@misc{YokoyamaLeimkuehler2015, author = {Yokoyama, Kenichi and Leimk{\"u}hler, Silke}, title = {The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria}, series = {Biochimica et biophysica acta : Molecular cell research}, volume = {1853}, journal = {Biochimica et biophysica acta : Molecular cell research}, number = {6}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-4889}, doi = {10.1016/j.bbamcr.2014.09.021}, pages = {1335 -- 1349}, year = {2015}, abstract = {The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{IshidaNozakiGrossartetal.2015, author = {Ishida, Seiji and Nozaki, Daiki and Grossart, Hans-Peter and Kagami, Maiko}, title = {Novel basal, fungal lineages from freshwater phytoplankton and lake samples}, series = {Environmental microbiology reports}, volume = {7}, journal = {Environmental microbiology reports}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.12268}, pages = {435 -- 441}, year = {2015}, abstract = {Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems.}, language = {en} } @article{DiGiacomoDiGiacomoKligeretal.2015, author = {Di Giacomo, Adrian S. and Di Giacomo, Alejandro G. and Kliger, Rafi and Reboreda, Juan C. and Tiedemann, Ralph and Mahler, Bettina}, title = {No evidence of genetic variation in microsatellite and mitochondrial DNA markers among remaining populations of the Strange-tailed Tyrant Alectrurus risora, an endangered grassland species}, series = {Bird conservation international}, volume = {25}, journal = {Bird conservation international}, number = {2}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {0959-2709}, doi = {10.1017/S0959270914000203}, pages = {127 -- 138}, year = {2015}, abstract = {The Strange-tailed Tyrant Alectrurus risora (Aves: Tyrannidae) is an endemic species of southern South American grasslands that suffered a 90\% reduction of its original distribution due to habitat transformation. This has led the species to be classified as globally Vulnerable. By the beginning of the last century, populations were partially migratory and moved south during the breeding season. Currently, the main breeding population inhabits the Ibera wetlands in the province of Corrientes, north-east Argentina, where it is resident all year round. There are two remaining small populations in the province of Formosa, north-east Argentina, and in southern Paraguay, which are separated from the main population by the Parana-Paraguay River and its continuous riverine forest habitat. The populations of Corrientes and Formosa are separated by 300 km and the grasslands between populations are non-continuous due to habitat transformation. We used mtDNA sequences and eight microsatellite loci to test if there were evidences of genetic isolation between Argentinean populations. We found no evidence of genetic structure between populations (Phi(ST) = 0.004, P = 0.32; Fst = 0.01, P = 0.06), which can be explained by either retained ancestral polymorphism or by dispersal between populations. We found no evidence for a recent demographic bottleneck in nuclear loci. Our results indicate that these populations could be managed as a single conservation unit on a regional scale. Conservation actions should be focused on preserving the remaining network of areas with natural grasslands to guarantee reproduction, dispersal and prevent further decline of populations.}, language = {en} } @article{CuiLvChenetal.2015, author = {Cui, Xiao and Lv, Yang and Chen, Miaolin and Nikoloski, Zoran and Twell, David and Zhang, Dabing}, title = {Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome}, series = {Molecular plant}, volume = {8}, journal = {Molecular plant}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1016/j.molp.2014.12.008}, pages = {935 -- 945}, year = {2015}, abstract = {The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens.