TY - JOUR A1 - Tucker, Marlee A. A1 - Boehning-Gaese, Katrin A1 - Fagan, William F. A1 - Fryxell, John M. A1 - Van Moorter, Bram A1 - Alberts, Susan C. A1 - Ali, Abdullahi H. A1 - Allen, Andrew M. A1 - Attias, Nina A1 - Avgar, Tal A1 - Bartlam-Brooks, Hattie A1 - Bayarbaatar, Buuveibaatar A1 - Belant, Jerrold L. A1 - Bertassoni, Alessandra A1 - Beyer, Dean A1 - Bidner, Laura A1 - van Beest, Floris M. A1 - Blake, Stephen A1 - Blaum, Niels A1 - Bracis, Chloe A1 - Brown, Danielle A1 - de Bruyn, P. J. Nico A1 - Cagnacci, Francesca A1 - Calabrese, Justin M. A1 - Camilo-Alves, Constanca A1 - Chamaille-Jammes, Simon A1 - Chiaradia, Andre A1 - Davidson, Sarah C. A1 - Dennis, Todd A1 - DeStefano, Stephen A1 - Diefenbach, Duane A1 - Douglas-Hamilton, Iain A1 - Fennessy, Julian A1 - Fichtel, Claudia A1 - Fiedler, Wolfgang A1 - Fischer, Christina A1 - Fischhoff, Ilya A1 - Fleming, Christen H. A1 - Ford, Adam T. A1 - Fritz, Susanne A. A1 - Gehr, Benedikt A1 - Goheen, Jacob R. A1 - Gurarie, Eliezer A1 - Hebblewhite, Mark A1 - Heurich, Marco A1 - Hewison, A. J. Mark A1 - Hof, Christian A1 - Hurme, Edward A1 - Isbell, Lynne A. A1 - Janssen, Rene A1 - Jeltsch, Florian A1 - Kaczensky, Petra A1 - Kane, Adam A1 - Kappeler, Peter M. A1 - Kauffman, Matthew A1 - Kays, Roland A1 - Kimuyu, Duncan A1 - Koch, Flavia A1 - Kranstauber, Bart A1 - LaPoint, Scott A1 - Leimgruber, Peter A1 - Linnell, John D. C. A1 - Lopez-Lopez, Pascual A1 - Markham, A. Catherine A1 - Mattisson, Jenny A1 - Medici, Emilia Patricia A1 - Mellone, Ugo A1 - Merrill, Evelyn A1 - Mourao, Guilherme de Miranda A1 - Morato, Ronaldo G. A1 - Morellet, Nicolas A1 - Morrison, Thomas A. A1 - Diaz-Munoz, Samuel L. A1 - Mysterud, Atle A1 - Nandintsetseg, Dejid A1 - Nathan, Ran A1 - Niamir, Aidin A1 - Odden, John A1 - Oliveira-Santos, Luiz Gustavo R. A1 - Olson, Kirk A. A1 - Patterson, Bruce D. A1 - de Paula, Rogerio Cunha A1 - Pedrotti, Luca A1 - Reineking, Bjorn A1 - Rimmler, Martin A1 - Rogers, Tracey L. A1 - Rolandsen, Christer Moe A1 - Rosenberry, Christopher S. A1 - Rubenstein, Daniel I. A1 - Safi, Kamran A1 - Said, Sonia A1 - Sapir, Nir A1 - Sawyer, Hall A1 - Schmidt, Niels Martin A1 - Selva, Nuria A1 - Sergiel, Agnieszka A1 - Shiilegdamba, Enkhtuvshin A1 - Silva, Joao Paulo A1 - Singh, Navinder A1 - Solberg, Erling J. A1 - Spiegel, Orr A1 - Strand, Olav A1 - Sundaresan, Siva A1 - Ullmann, Wiebke A1 - Voigt, Ulrich A1 - Wall, Jake A1 - Wattles, David A1 - Wikelski, Martin A1 - Wilmers, Christopher C. A1 - Wilson, John W. A1 - Wittemyer, George A1 - Zieba, Filip A1 - Zwijacz-Kozica, Tomasz A1 - Mueller, Thomas T1 - Moving in the Anthropocene BT - global reductions in terrestrial mammalian movements JF - Science N2 - Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral changes of individual animals and to the exclusion of species with long-range movements from areas with higher human impact. Global loss of vagility alters a key ecological trait of animals that affects not only population persistence but also ecosystem processes such as predator-prey interactions, nutrient cycling, and disease transmission. Y1 - 2018 U6 - https://doi.org/10.1126/science.aam9712 SN - 0036-8075 SN - 1095-9203 VL - 359 IS - 6374 SP - 466 EP - 469 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Sustr, David A1 - Hlaváček, Antonín A1 - Duschl, Claus A1 - Volodkin, Dmitry T1 - Multi-fractional analysis of molecular diffusion in polymer multilayers by FRAP BT - a new simulation-based approach JF - The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces & biophysical N2 - Comprehensive analysis of the multifractional molecular diffusion provides a deeper understanding of the diffusion phenomenon in the fields of material science, molecular and cell biology, advanced biomaterials, etc. Fluorescence recovery after photobleaching (FRAP) is commonly employed to probe the molecular diffusion. Despite FRAP being a very popular method, it is not easy to assess multifractional molecular diffusion due to limited possibilities of approaches for analysis. Here we present a novel simulation-optimization-based approach (S-approach) that significantly broadens possibilities of the analysis. In the S-approach, possible fluorescence recovery scenarios are primarily simulated and afterward compared with a real measurement while optimizing parameters of a model until a sufficient match is achieved. This makes it possible to reveal