TY - JOUR A1 - Wutke, Saskia A1 - Sandoval-Castellanos, Edson A1 - Benecke, Norbert A1 - Döhle, Hans-Jürgen A1 - Friederich, Susanne A1 - Gonzalez, Javier A1 - Hofreiter, Michael A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Malaspinas, Anna-Sapfo A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Reissmann, Monika A1 - Trinks, Alexandra A1 - Ludwig, Arne T1 - Decline of genetic diversity in ancient domestic stallions in Europe JF - Science Advances N2 - Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times. Y1 - 2018 U6 - https://doi.org/10.1126/sciadv.aap9691 SN - 2375-2548 VL - 4 IS - 4 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Spijkerman, Elly A1 - Behrend, Hella A1 - Fach, Bettina A1 - Gaedke, Ursula T1 - Decreased phosphorus incorporation explains the negative effect of high iron concentrations in the green microalga Chlamydomonas acidophila JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - The green microalga Chlamydomonas acidophila is an important primary producer in very acidic lakes (pH 2.0-3.5), characterized by high concentrations of ferric iron (up to 1 g total Fe L-1) and low rates of primary production. It was previously suggested that these high iron concentrations result in high iron accumulation and inhibit photosynthesis in C. acidophila. To test this, the alga was grown in sterilized lake water and in medium with varying total iron concentrations under limiting and sufficient inorganic phosphorus (Pi) supply, because Pi is an important growth limiting nutrient in acidic waters. Photosynthesis and growth of C. acidophila as measured over 5 days were largely unaffected by high total iron concentrations and only decreased if free ionic Fe3+ concentrations exceeded 100 mg Fe3+ L-1. Although C. acidophila was relatively rich in iron (up to 5 mmol Fe: mol C), we found no evidence of iron toxicity. In contrast, a concentration of 260 mg total Fe L-1 (i.e. 15 mg free ionic Fe3+ L-1), which is common in many acidic lakes, reduced Pi-incorporation by 50% and will result in Pi-limited photosynthesis. The resulting Pi-limitation present at high iron and Pi concentrations was illustrated by elevated maximum Pi-uptake rates. No direct toxic effects of high iron were found, but unfavourable chemical Pi-speciation reduced growth of the acidophile alga. KW - Chlamydomonas KW - Ecotoxicology KW - Extreme environment KW - Iron toxicity KW - Phosphate limitation KW - Phytoplankton Y1 - 2018 U6 - https://doi.org/10.1016/j.scitotenv.2018.01.188 SN - 0048-9697 SN - 1879-1026 VL - 626 SP - 1342 EP - 1349 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Dittmann, Thea A1 - Heinken, Thilo A1 - Schmidt, Marcus T1 - Die Wälder von Magdeburgerforth (Fläming, Sachsen-Anhalt) T1 - The forests of Magdeburgerforth (Flaming, NE Germany) BT - eine Wiederholungsuntersuchung nach sechs Jahrzehnten BT - a resurvey study after six decades JF - Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft N2 - In einem rund 2.200 ha großen Waldgebiet bei Magdeburgerforth (Fläming, Sachsen-Anhalt) wurden 1948 bis 1950 von Harro Passarge 120 Vegetationsaufnahmen sowie eine Vegetationskartierung erstellt. Das Gebiet zeichnet sich durch eine große Vielfalt an Waldtypen aus den Verbänden Agrostio-Quercion petraeae, Alnion glutinosae, Alnion incanae, Carpinion betuli, Dicrano-Pinion und Quercion roboris aus. Daher und weil viele der heute in Wäldern wirksamen Prozesse (z. B. Stickstoffeintrag, Klimawandel) vor 60 Jahren noch nicht spürbar waren, bietet sich das Gebiet für eine Wiederholungsuntersuchung besonders an. Da die Aufnahmeflächen von Passarge nicht punktgenau verortet waren, wurden im Jahr 2014 in einem über die Forstabteilungen und die Vegetationskarte definierten Suchraum immer die der Erstaufnahme ähnlichsten Waldbestände erfasst. Insgesamt konnten 97 (81 %) der Aufnahmen wiederholt werden. Vegetationsveränderungen werden mithilfe einer NMDS-Ordination, der Gegenüberstellung von α -Diversität, Zeigerwerten und Waldbindungskategorien für die beiden Aufnahmezeitpunkte sowie über die Identifikation von Gewinner- und Verlierer-Arten analysiert. Auch wenn methodenbedingt bei der Wiederholungsuntersuchung nur die jeweils geringstmögliche Vegetationsveränderung abgebildet wird, konnten Ergebnisse erzielt werden, die mit denen quasi permanenter Plots übereinstimmen. Die beobachteten allgemeinen Trends (Eutrophierung, Sukzession nach Nutzungswandel, Verlust lichtliebender und magerkeitszeigender Arten, Ausbreitung von stickstoffliebenden Arten und mesophilen Waldarten, Einwanderung von Neophyten, keine generelle Abnahme der Artenzahl) stimmen gut mit den in zahlreichen Studien aus mitteleuropäischen Wäldern festgestellten überein. Durch das von nassen bis trockenen sowie von bodensauer-nährstoffarmen bis zu relativ basenreichen Böden reichende Standortsspektrum innerhalb des Untersuchungsgebietes konnte aber – deutlicher als in den meisten bisherigen Fallstudien – gezeigt werden, dass sich die Resilienz der Wälder gegenüber Vegetationsveränderung je nach