TY - JOUR A1 - Elsner, Julia A1 - Schibler, Joerg A1 - Hofreiter, Michael A1 - Schlumbaum, Angela T1 - Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland JF - Archaeological and anthropological sciences N2 - Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the-inevitable-heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions. KW - Ancient DNA KW - DNA preservation KW - Horse KW - Cave KW - Switzerland Y1 - 2015 U6 - https://doi.org/10.1007/s12520-014-0213-4 SN - 1866-9557 SN - 1866-9565 VL - 7 IS - 4 SP - 505 EP - 515 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Eggers, Ute A1 - Arens, Michael A1 - Firla, Mario A1 - Wallschläger, Hans-Dieter T1 - 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 JF - Journal of ornithology N2 - 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. KW - Breeding success KW - Clutch size KW - Mortality causes KW - Weather impact KW - Land use KW - Arrival dates Y1 - 2015 U6 - https://doi.org/10.1007/s10336-015-1182-9 SN - 0021-8375 SN - 1439-0361 VL - 156 IS - 3 SP - 711 EP - 723 PB - Springer CY - New York ER - TY - JOUR A1 - Dubovskaya, Olga P. A1 - Tang, Kam W. A1 - Gladyshev, Michail I. A1 - Kirillin, Georgiy A1 - Buseva, Zhanna A1 - Kasprzak, Peter A1 - Tolomeev, Aleksandr P. A1 - Grossart, Hans-Peter T1 - Estimating In Situ Zooplankton Non-Predation Mortality in an Oligo-Mesotrophic Lake from Sediment Trap Data: Caveats and Reality Check JF - PLoS one N2 - Background Mortality is a main driver in zooplankton population biology but it is poorly constrained in models that describe zooplankton population dynamics, food web interactions and nutrient dynamics. Mortality due to non-predation factors is often ignored even though anecdotal evidence of non-predation mass mortality of zooplankton has been reported repeatedly. One way to estimate non-predation mortality rate is to measure the removal rate of carcasses, for which sinking is the primary removal mechanism especially in quiescent shallow water bodies. Objectives and Results We used sediment traps to quantify in situ carcass sinking velocity and non-predation mortality rate on eight consecutive days in 2013 for the cladoceran Bosmina longirostris in the oligo-mesotrophic Lake Stechlin; the outcomes were compared against estimates derived from in vitro carcass sinking velocity measurements and an empirical model correcting in vitro sinking velocity for turbulence resuspension and microbial decomposition of carcasses. Our results show that the latter two approaches produced unrealistically high mortality rates of 0.58-1.04 d(-1), whereas the sediment trap approach, when used properly, yielded a mortality rate estimate of 0.015 d(-1), which is more consistent with concurrent population abundance data and comparable to physiological death rate from the literature. Ecological implications Zooplankton carcasses may be exposed to water column microbes for days before entering the benthos; therefore, non-predation mortality affects not only zooplankton population dynamics but also microbial and benthic food webs. This would be particularly important for carbon and nitrogen cycles in systems where recurring mid-summer decline of zooplankton population due to non-predation mortality is observed. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0131431 SN - 1932-6203 VL - 10 IS - 7 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Di Giacomo, Adrian S. A1 - Di Giacomo, Alejandro G. A1 - Kliger, Rafi A1 - Reboreda, Juan C. A1 - Tiedemann, Ralph A1 - Mahler, Bettina T1 - 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 JF - Bird conservation international N2 - 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. Y1 - 2015 U6 - https://doi.org/10.1017/S0959270914000203 SN - 0959-2709 SN - 1474-0001 VL - 25 IS - 2 SP - 127 EP - 138 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Del Campo, Cristian A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Ignatova, Zoya T1 - Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005613 SN - 1553-7404 VL - 11 IS - 10 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Dammhahn, Melanie A1 - Rakotondramanana, Claude