}, language = {en} } @article{SeifertWeithoffVos2015, author = {Seifert, Linda I. and Weithoff, Guntram and Vos, Matthijs}, title = {Extreme heat changes post-heat wave community reassembly}, series = {Ecology and evolution}, volume = {5}, journal = {Ecology and evolution}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.1490}, pages = {2140 -- 2148}, year = {2015}, abstract = {Climate forecasts project further increases in extremely high-temperature events. These present threats to biodiversity, as they promote population declines and local species extinctions. This implies that ecological communities will need to rely more strongly on recovery processes, such as recolonization from a meta-community context. It is poorly understood how differences in extreme event intensity change the outcome of subsequent community reassembly and if such extremes modify the biotic environment in ways that would prevent the successful re-establishment of lost species. We studied replicated aquatic communities consisting of algae and herbivorous rotifers in a design that involved a control and two different heat wave intensity treatments (29 degrees C and 39 degrees C). Animal species that suffered heat-induced extinction were subsequently re-introduced at the same time and density, in each of the two treatments. The 39 degrees C treatment led to community closure in all replicates, meaning that a previously successful herbivore species could not re-establish itself in the postheat wave community. In contrast, such closure never occurred after a 29 degrees C event. Heat wave intensity determined the number of herbivore extinctions and strongly affected algal relative abundances. Re-introduced herbivore species were thus confronted with significantly different food environments. This ecological legacy generated by heat wave intensity led to differences in the failure or success of herbivore species re-introductions. Reassembly was significantly more variable, and hence less predictable, after an extreme heat wave, and was more canalized after a moderate one. Our results pertain to relatively simple communities, but they suggest that ecological legacies introduced by extremely high-temperature events may change subsequent ecological recovery and even prevent the successful re-establishment of lost species. Knowing the processes promoting and preventing ecological recovery is crucial to the success of species re-introduction programs and to our ability to restore ecosystems damaged by environmental extremes.}, language = {en} } @article{ThieleGrimm2015, author = {Thiele, Jan C. and Grimm, Volker}, title = {Replicating and breaking models: good for you and good for ecology}, series = {Oikos}, volume = {124}, journal = {Oikos}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.02170}, pages = {691 -- 696}, year = {2015}, abstract = {There are two major limitations to the potential of computational models in ecology for producing general insights: their design is path-dependent, reflecting different underlying questions, assumptions, and data, and there is too little robustness analysis exploring where the model mechanisms explaining certain observations break down. We here argue that both limitations could be overcome if modellers in ecology would more often replicate existing models, try to break the models, and explore modifications. Replication comprises the re-implementation of an existing model and the replication of its results. Breaking models means to identify under what conditions the mechanisms represented in a model can no longer explain observed phenomena. The benefits of replication include less effort being spent to enter the iterative stage of model development and having more time for systematic robustness analysis. A culture of replication would lead to increased credibility, coherence and efficiency of computational modelling and thereby facilitate theory development.}, language = {en} } @article{ManningGossnerBossdorfetal.2015, author = {Manning, Pete and Gossner, Martin M. and Bossdorf, Oliver and Allan, Eric and Zhang, Yuan-Ye and Prati, Daniel and Bl{\"u}thgen, Nico and Boch, Steffen and B{\"o}hm, Stefan and B{\"o}rschig, Carmen and H{\"o}lzel, Norbert and Jung, Kirsten and Klaus, Valentin H. and Klein, Alexandra-Maria and Kleinebecker, Till and Krauss, Jochen and Lange, Markus and M{\"u}ller, J{\"o}rg and Pasalic, Esther and Socher, Stephanie A. and Tschapka, Marco and T{\"u}rke, Manfred and Weiner, Christiane and Werner, Michael and Gockel, Sonja and Hemp, Andreas and Renner, Swen C. and Wells, Konstans and Buscot, Francois and Kalko, Elisabeth K. V. and Linsenmair, Karl Eduard and Weisser, Wolfgang W. and Fischer, Markus}, title = {Grassland management intensification weakens the associations among the diversities of multiple plant and animal taxa}, series = {Ecology : a publication of the Ecological Society of America}, volume = {96}, journal = {Ecology : a publication of the Ecological Society of America}, number = {6}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, doi = {10.1890/14-1307.1}, pages = {1492 -- 1501}, year = {2015}, abstract = {Land-use intensification is a key driver of biodiversity change. However, little is known about how it alters relationships between the diversities of different taxonomic groups, which are often correlated due to shared environmental drivers and trophic interactions. Using data from 150 grassland sites, we examined how land-use intensification (increased fertilization, higher livestock densities, and increased mowing frequency) altered correlations between the species richness of 15 plant, invertebrate, and vertebrate taxa. We found that 54\% of pairwise correlations between taxonomic groups were significant and positive among all grasslands, while only one was negative. Higher land-use intensity substantially weakened these correlations(35\% decrease in rand 43\% fewer significant pairwise correlations at high intensity), a pattern which may emerge as a result of biodiversity declines and the breakdown of specialized relationships in these conditions. Nevertheless, some groups (Coleoptera, Heteroptera, Hymenoptera and Orthoptera) were consistently correlated with multidiversity, an aggregate measure of total biodiversity comprised of the standardized diversities of multiple taxa, at both high and lowland-use intensity. The form of intensification was also important; increased fertilization and mowing frequency typically weakened plant-plant and plant-primary consumer correlations, whereas grazing intensification did not. This may reflect decreased habitat heterogeneity under mowing and fertilization and increased habitat heterogeneity under grazing. While these results urge caution in using certain taxonomic groups to monitor impacts of agricultural management on biodiversity, they also suggest that the diversities of some groups are reasonably robust indicators of total biodiversity across a range of conditions.}, language = {en} } @article{YildirimSemerciBenayahuAdamovskietal.2015, author = {Yildirim-Semerci, Cigdem and Benayahu, Dafna and Adamovski, Miriam and Wollenberger, Ursula}, title = {An Electrochemical Assay for Monitoring Differentiation of the Osteoblastic Cell Line (MBA-15) on the Sensor Chip}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {27}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, number = {6}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201400684}, pages = {1350 -- 1358}, year = {2015}, abstract = {An electrochemical assay for the indication of the activity of the cell bound differentiation marker alkaline phosphatase (ALP) is proposed using voltammetry on an in-vitro cell culture. The basis of the assay is cultivation of cells on gold microelectrodes in wells of a microplate, catalytic hydrolysis of p-aminophenyl phosphate by ALP and indication of p-aminophenol oxidation by square wave voltammetry (SWV) with the sensors onto which the cells attached. The morphology of the bone marrow stromal cell line (MBA-15) on the electrode surface was investigated and it exhibited in vitro osteogenic characteristics. Since ALP is expressed on the cell surface in early differentiation stage of osteoblastic cells, its activity was followed after different culture times over a period of 144 h by recording repetitive voltammograms at different time points upon addition of the substrate p-aminophenyl phosphate. The ALP activity was estimated from the signal increase related to formation rate of p-aminophenol and the number of cells. The highest value was measured at 120 h, when the cells reached confluence. The results of the electrochemical activity assay are consistent with the colorimetric acquired value from p-nitrophenol formation rate.}, language = {en} } @article{GraefBatsiosMeyer2015, author = {Gr{\"a}f, Ralph and Batsios, Petros and Meyer, Irene}, title = {Evolution of centrosomes and the nuclear lamina: Amoebozoan assets}, series = {European journal of cell biology}, volume = {94}, journal = {European journal of cell biology}, number = {6}, publisher = {Elsevier}, address = {Jena}, issn = {0171-9335}, doi = {10.1016/j.ejcb.2015.04.004}, pages = {249 -- 256}, year = {2015}, abstract = {The current eukaryotic tree of life groups most eukaryotes into one of five supergroups, the Opisthokonta, Amoebozoa, Archaeplastida, Excavata and SAR (Stramenopile, Alveolata, Rhizaria). Molecular and comparative morphological analyses revealed that the last eukaryotic common ancestor (LECA) already contained a rather sophisticated equipment of organelles including a mitochondrion, an endomembrane system, a nucleus with a lamina, a microtubule-organizing center (MTOC), and a flagellar apparatus. Recent studies of MTOCs, basal bodies/centrioles, and nuclear envelope organization of organisms in different supergroups have clarified our picture of how the nucleus and MTOCs co-evolved from LECA to extant eukaryotes. In this review we summarize these findings with special emphasis on valuable contributions of research on a lamin-like protein, nuclear envelope proteins, and the MTOC in the amoebozoan model organism Dictyostelium discoideum. (C) 2015 Elsevier GmbH. All rights reserved.