Ausgangsgesellschaft stark unterscheidet und jeweils unterschiedliche Treiber wirksam sind. Stellario-Carpinetum und Luzulo-Quercetum erwiesen sich als relativ stabil, und auch in den Feuchtwäldern des Circaeo-Alnetum gab es trotz eines Artenwechsels wenig Hinweise auf Umweltveränderungen. Dagegen wiesen die Wälder nährstoffarmer Standorte (Sphagno-Alnetum, Betulo-Quercetum, Dicrano-Pinion) viele Verliererarten und eine starke Eutrophierungstendenz auf. Die in besonderem Maße von historischen Waldnutzungsformen abhängigen thermophilen Wälder und die Flechten-Kiefernwälder gingen weitgehend verloren. N2 - Between 1948 and 1950 the German phytosociologist Harro Passarge conducted 120 relevés in a 2,200 ha large forest area near Magdeburgerforth (Fläming, Saxony-Anhalt, NE Germany). The study area is characterized by a remarkable diversity of forest communities of the alliances Agrostio- Quercion petraeae, Alnion glutinosae, Alnion incanae, Carpinion betuli, Dicrano-Pinion and Quercion roboris. Because of this broad ecological spectrum, and because many processes which impact Central European forests today (nitrogen deposition, climate change) were not noticeable at the date of the first survey, it provides a good opportunity for a resurvey study after 60 years. As the position of Passarge’s relevés were not marked in a map, in the 2014 resurvey we sampled the most similar forest stands within a search area defined by the forest compartment and the Passarge vegetation map. In this way, 97 (81%) of the relevés could be repeated. Vegetation change was analysed by NMDS ordination and the comparison of α diversity, Ellenberg indicator values and linkage to forest habitats of species from both censuses, as well as by the identification of winner and loser species. Although, due to the methodology, only the smallest possible vegetation change was indicated, we nevertheless gained results which conform to those of resurveys based on quasi-permanent plots. The main trends (eutrophication, succession after management change, loss of plant species that are light- demanding and linked to oligotrophic sites, spread of nitrophilous and mesophilous forest species, immigration of neophytes, no general decline in species richness) are in agreement with the results of several other resurvey studies in Central and Western European forests. Because of the wide spectrum of habitats within the study area (from wet to dry, as well as from acidic and nutrient-poor to relatively base-rich) we could demonstrate more clearly than in previous studies that the resilience of forests to vegetation change differs strongly according to the initial forest type, and that different drivers of tem- poral changes are active. Mesophilous forests (Stellario-Carpinetum and Luzulo-Quercetum) turned out to be relatively stable, while Circaeo-Alnetum forests also showed few signs of environmental change despite some species turnover. In contrast, forests of nutrient-poor habitats (Sphagno-Alnetum, Betulo-Quercetum, Dicrano-Pinion) were characterized by many loser species and a strong tendency towards eutrophication. Thermophilous forests and lichen-pine forests, which are especially dependent on historical forest management techniques, largely disappeared. KW - initial site conditions KW - nitrogen deposition KW - past land use KW - quasi-permanent plots KW - vegetation change KW - winner and loser species Y1 - 2018 U6 - https://doi.org/10.14471/2018.38.009 SN - 0722-494X IS - 38 SP - 11 EP - 42 PB - Floristisch-Soziologische Arbeitsgemeinschaft CY - Göttingen ER - TY - JOUR A1 - Laux, Eva-Maria A1 - Ermilova, Elena A1 - Pannwitz, Daniel A1 - Gibbons, Jessica A1 - Hölzel, Ralph A1 - Bier, Frank Fabian T1 - Dielectric Spectroscopy of Biomolecules up to 110 GHz JF - Frequenz N2 - Radio-frequency fields in the GHz range are increasingly applied in biotechnology and medicine. In order to fully exploit both their potential and their risks detailed information about the dielectric properties of biological material is needed. For this purpose a measuring system is presented that allows the acquisition of complex dielectric spectra over 4 frequency decade up to 110 GHz. Routines for calibration and for data evaluation according to physicochemical interaction models have been developed. The frequency dependent permittivity and dielectric loss of some proteins and nucleic acids, the main classes of biomolecules, and of their sub-units have been determined. Dielectric spectra are presented for the amino acid alanine, the proteins lysozyme and haemoglobin, the nucleotides AMP and ATP, and for the plasmid pET-21, which has been produced by bacterial culture. Characterisation of a variety of biomolecules is envisaged, as is the application to studies on protein structure and function. KW - dielectric KW - spectroscopy KW - permittivity KW - protein KW - DNA KW - amino acid KW - plasmid Y1 - 2018 U6 - https://doi.org/10.1515/freq-2018-0010 SN - 0016-1136 SN - 2191-6349 VL - 72 IS - 3-4 SP - 135 EP - 140 PB - De Gruyter CY - Berlin ER - TY - JOUR A1 - Laux, Eva-Maria A1 - Bier, Frank Fabian A1 - Hölzel, Ralph T1 - Dielectrophoretic Stretching of DNA JF - DNA Nanotechnology N2 - The spatial control of DNA and of self-assembled DNA constructs is a prerequisite for the preparation of DNA-based nanostructures and microstructures and a useful tool for studies on single DNA molecules. Here we describe a protocol for the accumulation of dissolved lambda-DNA molecules between planar microelectrodes by the action of inhomogeneous radiofrequency electric fields. The resulting AC electrokinetic forces stretch the DNA molecules and align them parallel to the electric field. The electrode preparation from off-the-shelf electronic components is explained, and a detailed description of the electronic setup is given. The experimental procedure is controlled in real-time by fluorescence microscopy. KW - Alignment KW - Dielectrophoresis KW - DNA KW - Electrokinetics KW - Interdigitated electrodes KW - Stretching Y1 - 2018 SN - 978-1-4939-8582-1 SN - 978-1-4939-8581-4 U6 - https://doi.org/10.1007/978-1-4939-8582-1_14 SN - 1064-3745 SN - 1940-6029 SP - 199 EP - 208 PB - Humana Press Inc. CY - New York ET - 2 ER - TY - JOUR A1 - Weyrich, Alexandra A1 - Jeschek, Marie A1 - Schrapers, Katharina T. A1 - Lenz, Dorina A1 - Chung, Tzu Hung A1 - Ruebensam, Kathrin A1 - Yasar, Sermin A1 - Schneemann, Markus A1 - Ortmann, Sylvia A1 - Jewgenow, Katarina A1 - Fickel, Jörns T1 - Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs JF - Environmental Epigenetics N2 - Epigenetic modifications, of which DNA methylation is the most stable, are a mechanism conveying environmental information to subsequent generations via parental germ lines. The paternal contribution to adaptive processes in the offspring might be crucial, but has been widely neglected in comparison to the maternal one. To address the paternal impact on the offspring’s adaptability to changes in diet composition, we investigated if low protein diet (LPD) in F0 males caused epigenetic alterations in their subsequently sired sons. We therefore fed F0 male Wild guinea pigs with a diet lowered in protein content (LPD) and investigated DNA methylation in sons sired before and after their father’s LPD treatment in both, liver and testis tissues. Our results point to a ‘heritable epigenetic response’ of the sons to the fathers’ dietary change. Because we detected methylation changes also in the testis tissue, they are likely to be transmitted to the F2 generation. Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming (‘metabolic shift’). Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change. KW - DNA methylation KW - exposure KW - wild mammal species KW - inheritance KW - plasticity KW - adaptation Y1 - 2018 U6 - https://doi.org/10.1093/eep/dvy011 SN - 2058-5888 VL - 4 IS - 2 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Paraskevopoulou, Sofia A1 - Tiedemann, Ralph A1 - Weithoff, Guntram T1 - Differential response to heat stress among evolutionary lineages of an aquatic invertebrate species complex JF - Biology letters N2 - Under global warming scenarios, rising temperatures can constitute heat stress to which species may respond differentially. Within a described species, knowledge on cryptic diversity is of further relevance, as different lineages/cryptic species may respond differentially to environmental change. The Brachionus calyciflorus species complex (Rotifera), which was recently described using integrative taxonomy, is an essential component of aquatic ecosystems. Here, we tested the hypothesis that these (formerly cryptic) species differ in their heat tolerance. We assigned 47 clones with nuclear ITS1 (nuITS1) and mitochondrial COI (mtCOI) markers to evolutionary lineages, now named B. calyciflorus sensu stricto (s.s.) and B. fernandoi. We selected 15 representative clones and assessed their heat tolerance as a bi-dimensional phenotypic trait affected by both the intensity and duration of heat stress. We found two distinct groups, with B. calyciflorus s.s. clones having higher heat tolerance than the novel species B. fernandoi. This apparent temperature specialization among former cryptic species underscores the necessity of a sound species delimitation and assignment, when organismal responses to environmental changes are investigated. KW - Brachionus calyciflorus KW - critical thermal maximum KW - cryptic species KW - ecological speciation KW - rotifers KW - heat tolerance Y1 - 2018 U6 - https://doi.org/10.1098/rsbl.2018.0498 SN - 1744-9561 SN - 1744-957X VL - 14 IS - 11 PB - Royal Society CY - London ER - TY - JOUR A1 - Heger, Tina A1 - Nikles, Gabriele A1 - Jacobs, Brooke S. T1 - Differentiation in native as well as introduced ranges BT - germination reflects mean and variance in cover of surrounding vegetation JF - AoB PLANTS N2 - Germination, a crucial phase in the life cycle of a plant, can be significantly influenced by competition and facilitation. The aim of this study was to test whether differences in cover of surrounding vegetation can lead