Fabienne A1 - Goodman, Steven M. T1 - Coexistence of morphologically similar bats (Vespertilionidae) on Madagascar: stable isotopes reveal fine-grained niche differentiation among cryptic species JF - Journal of tropical ecology N2 - Based on niche theory, closely related and morphologically similar species are not predicted to coexist due to overlap in resource and habitat use. Local assemblages of bats often contain cryptic taxa, which co-occur despite notable similarities in morphology and ecology. We measured in two different habitat types on Madagascar levels of stable carbon and nitrogen isotopes in hair (n = 103) and faeces (n = 57) of cryptic Vespertilionidae taxa to indirectly examine whether fine-grained trophic niche differentiation explains their coexistence. In the dry deciduous forest (Kirindy), six sympatric species ranged over 6.0% in delta N-15, i.e. two trophic levels, and 4.2% in delta C-13 with a community mean of 11.3% in delta N-15 and - 21.0% in delta C-13. In the mesic forest (Antsahabe), three sympatric species ranged over one trophic level (delta N-15: 2.4%, delta C-13: 1.0%) with a community mean of 8.0% delta N-15 and - 21.7% in delta C-13. Multivariate analyses and residual permutation of Euclidian distances in delta C-13- delta N-15 bi-plots revealed in both communities distinct stable isotope signatures and species separation for the hair samples among coexisting Vespertilionidae. Intraspecific variation in faecal and hair stable isotopes did not indicate that seasonal migration might relax competition and thereby facilitate the local co-occurrence of sympatric taxa. KW - Chiroptera KW - community structure KW - congeneric species KW - ecological niches KW - migration KW - Neoromicia KW - Pipistrellus KW - Scotophilus KW - stable carbon KW - stable nitrogen Y1 - 2015 U6 - https://doi.org/10.1017/S0266467414000741 SN - 0266-4674 SN - 1469-7831 VL - 31 SP - 153 EP - 164 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Czesnick, Hjördis A1 - Lenhard, Michael T1 - Size Control in Plants-Lessons from Leaves and Flowers JF - Cold Spring Harbor perspectives in biology N2 - To achieve optimal functionality, plant organs like leaves and petals have to grow to a certain size. Beginning with a limited number of undifferentiated cells, the final size of an organ is attained by a complex interplay of cell proliferation and subsequent cell expansion. Regulatory mechanisms that integrate intrinsic growth signals and environmental cues are required to enable optimal leaf and flower development. This review focuses on plant-specific principles of growth reaching from the cellular to the organ level. The currently known genetic pathways underlying these principles are summarized and network connections are highlighted. Putative non-cell autonomously acting mechanisms that might coordinate plant-cell growth are discussed. Y1 - 2015 U6 - https://doi.org/10.1101/cshperspect.a019190 SN - 1943-0264 VL - 7 IS - 8 PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, NY ER - TY - JOUR A1 - Cui, Xiao A1 - Lv, Yang A1 - Chen, Miaolin A1 - Nikoloski, Zoran A1 - Twell, David A1 - Zhang, Dabing T1 - Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome JF - Molecular plant N2 - 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. KW - pollen KW - evolution KW - young genes KW - transcriptome Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2014.12.008 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 6 SP - 935 EP - 945 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Corno, Gianluca A1 - Salka, Ivette A1 - Pohlmann, Kirsten A1 - Hall, Alex R. A1 - Grossart, Hans-Peter T1 - Interspecific interactions drive chitin and cellulose degradation by aquatic microorganisms JF - Aquatic microbial ecology : international journal N2 - Complex biopolymers (BPs) such as chitin and cellulose provide the majority of organic carbon in aquatic ecosystems, but the mechanisms by which communities of bacteria in natural systems exploit them are unclear. Previous degradation experiments in artificial systems predominantly used microcosms containing a single bacterial