}, language = {en} } @article{CamargodosReisRiccardiTeixeiraRibeiroetal.2015, author = {Camargo, Rodolfo Gonzalez and dos Reis Riccardi, Daniela Mendes and Teixeira Ribeiro, Henrique Quintas and Carnevali Junior, Luiz Carlos and de Matos-Neto, Emidio Marques and Enjiu, Lucas and Neves, Rodrigo Xavier and Carola Correia Lima, Joanna Darck and Figueredo, Raquel Galvao and Martins de Alcantara, Paulo Sergio and Maximiano, Linda and Otoch, Jose and Batista Jr., Miguel Luiz and P{\"u}schel, Gerhard Paul and Seelaender, Marilia}, title = {NF-kappa Bp65 and Expression of Its Pro-Inflammatory Target Genes Are Upregulated in the Subcutaneous Adipose Tissue of Cachectic Cancer Patients}, series = {Nutrients}, volume = {7}, journal = {Nutrients}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2072-6643}, doi = {10.3390/nu7064465}, pages = {4465 -- 4479}, year = {2015}, abstract = {Cancer cachexia, of which the most notable symptom is severe and rapid weight loss, is present in the majority of patients with advanced cancer. Inflammatory mediators play an important role in the development of cachexia, envisaged as a chronic inflammatory syndrome. The white adipose tissue (WAT) is one of the first compartments affected in cancer cachexia and suffers a high rate of lipolysis. It secretes several cytokines capable of directly regulating intermediate metabolism. A common pathway in the regulation of the expression of pro-inflammatory cytokines in WAT is the activation of the nuclear transcription factor kappa-B (NF-B). We have examined the gene expression of the subunits NF-Bp65 and NF-Bp50, as well as NF-Bp65 and NF-Bp50 binding, the gene expression of pro-inflammatory mediators under NF-B control (IL-1, IL-6, INF-, TNF-, MCP-1), and its inhibitory protein, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IB-). The observational study involved 35 patients (control group, n = 12 and cancer group, n = 23, further divided into cachectic and non-cachectic). NF-Bp65 and its target genes expression (TNF-, IL-1, MCP-1 and IB-) were significantly higher in cachectic cancer patients. Moreover, NF-Bp65 gene expression correlated positively with the expression of its target genes. The results strongly suggest that the NF-B pathway plays a role in the promotion of WAT inflammation during cachexia.}, language = {en} } @inproceedings{HankeGogokhiaFrederickZhangetal.2015, author = {Hanke-Gogokhia, Christin and Frederick, Jeanne M. and Zhang, Houbin and Baehr, Wolfgang}, title = {ARL3 regulates transport of prenylated and acylated proteins to photoreceptor outer segment in mouse retina}, series = {Investigative ophthalmology \& visual science}, volume = {56}, booktitle = {Investigative ophthalmology \& visual science}, number = {7}, publisher = {Association for Research in Vision and Opthalmology}, address = {Rockville}, issn = {0146-0404}, pages = {2}, year = {2015}, language = {en} } @article{AdamlaIgnatova2015, author = {Adamla, Frauke and Ignatova, Zoya}, title = {Somatic expression of unc-54 and vha-6 mRNAs declines but not pan-neuronal rgef-1 and unc-119 expression in aging Caenorhabditis elegans}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep10692}, pages = {10}, year = {2015}, abstract = {Aging is a highly controlled biological process characterized by a progressive deterioration of various cellular activities. One of several hallmarks of aging describes a link to transcriptional alteration, suggesting that it may impact the steady-state mRNA levels. We analyzed the mRNA steady-state levels of polyCAG-encoding transgenes and endogenous genes under the control of well-characterized promoters for intestinal (vha-6), muscular (unc-54, unc-15) and pan-neuronal (rgef-1, unc-119) expression in the nematode Caenorhabditis elegans. We find that there is not a uniform change in transcriptional profile in aging, but rather a tissue-specific difference in the mRNA levels of these genes. While levels of mRNA in the intestine (vha-6) and muscular (unc-54, unc-15) cells decline with age, pan-neuronal tissue shows more stable mRNA expression (rgef-1, unc-119) which even slightly increases with the age of the animals. Our data on the variations in the mRNA abundance from exemplary cases of endogenous and transgenic gene expression contribute to the emerging evidence for tissue-specific variations in the aging process.