multifractional molecular diffusion. Fluorescent latex particles of different size and fluorescein isothiocyanate in an aqueous medium were utilized as test systems. Finally, the S-approach has been used to evaluate diffusion of cytochrome c loaded into multilayers made of hyaluronan and polylysine. Software for evaluation of multifractional molecular diffusion by S-approach has been developed aiming to offer maximal versatility and user-friendly way for analysis. Y1 - 2017 U6 - https://doi.org/10.1021/acs.jpcb.7b11051 SN - 1520-6106 VL - 122 IS - 3 SP - 1323 EP - 1333 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Thorpe, Roger A1 - Barlow, Axel A1 - Surget-Groba, Yann A1 - Malhotra, Anita T1 - Multilocus phylogeny, species age and biogeography of the Lesser Antillean anoles JF - Molecular phylogenetics and evolution N2 - Lesser Antillean anoles provide classic examples of island radiations. A detailed knowledge of their phylogeny and biogeography, in particular how the age of species relate to the ages of their respective islands and the age of their radiation, is essential to elucidate the tempo and mechanisms of these radiations. We conduct a large-scale phylogenetic and phylogeographic investigation of the Lesser Antillean anoles using multiple genetic markers and comprehensive geographic sampling of most species. The multilocus phylogeny gives the first well-supported reconstruction of the interspecific relationships, and the densely sampled phylogeography reveals a highly dynamic system, driven by overseas dispersal, with several alternative post-dispersal colonisation trajectories. These radiations currently occupy both the outer-older (Eocene to Miocene), and the inner-younger (< 8mybp), Lesser Antillean arcs. The origin of these radiations corresponds with the age of the ancient outer arc. However, the ages of extant species (compatible with the age of other small terrestrial amniotes) are much younger, about the age of the emergence of the younger arc, or less. The difference between the age of the radiation and the age of the extant species suggests substantial species turnover on older arc islands, most likely through competitive replacement. Although extant anoles are extremely speciose, this may represent only a fraction of their biodiversity over time. While paraphyly enables us to infer several recent colonization events, the absence of the younger arc islands and extant species at the earlier and middle stages of the radiation, does not allow the earlier inter-island colonization to be reliably inferred. Reproductive isolation in allopatry takes a very considerable time (in excess of 8my) and sympatry appears to occur only late in the radiation. The resolved multilocus phylogeny, and relative species age, raise difficulties for some earlier hypotheses regarding size evolution, and provide no evidence for within-island speciation. KW - Anolis KW - Multilocus phylogeny KW - Lesser antilles KW - Species age KW - Species turnover KW - Island colonization Y1 - 2018 U6 - https://doi.org/10.1016/j.ympev.2018.06.014 SN - 1055-7903 SN - 1095-9513 VL - 127 SP - 682 EP - 695 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Dey, Pradip A1 - Bergmann, Tobias A1 - Cuellar-Camacho, Jose Luis A1 - Ehrmann, Svenja A1 - Chowdhury, Mohammad Suman A1 - Zhang, Minze A1 - Dahmani, Ismail A1 - Haag, Rainer A1 - Azad, Walid T1 - Multivalent flexible nanogels exhibit broad-spectrum antiviral activity by blocking virus entry JF - ACS nano N2 - The entry process of viruses into host cells is complex and involves stable but transient multivalent interactions with different cell surface receptors. The initial contact of several viruses begins with attachment to heparan sulfate (HS) proteoglycans on the cell surface, which results in a cascade of events that end up with virus entry. The development of antiviral agents based on multivalent interactions to shield virus particles and block initial interactions with cellular receptors has attracted attention in antiviral research. Here, we designed nanogels with different degrees of flexibility based on dendritic polyglycerol sulfate to mimic cellular HS. The designed nanogels are nontoxic and broad-spectrum, can multivalently interact with viral glycoproteins, shield virus surfaces, and efficiently block infection. We also visualized virus-nanogel interactions as well as the uptake of nanogels by the cells