to population differentiation in germination behaviour of an annual grassland species, and if so, whether such a differentiation can be found in the native as well as in the introduced range. We used maternal progeny of Erodium cicutarium previously propagated under uniform conditions that had been collected in multiple populations in the native and two introduced ranges, in populations representing extremes in terms of mean and variability of the cover of surrounding vegetation. In the first experiment, we tested the effect of germination temperature and mean cover at the source site on germination, and found interlinked effects of these factors. In seeds from one of the introduced ranges (California), we found indication for a 2-fold dormancy, hindering germination at high temperatures even if physical dormancy was broken and water was available. This behaviour was less strong in high cover populations, indicating cross-generational facilitating effects of dense vegetation. In the second experiment, we tested whether spatial variation in cover of surrounding vegetation has an effect on the proportion of dormant seeds. Contrary to our expectations, we found that across source regions, high variance in cover was associated with higher proportions of seeds germinating directly after storage. In all three regions, germination seemed to match the local environment in terms of climate and vegetation cover. We suggest that this is due to a combined effect of introduction of preadapted genotypes and local evolutionary processes. KW - Bet-hedging KW - competition KW - eco-evolutionary experience KW - facilitation KW - genetic adaptation KW - physical and physiological dormancy KW - preadaptation Y1 - 2018 U6 - https://doi.org/10.1093/aobpla/ply009 SN - 2041-2851 VL - 10 IS - 1 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Olmer, Ruth A1 - Engels, Lena A1 - Usman, Abdulai A1 - Menke, Sandra A1 - Malik, Muhammad Nasir Hayat A1 - Pessler, Frank A1 - Goehring, Gudrun A1 - Bornhorst, Dorothee A1 - Bolten, Svenja A1 - Abdelilah-Seyfried, Salim A1 - Scheper, Thomas A1 - Kempf, Henning A1 - Zweigerdt, Robert A1 - Martin, Ulrich T1 - Differentiation of Human Pluripotent Stem Cells into Functional Endothelial Cells in Scalable Suspension Culture JF - Stem Cell Reports N2 - Endothelial cells (ECs) are involved in a variety of cellular responses. As multifunctional components of vascular structures, endothelial (progenitor) cells have been utilized in cellular therapies and are required as an important cellular component of engineered tissue constructs and in vitro disease models. Although primary ECs from different sources are readily isolated and expanded, cell quantity and quality in terms of functionality and karyotype stability is limited. ECs derived from human induced pluripotent stem cells (hiPSCs) represent an alternative and potentially superior cell source, but traditional culture approaches and 2D differentiation protocols hardly allow for production of large cell numbers. Aiming at the production of ECs, we have developed a robust approach for efficient endothelial differentiation of hiPSCs in scalable suspension culture. The established protocol results in relevant numbers of ECs for regenerative approaches and industrial applications that show in vitro proliferation capacity and a high degree of chromosomal stability. KW - virus infection KW - progenitor cells KW - in vitro KW - telomere dysfunction KW - cord blood KW - cardiomyogenic differentiation KW - angiogenesis KW - efficient KW - aberrations KW - expression Y1 - 2017 U6 - https://doi.org/10.1016/j.stemcr.2018.03.017 SN - 2213-6711 VL - 10 IS - 5 PB - Springer CY - New York ER - TY - JOUR A1 - Küçükgöze, Gökhan A1 - Leimkühler, Silke T1 - Direct comparison of the four aldehyde oxidase enzymes present in mouse gives insight into their substrate specificities JF - PLOS ONE N2 - Mammalian aldehyde oxidases (AOXs) are molybdo-flavoenzymes which are present in many tissues in various mammalian species, including humans and rodents. Different species contain a different number of AOX isoforms. In particular, the reasons why mammals other than humans express a multiplicity of tissue-specific AOX enzymes is unknown. In mouse, the isoforms mAOX1, mAOX3, mAOX4 and mAOX2 are present. We previously established a codon-optimized heterologous expression systems for the mAOX1-4 isoforms in Escherichia coli that gives yield to sufficient amounts of active protein for kinetic characterizations and sets the basis in this study for site-directed mutagenesis and structure-function studies. A direct and simultaneous comparison of the enzymatic properties and characteristics of the four enzymes on a larger number of substrates has never been performed. Here, thirty different structurally related aromatic, aliphatic and N-heterocyclic compounds were used as substrates, and the kinetic parameters of all four mAOX enzymes were directly compared. The results show that especially mAOX4 displays a higher substrate selectivity, while no major differences between mAOX1, mAOX2 and mAOX3 were identified. Generally, mAOX1 was the enzyme with the highest catalytic turnover for most substrates. To understand the factors that contribute to the substrate specificity of mAOX4, site-directed mutagenesis was applied to substitute amino acids in the substrate-binding funnel by the ones present in mAOX1, mAOX3, and mAOX2. An increase in activity was obtained by the amino acid exchange M1088V in the active site identified to be specific for mAOX4, to the amino acid identified in mAOX3. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0191819 SN - 1932-6203 VL - 13 IS - 1 PB - Public Library of Science CY - San Fransisco ER - TY - JOUR A1 - Liu, Hsiang-chin A1 - Lämke, Jörn A1 - Lin, Siou-ying A1 - Hung, Meng-Ju A1 - Liu, Kuan-Ming A1 - Charng, Yee-yung A1 - Bäurle, Isabel T1 - Distinct heat shock factors and chromatin modifications mediate the organ-autonomous transcriptional memory of heat stress JF - The plant journal N2 - Plants can be primed by a stress cue to mount a faster or stronger activation of defense mechanisms upon subsequent stress. A crucial component of such stress priming is the modified reactivation of genes upon recurring stress; however, the underlying mechanisms of this are poorly understood. Here, we report that dozens of Arabidopsis thaliana genes display transcriptional memory, i.e. stronger upregulation after a recurring heat stress, that lasts for at least 3 days. We define a set of transcription factors involved in this memory response and show that the transcriptional memory results in enhanced transcriptional activation within minutes of the onset of a heat stress cue. Further, we show that the transcriptional memory is active in all tissues. It may last for up to a week, and is associated during this time with histone H3 lysine 4 hypermethylation. This transcriptional memory is cis-encoded, as we identify a promoter fragment that confers memory onto a heterologous gene. In summary, heat-induced transcriptional memory is a widespread and sustained response, and our study provides a framework for future mechanistic studies of somatic stress memory in higher plants. KW - epigenetics KW - priming KW - heat stress KW - H3K4 methylation KW - transcriptional memory KW - Arabidopsis thaliana KW - HSF Y1 - 2018 U6 - https://doi.org/10.1111/tpj.13958 SN - 0960-7412 SN - 1365-313X VL - 95 IS - 3 SP - 401 EP - 413 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Kolora, Sree Rohit Raj A1 - Weigert, Anne A1 - Saffari, Amin A1 - Kehr, Stephanie A1 - Walter Costa, Maria Beatriz A1 - Spröer, Cathrin A1 - Indrischek, Henrike A1 - Chintalapati, Manjusha A1 - Lohse, Konrad A1 - Doose, Gero A1 - Overmann, Jörg A1 - Bunk, Boyke A1 - Bleidorn, Christoph A1 - Grimm-Seyfarth, Annegret A1 - Henle, Klaus A1 - Nowick, Katja A1 - Faria, Rui A1 - Stadler, Peter F. A1 - Schlegel, Martin T1 - Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation JF - GigaScience N2 - Background Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. Findings Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. Conclusion The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids. KW - sister species KW - PacBio and Illumina KW - de novo hybrid assembly KW - transcripts KW - noncoding RNA KW - zinc fingers KW - positive selection KW - UV response KW - inversions KW - gene flow Y1 - 2018 U6 - https://doi.org/10.1093/gigascience/giy160 SN - 2047-217X VL - 8 IS - 2 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Van den Wyngaert, Silke A1 - Rojas-Jimenez, Keilor A1 - Seto, Kensuke A1 - Kagami, Maiko A1 - Grossart, Hans-Peter T1 - Diversity and Hidden Host Specificity of Chytrids Infecting Colonial Volvocacean Algae JF - Journal of Eukaryotic Microbiology N2 - Chytrids are zoosporic fungi that play an important, but yet understudied, ecological role in aquatic ecosystems. Many chytrid species have been morphologically described as parasites on phytoplankton. However, the majority of them have rarely been isolated and lack DNA sequence data. In this study we isolated and cultivated three parasitic chytrids, infecting a common volvocacean host species, Yamagishiella unicocca. To identify the chytrids, we characterized morphology and life cycle, and analyzed phylogenetic relationships based on 18S and 28S rDNA genes. Host range and specificity of the chytrids was determined by cross-infection assays with host strains, characterized by rbcL and ITS markers. We were able to confirm the identity of two chytrid strains as Endocoenobium eudorinae Ingold and Dangeardia mamillata Schroder and described the third chytrid strain as Algomyces stechlinensis gen. et sp. nov. The three chytrids were assigned to novel and phylogenetically distant clades within the phylum Chytridiomycota, each exhibiting different host specificities. By integrating morphological and molecular data of both the parasitic chytrids and their respective host species, we unveiled cryptic host-parasite associations. This study highlights that a high prevalence