}, language = {en} } @article{TedderCarleialGolebiewskaetal.2015, author = {Tedder, Andrew and Carleial, Samuel and Golebiewska, Martyna and Kappel, Christian and Shimizu, Kentaro K. and Stift, Marc}, title = {Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae)}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {6}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0126618}, pages = {17}, year = {2015}, abstract = {Introduction The transition from cross-fertilisation (outcrossing) to self-fertilisation (selfing) frequently coincides with changes towards a floral morphology that optimises self-pollination, the selfing syndrome. Population genetic studies have reported the existence of both outcrossing and selfing populations in Arabis alpina (Brassicaceae), which is an emerging model species for studying the molecular basis of perenniality and local adaptation. It is unknown whether its selfing populations have evolved a selfing syndrome. Methods Using macro-photography, microscopy and automated cell counting, we compared floral syndromes (size, herkogamy, pollen and ovule numbers) between three outcrossing populations from the Apuan Alps and three selfing populations from the Western and Central Alps (Maritime Alps and Dolomites). In addition, we genotyped the plants for 12 microsatellite loci to confirm previous measures of diversity and inbreeding coefficients based on allozymes, and performed Bayesian clustering. Results and Discussion Plants from the three selfing populations had markedly smaller flowers, less herkogamy and lower pollen production than plants from the three outcrossing populations, whereas pistil length and ovule number have remained constant. Compared to allozymes, microsatellite variation was higher, but revealed similar patterns of low diversity and high Fis in selfing populations. Bayesian clustering revealed two clusters. The first cluster contained the three outcrossing populations from the Apuan Alps, the second contained the three selfing populations from the Maritime Alps and Dolomites. Conclusion We conclude that in comparison to three outcrossing populations, three populations with high selfing rates are characterised by a flower morphology that is closer to the selfing syndrome. The presence of outcrossing and selfing floral syndromes within a single species will facilitate unravelling the genetic basis of the selfing syndrome, and addressing which selective forces drive its evolution.}, language = {en} } @article{AllhoffRitterskampRalletal.2015, author = {Allhoff, Korinna Theresa and Ritterskamp, Daniel and Rall, Bj{\"o}rn C. and Drossel, Barbara and Guill, Christian}, title = {Evolutionary food web model based on body masses gives realistic networks with permanent species turnover}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep10955}, pages = {12}, year = {2015}, abstract = {The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the complexity and stability of such food webs, we developed an eco-evolutionary model in which new species emerge as modifications of existing ones and dynamic ecological interactions determine which species are viable. The food-web structure thereby emerges from the dynamical interplay between speciation and trophic interactions. The proposed model is less abstract than earlier evolutionary food web models in the sense that all three evolving traits have a clear biological meaning, namely the average body mass of the individuals, the preferred prey body mass, and the width of their potential prey body mass spectrum. We observed networks with a wide range of sizes and structures and high similarity to natural food webs. The model networks exhibit a continuous species turnover, but massive extinction waves that affect more than 50\% of the network are not observed.