species, neglecting effects of interspecific interactions. By constructing simplified aquatic microbial communities, we tested how the addition of other bacterial species, of a nanoflagellate protist capable of consuming bacteria, or of both, affect utilization of BPs. Surprisingly, total abundance of resident bacteria in mixed communities increased upon addition of the protist. Concomitantly, bacteria shifted from free-living to aggregated morphotypes that seemed to promote utilization of BPs. In our model system, these interactions significantly increased productivity in terms of overall bacterial numbers and carbon transfer efficiency. This indicates that interactions on microbial aggregates may be crucial for chitin and cellulose degradation. We therefore suggest that interspecific microbial interactions must be considered when attempting to model the turnover of the vast pool of complex biopolymers in aquatic ecosystems. KW - Aggregation KW - Flagellate grazing KW - Ecological interactions KW - Microbial carbon transfer KW - Polymer degradation KW - System ecology Y1 - 2015 U6 - https://doi.org/10.3354/ame01765 SN - 0948-3055 SN - 1616-1564 VL - 76 IS - 1 SP - 27 EP - + PB - Institute of Mathematical Statistics CY - Oldendorf Luhe ER - TY - JOUR A1 - Cornetti, Luca A1 - Valente, Luis M. A1 - Dunning, Luke T. A1 - Quan, Xueping A1 - Black, Richard A. A1 - Hebert, Olivier A1 - Savolainen, Vincent T1 - The Genome of the "Great Speciator" Provides Insights into Bird Diversification JF - Genome biology and evolution N2 - Among birds, white-eyes (genusZosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the 'great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation. KW - genome evolution KW - positive selection KW - gene duplication KW - phylogenomics KW - demography KW - morphological divergence Y1 - 2015 U6 - https://doi.org/10.1093/gbe/evv168 SN - 1759-6653 VL - 7 IS - 9 SP - 2680 EP - 2691 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Contin, Andrea A1 - Frasca, Stefano A1 - Vivekananthan, Jeevanthi A1 - Leimkühler, Silke A1 - Wollenberger, Ursula A1 - Plumere, Nicolas A1 - Schuhmann, Wolfgang T1 - A pH Responsive Redox Hydrogel for Electrochemical Detection of Redox Silent Biocatalytic Processes. Control of Hydrogel Solvation JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - The control of bioelectrocatalytic processes by external stimuli for the indirect detection of non-redox active species was achieved using an esterase and a redox enzyme both integrated within a redox hydrogel. The poly( vinyl) imidazole Os(bpy)(2)Cl hydrogel displays pH-responsive properties. The esterase catalysed reaction leads to a local pH decrease causing protonation of imidazole moieties thus increasing hydrogel solvation and mobility of the tethered Os-complexes. This is the key step to enable improved electron transfer between an aldehyde oxidoreductase and the polymer-bound Os-complexes. The off-on switch is further integrated in a biofuel cell system for self-powered signal generation. KW - pH responsive hydrogel KW - External stimuli KW - Biofuel cell KW - Self-powered biosensor KW - Solvation Y1 - 2015 U6 - https://doi.org/10.1002/elan.201400621 SN - 1040-0397 SN - 1521-4109 VL - 27 IS - 4 SP - 938 EP - 944 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Coelho, Catarina A1 - Foti, Alessandro A1 - Hartmann, Tobias A1 - Santos-Silva, Teresa A1 - Leimkühler, Silke A1 - Romao, Maria Joao T1 - Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase JF - Nature chemical biology N2 - Aldehyde oxidase (AOX) is a xanthine oxidase (XO)-related enzyme with emerging importance due to its role in the metabolism of drugs and xenobiotics. We report the first crystal structures of human AOX1, substrate free (2.6-angstrom resolution) and in complex with the substrate phthalazine and the inhibitor thioridazine (2.7-angstrom resolution). Analysis of the protein active site combined with steady-state kinetic studies highlight the unique features, including binding and substrate orientation at the active site, that characterize human AOX1 as an important drug-metabolizing enzyme. Structural