of (pseudo)cryptic diversity requires molecular characterization of both phytoplankton host and parasitic chytrid to accurately identify and compare host range and specificity, and to study phytoplankton-chytrid interactions in general. KW - Chytridiomycota KW - Dangeardia mamillata KW - Endocoenobium eudorinae KW - fungal parasites KW - life cycle KW - phytoplankton Y1 - 2018 U6 - https://doi.org/10.1111/jeu.12632 SN - 1066-5234 SN - 1550-7408 VL - 65 IS - 6 SP - 870 EP - 881 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Pereus, D. A1 - Otieno, J. N. A1 - Ghorbani, Abdolbaset A1 - Kocyan, Alexander A1 - Hilonga, S. A1 - de Boer, H. J. T1 - Diversity of Hypoxis species used in ethnomedicine in Tanzania JF - South African journal of botany : an international interdisciplinary journal for botanical sciences N2 - The corms of different Hypoxis species (Hypoxidaceae) are used for the treatment and management of a variety of human ailments and disorders in African traditional medicine. However, the used corms are morphologically similar and it is not known whether this has resulted in different species being harvested, prescribed and sold as the same species. Ethnomedicinal information regarding its use in Tanzania is scanty and the available ethnobotanical information about the plants is mostly from various studies done outside Tanzania. The objective of the study was to document the diverse uses of Hypoxis in Tanzania and study what species are used and whether preferences exist for specific species. Focus group discussions and in depth interviews with informants were done in 15 regions of Tanzania to document local uses of Hypoxis species and collect vouchers for identification. Traditional practitioners use Hypoxis to manage a variety of human illness in Tanzania, and appear to use different species indiscriminately for medicine, socio-cultural applications and for food. Medicinal uses include treatment of benign prostate hypertrophy, cancer, diabetes, gout, headache, HIV/AIDS, infertility, ringworms, stomachache, and urinary tract infections. In Tanzania, different Hypoxis species are used indiscriminately for a range of sociocultural and medicinal purposes. The reported medicinal uses could aid testing and evaluation of traditional herbal medicine and more research is needed to test their pharmacological effects. (C) 2018 SAAB. Published by Elsevier B.V. All rights reserved. KW - Corms KW - Ethnobotany KW - Hypoxis KW - Tanzania KW - Traditional medicine Y1 - 2018 U6 - https://doi.org/10.1016/j.sajb.2018.03.004 SN - 0254-6299 SN - 1727-9321 VL - 122 SP - 336 EP - 341 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Reverey, Florian A1 - Ganzert, Lars A1 - Lischeid, Gunnar A1 - Ulrich, Andreas A1 - Premke, Katrin A1 - Grossart, Hans-Peter T1 - Dry-wet cycles of kettle hole sediments leave a microbial and biogeochemical legacy JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Understanding interrelations between an environment's hydrological past and its current biogeochemistry is necessary for the assessment of biogeochemical and microbial responses to changing hydrological conditions. The question how previous dry-wet events determine the contemporary microbial and biogeochemical state is addressed in this study. Therefore, sediments exposed to the atmosphere of areas with a different hydrological past within one kettle hole, i.e. (1) the predominantly inundated pond center, (2) the pond margin frequently desiccated for longer periods and (3) an intermediate zone, were incubated with the same rewetting treatment. Physicochemical and textural characteristics were related to structural microbial parameters regarding carbon and nitrogen turnover, i.e. abundance of bacteria and fungi, denitrifiers (targeted by the nirK und nirS functional genes) and nitrate ammonifiers (targeted by the nrfA functional gene). Our study reveals that, in combination with varying sediment texture, the hydrological history creates distinct microbial habitats with defined boundary conditions within the kettle hole, mainly driven by redox conditions, pH and organic matter (OM) composition. OM mineralization, as indicated by CO2-outgassing, was most efficient in exposed sediments with a less stable hydrological past. The potential for nitrogen retention via nitrate ammonification was highest in the hydrologically rather stable pond center, counteracting nitrogen loss due to denitrification. Therefore, the degree of hydrological stability is an important factor leaving a microbial and biogeochemical legacy, which determines carbon and nitrogen losses from small lentic freshwater systems in the long term run. KW - Desiccation KW - DNRA KW - Denitrifiers KW - Organic matter mineralization KW - Carbon KW - Nitrogen Y1 - 2018 U6 - https://doi.org/10.1016/j.scitotenv.2018.01.220 SN - 0048-9697 SN - 1879-1026 VL - 627 SP - 985 EP - 996 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Eisold, Ursula A1 - Sellrie, Frank A1 - Memczak, Henry A1 - Andersson, Anika A1 - Schenk, Jörg A. A1 - Kumke, Michael Uwe T1 - Dye tool box for a fluorescence enhancement immunoassay JF - Bioconjugate chemistry N2 - Immunochemical analytical methods are very successful in clinical diagnostics and are nowadays also emerging in the control of food as well as monitoring of environmental issues. Among the different immunoassays, luminescence based formats are characterized by their outstanding sensitivity making this format especially attractive for future applications. The need for multiparameter detection capabilities calls for a tool box of dye labels in order to transduce the biochemical reaction into an optically detectable signal. Here, in a multiparameter approach each analyte may be detected by a different dye with a unique emission color (covering the blue to red spectral range) or a unique luminescence decay kinetics. In the case of a competitive immunoassay format for each of the different dye labels an individual antibody would be needed. In the present paper a slightly modified approach is presented using a 7-aminocoumarin unit as the basic antigen against which highly specific antibodies were generated. Leaving the epitope region in the dyes unchanged but introducing a side group in positon 3 of the coumarin system allowed us to tune the optical properties of the coumarin dyes without the necessity of new antibody generation. Upon modification of the parent coumarin unit the full spectral range from blue to deep red was accessed. In the manuscript the photophysical characterization of the coumarin derivatives and their corresponding immunocomplexes with two highly specific antibodies is presented. The coumarin dyes and their immunocomplexes were characterized by steady-state and time-resolved absorption as well as emission spectroscopy. Moreover, fluorescence depolarization measurements were carried out to complement the data stressing the different binding modes of the two antibodies. The binding modes were evaluated using the photophysics of 7-aminocoumarins and how it was affected in the respective immunocomplexes, namely, the formation of the intramolecular charge transfer (ICT) as well as the twisted intramolecular charge transfer (TICT). In contrast to other antibody-dye pairs reported a distinct fluorescence enhancement upon formation of the antibody-dye complex up to a factor of SO was found. Because of the easy emission color tuning by tailoring the coumarin substitution for the antigen binding in nonrelevant position 3 of the parent molecule, a dye tool box is on hand which can be used in the construction of competitive multiparameter fluorescence enhancement immunoassays (FenIA). Y1 - 2018 U6 - https://doi.org/10.1021/acs.bioconjchem.7b00731 SN - 1043-1802 VL - 29 IS - 1 SP - 203 EP - 214 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Malinova, Irina A1 - Mahto, Harendra A1 - Brandt, Felix A1 - AL-Rawi, Shadha A1 - Qasim, Hadeel A1 - Brust, Henrike A1 - Hejazi, Mahdi A1 - Fettke, Jörg T1 - EARLY STARVATION1 specifically affects the phosphorylation action of starch-related dikinases JF - The plant journal N2 - Starch phosphorylation by starch-related dikinases glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD) is a key step in starch degradation. Little information is known about the precise structure of the glucan substrate utilized by the dikinases and about the mechanisms by which these structures may be influenced. A 50-kDa starch-binding protein named EARLY STARVATION1 (ESV1) was analyzed regarding its impact on starch phosphorylation. In various invitro assays, the influences of the recombinant protein ESV1 on the actions of GWD and PWD on the surfaces of native starch granules were analyzed. In addition, we included starches from various sources as well as truncated forms of GWD. ESV1 preferentially binds to highly ordered, -glucans, such as starch and crystalline maltodextrins. Furthermore, ESV1 specifically influences the action of GWD and PWD at the starch granule surface. Starch phosphorylation by GWD is decreased in the presence of ESV1, whereas the action of PWD increases in the presence of ESV1. The unique alterations observed in starch phosphorylation by the two dikinases are discussed in regard to altered glucan structures at the starch granule surface. KW - Arabidopsis thaliana KW - EARLY STARVATION1 KW - glucan KW - phosphoglucan KW - starch granule surface KW - starch phosphorylation KW - water dikinase Y1 - 2018 U6 - https://doi.org/10.1111/tpj.13937 SN - 0960-7412 SN - 1365-313X VL - 95 IS - 1 SP - 126 EP - 137 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Müller, Jörg A1 - Boch, Steffen A1 - Prati, Daniel A1 - Socher, Stephanie A. A1 - Pommer, Ulf A1 - Hessenmöller, Dominik A1 - Schall, Peter A1 - Schulze, Ernst Detlef A1 - Fischer, Markus T1 - Effects of forest management on bryophyte species richness in Central European forests JF - Forest ecology and management N2 - We studied the effect of three major forest management types (unmanaged beech, selection beech, and age class forests) and stand variables (SMId, soil pH, proportion of conifers, litter cover, deadwood cover, rock cover and cumulative cover of woody trees and shrubs) on bryophyte species richness in 1050 forest plots in three regions in Germany. In addition, we analysed the species richness of four ecological guilds of bryophytes according to their colonized substrates (deadwood, rock, soil, bark) and the number of woodland indicator bryophyte species. Beech selection forests turned out to be the most species rich management type, whereas unmanaged beech forests revealed even lower species numbers than age-class forests. Increasing conifer proportion increased bryophyte species richness but not the number of woodland indicator bryophyte species. The richness of the four ecological guilds mainly responded to the abundance of their respective substrate. We conclude that the permanent availability of suitable substrates is most important for bryophyte species richness in forests, which is not stringently linked to management type. Therefore, managed age-class forests and selection forests may even exceed unmanaged forests in bryophyte species richness due to higher substrate supply and therefore represent important habitats for bryophytes. Typical woodland indicator bryophytes and their species richness were negatively affected by SMId (management intensity) and therefore better indicate forest integrity than the species richness of all bryophytes. Nature conservation efforts should focus on the reduction of management intensity. Moreover, maintaining and increasing a variability of substrates and habitats, such as coarse woody debris, increasing structural heterogeneity by retaining patches with groups of old, mature to over-mature trees in managed forests, maintaining forest climate conditions by silvicultural methods that assure stand continuity, e.g. by selection cutting rather than clear cutting and shelterwood logging might promote bryophyte diversity and in particular the one of woodland indicator bryophytes. KW - Beech forests KW - Conifer plantations KW - Cryptogams KW - Ecological guilds KW - Forest management KW - Temperate forests KW - Selection vs. age-class forests KW - Unmanaged vs. managed forests KW - Woodland indicator species Y1 - 2018 U6 - https://doi.org/10.1016/j.foreco.2018.10.019 SN - 0378-1127 SN - 1872-7042 VL - 432 SP - 850 EP - 859 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Küken, Anika A1 - Sommer, Frederik A1 - Yaneva-Roder, Liliya A1 - Mackinder, Luke C. M. A1 - Hoehne, Melanie A1 - Geimer, Stefan A1 - Jonikas, Martin C. A1 - Schroda, Michael A1 - Stitt, Mark A1 - Nikoloski, Zoran A1 - Mettler-Altmann, Tabea T1 - Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts JF - eLife N2 - Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms. Y1 - 2018 U6 - https://doi.org/10.7554/eLife.37960 SN - 2050-084X VL - 7 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Nagel, Rebecca A1 - Kirschbaum, Frank A1 - Hofmann, Volker A1 - Engelmann, Jacob A1 - Tiedemann, Ralph T1 - Electric pulse characteristics can enable species recognition in African weakly electric fish species JF - Scientific Reports N2 - Communication is key to a wide variety of animal behaviours and multiple modalities are often involved in this exchange of information from sender to receiver. The communication of African weakly electric fish, however, is thought to be predominantly unimodal and is mediated by their electric sense, in which species-specific electric organ discharges (EODs) are generated in a context-dependent and thus variable sequence of pulse intervals (SPI). While the primary function of the electric sense is considered to be electrolocation, both of its components likely carry information regarding identity of the sender. However, a clear understanding of their contribution to species recognition is incomplete. We therefore analysed these two electrocommunication components (EOD waveform and SPI statistics) in two sympatric mormyrid Campylomormyrus species. In a set of five playback conditions, we further investigated which components may drive interspecific recognition and discrimination. While we found that both electrocommunication components are species-specific, the cues necessary for species recognition differ between the two species studied. While the EOD waveform and SPI were both necessary and sufficient for species recognition in C. compressirostris males, C. tamandua males apparently utilize other, non-electric modalities. Mapped onto a recent phylogeny, our results suggest that discrimination by electric cues alone may be an apomorphic trait evolved during a recent radiation in this taxon. KW - Dwelling Atlantic Mollies KW - Organ Discharge Patterns KW - Mormyrid Fish KW - Pollimyrus-Isidori KW - Acoustic-Signals KW - Sexual Selection KW - Phylogenetic-Relationships KW - Hypopomus-Occidentalis KW - Convergent Evolution KW - Poecili-Mexicana Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-29132-z SN - 2045-2322 VL - 8 SP - 1 EP - 12 PB - Nature Publishing Group CY - London ER -