}, language = {en} } @article{PinhasiFernandesSiraketal.2015, author = {Pinhasi, Ron and Fernandes, Daniel and Sirak, Kendra and Novak, Mario and Connell, Sarah and Alpaslan-Roodenberg, Songul and Gerritsen, Fokke and Moiseyev, Vyacheslav and Gromov, Andrey and Raczky, Pal and Anders, Alexandra and Pietrusewsky, Michael and Rollefson, Gary and Jovanovic, Marija and Trinhhoang, Hiep and Bar-Oz, Guy and Oxenham, Marc and Matsumura, Hirofumi and Hofreiter, Michael}, title = {Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {6}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0129102}, pages = {13}, year = {2015}, abstract = {The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (similar to 1\% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,0001,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1\% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.}, language = {en} } @article{KielbSezerKatzetal.2015, author = {Kielb, Patrycja and Sezer, Murat and Katz, Sagie and Lopez, Francesca and Schulz, Christopher and Gorton, Lo and Ludwig, Roland and Wollenberger, Ursula and Zebger, Ingo and Weidinger, Inez M.}, title = {Spectroscopic Observation of Calcium-Induced Reorientation of Cellobiose Dehydrogenase Immobilized on Electrodes and its Effect on Electrocatalytic Activity}, series = {ChemPhysChem : a European journal of chemical physics and physical chemistry}, volume = {16}, journal = {ChemPhysChem : a European journal of chemical physics and physical chemistry}, number = {9}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1439-4235}, doi = {10.1002/cphc.201500112}, pages = {1960 -- 1968}, year = {2015}, abstract = {Cellobiose dehydrogenase catalyzes the oxidation of various carbohydrates and is considered as a possible anode catalyst in biofuel cells. It has been shown that the catalytic performance of this enzyme immobilized on electrodes can be increased by presence of calcium ions. To get insight into the Ca2+-induced changes in the immobilized enzyme we employ surface-enhanced vibrational (SERR and SEIRA) spectroscopy together with electrochemistry. Upon addition of Ca2+ ions electrochemical measurements show a shift of the catalytic turnover signal to more negative potentials while SERR measurements reveal an offset between the potential of heme reduction and catalytic current. Comparing SERR and SEIRA data we propose that binding of Ca2+ to the heme induces protein reorientation in a way that the electron transfer pathway of the catalytic FAD center to the electrode can bypass the heme cofactor, resulting in catalytic activity at more negative potentials.}, language = {en} } @article{ReinhardKupfer2015, author = {Reinhard, Sandy and Kupfer, Alexander}, title = {Sexual dimorphism in a French population of the marbled newt, Triturus marmoratus (Urodela: Salamandridae)}, series = {Salamandra : German journal of herpetology}, volume = {51}, journal = {Salamandra : German journal of herpetology}, number = {2}, publisher = {Deutsche Gesellschaft f{\"u}r Herpetologie und Terrarienkunde}, address = {Darmstadt}, issn = {0036-3375}, pages = {121 -- 128}, year = {2015}, abstract = {Amphibians have developed a large set of life-history strategies and demonstrate an impressive diversity of reproductive patterns compared to other vertebrates. Various selection pressures impact on males and females and see them produce different degrees of sexual dimorphism in order to maximise their reproductive success. In an extended morphometric analysis that included 27 body-and head-related characters, we studied the pattern of sexual dimorphism of a French population of the marbled newt, Triturus marmoratus. We analysed the characters by employing GLM methods (ANCOVA) and found 16 of them to be dimorphic between the sexes. In general, females differ in head-body size, such as snout-vent length, but males rather in shape or body proportions (e.g., limb proportions). The various expressions of sexual size dimorphism among large-bodied marbled newts and allies demonstrate that more than one evolutionary model works simultaneously on different traits.}, language = {en} } @article{SreeKeresztesMuellerRoeberetal.2015, author = {Sree, K. Sowjanya and Keresztes, Aron and M{\"u}ller-R{\"o}ber, Bernd and Brandt, Ronny and Eberius, Matthias and Fischer, Wolfgang and Appenroth, Klaus-J.