analysis of the complex with the noncompetitive inhibitor thioridazine revealed a new, unexpected and fully occupied inhibitor-binding site that is structurally conserved among mammalian AOXs and XO. The new structural insights into the catalytic and inhibition mechanisms of human AOX that we now report will be of great value for the rational analysis of clinical drug interactions involving inhibition of AOX1 and for the prediction and design of AOX-stable putative drugs. Y1 - 2015 U6 - https://doi.org/10.1038/NCHEMBIO.1895 SN - 1552-4450 SN - 1552-4469 VL - 11 IS - 10 SP - 779 EP - + PB - Nature Publ. Group CY - New York ER - TY - JOUR A1 - Cochard, Roland A1 - Edwards, Peter J. A1 - Weber, Ewald T1 - Post-ranching tree-grass interactions in secondary Acacia zanzibarica woodlands in coastal Tanzania - an experimental study JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - Questions: We studied a humid savanna rangeland., abandoned in 2000, where intensive cattle grazing had led to widespread encroachment by Acacia zanzibarica. We asked whether the acacia trees were able to regenerate in the absence of domesJic livestock, either beneath acacia canopies or in artificial clearings. Location: Tropical coastal Tanzania (former Mkwaja Ranch, now in Saadani National Park). Methods: We set out a total of 48 plots on four sites in November 2001, and assigned them to three treatments: trees felled (FN), trees felled and the stumps poisoned (FP) with Triclopyr, and no intervention (controls, NN). We analysed soils of plots for texture and nutrients. In two wet (July 2002 and 2003) and one dry (February 2003) seasons we assessed grass and tree leaf biomass and transpiration rates, and counted acacia seedlings and resprouts. The effects of treatments (controlled for site and other co-variables) on grass growth and acacia rectaiitment were determined statistically using general linear models (GLM). Results: Acacia leaves had a much higher stomatal conductance than grasses, with the consequence that total evapotranspiration in woodland was higher than in clearings. In the wet seasons, grass biomass and seedling densities were significantly higher in clearings than in control plots, which we attributed to more.favourable moisture conditions, In the dry season, by contrast, we found no differences, and all seedlings had died. On FN plots, 71% of stumps, and on FP plots, 11% resprouted (coppicing), but only a quarter of these shoots survived until July 2003. Root suckering occurred spontaneously at low densities. No root suckers or resprouts grew beyond the grass layer. Conclusions: Acacia woodlands do not regenerate in the absence of cattle grazing, and tree cutting in combination with appropriate fire management could potentially accelerate re-establishment of open grassland. However, regeneration might occur in the future due to the increasing wildlife populations within the new national park. KW - Bush encroachment KW - Clearing formation KW - Grass flush KW - Savanna rangeland dynamics KW - Sprouting KW - Tree recruitment Y1 - 2015 U6 - https://doi.org/10.1111/avsc.12134 SN - 1402-2001 SN - 1654-109X VL - 18 IS - 2 SP - 297 EP - 310 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Cisek, Richard A1 - Tokarz, Danielle A1 - Steup, Martin A1 - Tetlow, Ian J. A1 - Emes, Michael J. A1 - Hebelstrup, Kim H. A1 - Blennow, Andreas A1 - Barzda, Virginijus T1 - Second harmonic generation microscopy investigation of the crystalline ultrastructure of three barley starch lines affected by hydration JF - Biomedical optics express N2 - Second harmonic generation (SHG) microscopy is employed to study changes in crystalline organization due to altered gene expression and hydration in barley starch granules. SHG intensity and susceptibility ratio values (R'(SHG)) are obtained using reduced Stokes-Mueller polarimetric microscopy. The maximum R'(SHG) values occur at moderate moisture indicating the narrowest orientation distribution of nonlinear dipoles from the cylindrical axis of glucan helices. The maximum SHG intensity occurs at the highest moisture and amylopectin content. These results