {1655 -- 1679},
  year      = {2018},
  abstract  = {Manganese (Mn) is an essential nutrient for intracellular activities; it functions as a cofactor for a variety of enzymes, including arginase, glutamine synthetase (GS), pyruvate carboxylase and Mn superoxide dismutase (Mn-SOD). Through these metalloproteins, Mn plays critically important roles in development, digestion, reproduction, antioxidant defense, energy production, immune response and regulation of neuronal activities. Mn deficiency is rare. In contrast Mn poisoning may be encountered upon overexposure to this metal. Excessive Mn tends to accumulate in the liver, pancreas, bone, kidney and brain, with the latter being the major target of Mn intoxication. Hepatic cirrhosis, polycythemia, hypermanganesemia, dystonia and Parkinsonism-like symptoms have been reported in patients with Mn poisoning. In recent years, Mn has come to the forefront of environmental concerns due to its neurotoxicity. Molecular mechanisms of Mn toxicity include oxidative stress, mitochondrial dysfunction, protein misfolding, endoplasmic reticulum (ER) stress, autophagy dysregulation, apoptosis, and disruption of other metal homeostasis. The mechanisms of Mn homeostasis are not fully understood. Here, we will address recent progress in Mn absorption, distribution and elimination across different tissues, as well as the intracellular regulation of Mn homeostasis in cells. We will conclude with recommendations for future research areas on Mn metabolism.},
  language  = {en}
}
@misc{CisekTokarzKontenisetal.2018,
  author    = {Cisek, Richard and Tokarz, Danielle and Kontenis, Lukas and Barzda, Virginijus and Steup, Martin},
  title     = {Polarimetric second harmonic generation microscopy},
  series = {Starch-Starke},
  volume    = {70},
  journal   = {Starch-Starke},
  number    = {1-2},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {0038-9056},
  doi       = {10.1002/star.201700031},
  pages     = {15},
  year      = {2018},
  abstract  = {Second harmonic generation (SHG) is a nonlinear optical process that inherently generates signal in non-centrosymmetric materials, such as starch granules, and therefore can be used for label-free imaging. Both intensity and polarization of SHG are determined by material properties that are characterized by the nonlinear susceptibility tensor, ((2)). Examination of the tensor is performed for each focal volume of the image by measuring the outgoing polarization state of the SHG signal for a set of incoming laser beam polarizations. Mapping of nonlinear properties expressed as the susceptibility ratio reveals structural features including the organization of crystalline material within a single starch granule, and the distribution of structural properties in a population of granules. Isolated granules, as well as in situ starch, can be analyzed using polarimetric SHG microscopy. Due to the fast sample preparation and short imaging times, polarimetric SHG microscopy allows for a quick assessment of starch structure and permits rapid feedback for bioengineering applications. This article presents the basics of SHG theory and microscopy applications for starch-containing materials. Quantification of ultrastructural features within individual starch granules is described. New results obtained by polarization resolved SHG microscopy of starch granules are presented for various maize genotypes revealing heterogeneity within a single starch particle and between various granules.},
  language  = {en}
}