}, title = {Phytotoxicity of cobalt ions on the duckweed Lemna minor - Morphology, ion uptake, and starch accumulation}, series = {Chemosphere : chemistry, biology and toxicology as related to environmental problems}, volume = {131}, journal = {Chemosphere : chemistry, biology and toxicology as related to environmental problems}, publisher = {Elsevier}, address = {Oxford}, issn = {0045-6535}, doi = {10.1016/j.chemosphere.2015.03.008}, pages = {149 -- 156}, year = {2015}, abstract = {Cobalt (Co2+) inhibits vegetative growth of Lemna minor gradually from 1 mu M to 100 mu M. Fronds accumulated up to 21 mg Co2+ g(-1) dry weight at 10 mu M external Co2+ indicating hyperaccumulation. Interestingly, accumulation of Co2+ did not decrease the iron (Fe) content in fronds, highlighting L. minor as a suitable system for studying effects of Co2+ undisturbed by Fe deficiency symptoms unlike most other plants. Digital image analysis revealed the size distribution of fronds after Co2+ treatment and also a reduction in pigmentation of newly formed daughter fronds unlike the mother fronds during the 7-day treatment. Neither chlorophyll nor photosystem II fluorescence changed significantly during the initial 4 d, indicating effective photosynthesis. During the later phase of the 7-day treatment, however, chlorophyll content and photosynthetic efficiency decreased in the Co2+-treated daughter fronds, indicating that Co2+ inhibits the biosynthesis of chlorophyll rather than leading to the destruction of pre-existing pigment molecules. In addition, during the first 4 d of Co2+ treatment starch accumulated in the fronds and led to the transition of chloroplasts to chloro-amyloplasts and amylo-chloroplasts, while starch levels strongly decreased thereafter. (C) 2015 Elsevier Ltd. All rights reserved.}, language = {en} } @article{BreitkopfOnsteinCafassoetal.2015, author = {Breitkopf, Hendrik and Onstein, Renske E. and Cafasso, Donata and Schl{\"u}ter, Philipp M. and Cozzolino, Salvatore}, title = {Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptive Ophrys orchids}, series = {New phytologist : international journal of plant science}, volume = {207}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.13219}, pages = {377 -- 389}, year = {2015}, abstract = {Episodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys). Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework. It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history. Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic.}, language = {en} } @article{EggersArensFirlaetal.2015, author = {Eggers, Ute and Arens, Michael and Firla, Mario and Wallschl{\"a}ger, Hans-Dieter}, title = {To fledge or not to fledge: factors influencing the number of eggs and the eggs-to-fledglings rate in White Storks Ciconia ciconia in an agricultural environment}, series = {Journal of ornithology}, volume = {156}, journal = {Journal of ornithology}, number = {3}, publisher = {Springer}, address = {New York}, issn = {0021-8375}, doi = {10.1007/s10336-015-1182-9}, pages = {711 -- 723}, year = {2015}, abstract = {Numerous studies have explored the relationship between environmental factors and White Stork Ciconia ciconia reproduction, mainly expressing breeding success as the number of fledglings. Nonetheless, one of the most critical life-history stages in birds falls between egg-laying and fledging, and identifying the factors causing offspring mortality during this period provides valuable knowledge. We quantified the number of laid White Stork eggs and the proportion of eggs that turned into fledglings in an agriculture-dominated region in Eastern Germany. Moreover, we identified the factors among land cover, weather and arrival dates, which influenced these two reproductive measures the most, and analysed the monitored mortality causes. On average, four eggs were laid per nest, and 57.8 \% of the eggs turned into fledglings. The number of eggs laid was best explained by the negative effect of the arrival date of the second stork, while the percentage of eggs that turned into fledglings was more dependent on weather: most important parameters were mean temperature in the fifth and seventh weeks after the assumed breeding start (i.e. around the assumed hatching date), and the number of consecutive days with precipitation when nestlings are assumed to be approximately 3 weeks old. In an agricultural environment, weather effects that potentially disturb food availability might be more important than effects directly affecting the survival of White Stork offspring. The most frequent observed mortality cause, nest fights, furthermore revealed the relevance of intraspecific competition in the study population.}, language = {en} }