support the hypothesis that SHG is caused by ordered hydrogen and hydroxyl bond networks which increase with hydration of starch granules. (C) 2015 Optical Society of America Y1 - 2015 U6 - https://doi.org/10.1364/BOE.6.003694 SN - 2156-7085 VL - 6 IS - 10 SP - 3694 EP - 3700 PB - Optical Society of America CY - Washington ER - TY - JOUR A1 - Choi, Young-Joon A1 - Klosterman, Steven J. A1 - Kummer, Volker A1 - Voglmayr, Hermann A1 - Shin, Hyeon-Dong A1 - Thines, Marco T1 - Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach JF - Molecular phylogenetics and evolution N2 - Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. (C) 2015 Elsevier Inc. All rights reserved. KW - Cospeciation KW - Host shift KW - Multi-locus phylogeny KW - Oomycetes KW - Peronospora farinosa KW - Species tree Y1 - 2015 U6 - https://doi.org/10.1016/j.ympev.2015.03.003 SN - 1055-7903 SN - 1095-9513 VL - 86 SP - 24 EP - 34 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Castellini, Alberto A1 - Paltrinieri, Daniele A1 - Manca, Vincenzo T1 - MP-GeneticSynth: inferring biological network regulations from time series JF - Bioinformatics N2 - MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations. The software makes use of: (i) metabolic P systems as a modeling framework, (ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, (iii) a suitable reformulation of the least squares method to estimate function parameters considering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis. Y1 - 2015 U6 - https://doi.org/10.1093/bioinformatics/btu694 SN - 1367-4803 SN - 1460-2059 VL - 31 IS - 5 SP - 785 EP - 787 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Caron, Maria Mercedes A1 - De Frenne, Pieter A1 - Brunet, Jörg A1 - Chabrerie, Olivier A1 - Cousins, Sara A. O. A1 - Decocq, Guillaume A1 - Diekmann, Martin A1 - Graae, Bente Jessen A1 - Heinken, Thilo A1 - Kolb, Annette A1 - Lenoir, Jonathan A1 - Naaf, Tobias A1 - Plue, Jan A1 - Selvi, Federico A1 - Wulf, Monika A1 - Verheyen, Kris T1 - Divergent regeneration responses of two closely related tree species to direct abiotic and indirect biotic effects of climate change JF - Forest ecology and management N2 - Changing temperature and precipitation can strongly influence plant reproduction. However, also biotic interactions might indirectly affect the reproduction and recruitment success of plants in the context of climate change. Information about the interactive effects of changes in abiotic and biotic factors is essential, but still largely lacking, to better understand the potential effects of a changing climate on plant populations. Here we analyze the regeneration from seeds of Acer platanoides and Acer pseudoplatanus, two currently secondary forest tree species from seven regions along a 2200 km-wide latitudinal gradient in Europe. We assessed the germination, seedling survival and growth during two years in a common garden experiment where temperature, precipitation and competition with the understory vegetation were manipulated. A. platanoides was more sensitive to changes in biotic conditions while A. pseudoplatanus was affected by both abiotic and biotic changes. In general, competition reduced (in A. platanoides) and warming enhanced (in A. pseudoplatanus) germination and survival, respectively. Reduced competition strongly increased the growth of A. platanoides seedlings. Seedling responses were independent of the conditions experienced by the mother tree during seed production and maturation. Our results indicate that, due to the negative effects of competition on the regeneration of A. platanoides, it is likely that under stronger competition (projected under future climatic conditions) this species will be negatively affected in terms of germination, survival and seedling biomass. Climate-change experiments including both abiotic and biotic factors constitute a key step forward to better understand the response of tree species' regeneration to climate change. (C) 2015 Elsevier B.V. All rights reserved. KW - Acer KW - Regeneration KW - Latitudinal gradient KW - Temperature KW - Precipitation KW - Competition Y1 - 2015 U6 - https://doi.org/10.1016/j.foreco.2015.01.003 SN - 0378-1127 SN - 1872-7042 VL - 342 SP - 21 EP - 29 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Caron, Maria Mercedes A1 - De Frenne, Pieter A1 - Brunet, J. A1 - Chabrerie, Olivier A1 - Cousins, S. A. O. A1 - De Backer, L. A1 - Decocq, G. A1 - Diekmann, M. A1 - Heinken, Thilo A1 - Kolb, A. A1 - Naaf, T. A1 - Plue, J. A1 - Selvi, Federico A1 - Strimbeck, G. R. A1 - Wulf, Monika A1 - Verheyen, Kris T1 - Interacting effects of warming and drought on regeneration and early growth of Acer pseudoplatanus and A. platanoides JF - Plant biology N2 - Climate change is acting on several aspects of plant life cycles, including the sexual reproductive stage, which is considered amongst the most sensitive life-cycle phases. In temperate forests, it is expected that climate change will lead to a compositional change in community structure due to changes in the dominance of currently more abundant forest tree species. Increasing our understanding of the effects of climate change on currently secondary tree species recruitment is therefore important to better understand and forecast population and community dynamics in forests. Here, we analyse the interactive effects of rising temperatures and soil moisture reduction on germination, seedling survival and early growth of two important secondary European tree species, Acer pseudoplatanus and A.platanoides. Additionally, we analyse the effect of the temperature experienced by the mother tree during seed production by collecting seeds of both species along a 2200-km long latitudinal gradient. For most of the responses, A.platanoides showed higher sensitivity to the treatments applied, and especially to its joint manipulation, which for some variables resulted in additive effects while for others only partial compensation. In both species, germination and survival decreased with rising temperatures and/or soil moisture reduction while early growth decreased with declining soil moisture content. We conclude that although A.platanoides germination and survival were more affected after the applied treatments, its initial higher germination and larger seedlings might allow this species to be relatively more successful than A.pseudoplatanus in the face of climate change. KW - Acer platanoides KW - Acer pseudoplatanus KW - climate change KW - drought KW - reproduction KW - seed KW - temperature Y1 - 2015 U6 - https://doi.org/10.1111/plb.12177 SN - 1435-8603 SN - 1438-8677 VL - 17 IS - 1 SP - 52 EP - 62 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Caron, Maria Mercedes A1 - De Frenne, P. A1 - Chabrerie, Olivier A1 - Cousins, S. A. O. A1 - De Backer, L. A1 - Decocq, G. A1 - Diekmann, M. A1 - Heinken, Thilo A1 - Kolb, A. A1 - Naaf, T. A1 - Plue, J. A1 - Selvi, F. A1 - Strimbeck, G. R. A1 - Wulf, M. A1 - Verheyen, Kris T1 - Impacts of warming and changes in precipitation frequency on the regeneration of two Acer species JF - Flora : morphology, distribution, functional ecology of plants KW - Seed provenance KW - Germination KW - Climate change KW - Interactive effects Y1 - 2015 U6 - https://doi.org/10.1016/j.flora.2015.05.005 SN - 0367-2530 SN - 1618-0585 VL - 214 SP - 24 EP - 33 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Camargo, Rodolfo Gonzalez A1 - dos Reis Riccardi, Daniela Mendes A1 - Teixeira Ribeiro, Henrique Quintas A1 - Carnevali Junior, Luiz Carlos A1 - de Matos-Neto, Emidio Marques A1 - Enjiu, Lucas A1 - Neves, Rodrigo Xavier A1 - Carola Correia Lima, Joanna Darck A1 - Figueredo, Raquel Galvao A1 - Martins de Alcantara, Paulo Sergio A1 - Maximiano, Linda A1 - Otoch, Jose A1 - Batista Jr., Miguel Luiz A1 - Püschel, Gerhard Paul A1 - Seelaender, Marilia T1 - NF-kappa Bp65 and Expression of Its Pro-Inflammatory Target Genes Are Upregulated in the Subcutaneous Adipose Tissue of Cachectic Cancer Patients JF - Nutrients N2 - 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. KW - cancer cachexia KW - inflammation KW - white adipose tissue KW - NF-B KW - IB Y1 - 2015 U6 - https://doi.org/10.3390/nu7064465 SN - 2072-6643 VL - 7 IS - 6 SP - 4465 EP - 4479 PB - MDPI CY - Basel ER -