through clathrin-mediated endocytosis using confocal microscopy. As many human viruses attach to the cells through HS moieties, we introduce our flexible nanogels as robust inhibitors for these viruses. KW - multivalent KW - herpes simplex virus KW - heparan sulfate KW - nanoparticles KW - click chemistry KW - polyglycerol Y1 - 2018 U6 - https://doi.org/10.1021/acsnano.8b01616 SN - 1936-0851 SN - 1936-086X VL - 12 IS - 7 SP - 6429 EP - 6442 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Hu, Chenlin A1 - Ludsin, Stuart A. A1 - Martin, Jay F. A1 - Dittmann, Elke A1 - Lee, Jiyoung T1 - Mycosporine-like amino acids (MAAs)-producing Microcystis in Lake Erie BT - Development of a qPCR assay and insight into its ecology JF - Harmful algae N2 - Mycosporine-like amino acids (MAAs) are UV-absorbing metabolites found in cyanobacteria. While their protective role from UV in Microcystis has been studied in a laboratory setting, a full understanding of the ecology of MAA-producing versus non-MAA-producing Microcystis in natural environments is lacking. This study presents a new tool for quantifying MAA-producing Microcystis and applies it to obtain insight into the dynamics of MAA-producing and non-MAA-producing Microcystis in Lake Erie. This study first developed a sensitive, specific TaqMan real-time PCR assay that targets MAA synthetase gene C (mysC) of Microcystis (quantitative range: 1.7 × 101 to 1.7 × 107 copies/assay). Using this assay, Microcystis was quantified with a MAA-producing genotype (mysC+) in water samples (n = 96) collected during March-November 2013 from 21 Lake Erie sites (undetectable − 8.4 × 106 copies/ml). The mysC+ genotype comprised 0.3–37.8% of the Microcystis population in Lake Erie during the study period. The proportion of the mysC+ genotype during high solar UV irradiation periods (mean = 18.8%) was significantly higher than that during lower UV periods (mean = 9.7%). Among the MAAs, shinorine (major) and porphyra (minor) were detected with HPLC-PDA-MS/MS from the Microcystis isolates and water samples. However, no significant difference in the MAA concentrations existed between higher and lower solar UV periods when the MAA concentrations were normalized with Microcystis mysC abundance. Collectively, this study’s findings suggest that the MAA-producing Microcystis are present in Lake Erie, and they may be ecologically advantageous under high UV conditions, but not to the point that they exclusively predominate over the non-MAA-producers. KW - Shinorine KW - Porphyra KW - UV irradiation KW - Sunscreen KW - Eutrophication KW - Harmful algal bloom Y1 - 2018 U6 - https://doi.org/10.1016/j.hal.2018.05.010 SN - 1568-9883 SN - 1878-1470 VL - 77 SP - 1 EP - 10 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Kurze, Susanne A1 - Heinken, Thilo A1 - Fartmann, Thomas T1 - Nitrogen enrichment in host plants increases the mortality of common Lepidoptera species JF - Oecologia N2 - The recent decline of Lepidoptera species strongly correlates with the increasing intensification of agriculture in Western and Central Europe. However, the effects of changed host-plant quality through agricultural fertilization on this insect group remain largely unexplored. For this reason, we tested the response of six common butterfly and moth species to host-plant fertilization using fertilizer quantities usually applied in agriculture. The larvae of the study species Coenonympha pamphilus, Lycaena phlaeas, Lycaena tityrus, Pararge aegeria, Rivula sericealis and Timandra comae were distributed according to a split-brood design to three host-plant treatments comprising one control treatment without fertilization and two fertilization treatments with an input of 150 and 300kgNha(-1)year(-1), respectively. In L.tityrus, we used two additional fertilization treatments with an input of 30 and 90kgNha(-1)year(-1), respectively. Fertilization increased the nitrogen concentration of both host-plant species, Rumex acetosella and Poa pratensis, and decreased the survival of larvae in all six Lepidoptera species by at least one-third, without clear differences between sorrel- and grass-feeding species. The declining survival rate in all species contradicts the well-accepted nitrogen-limitation hypothesis, which predicts a positive response in species performance to dietary nitrogen content. In contrast, this study presents the first evidence that current fertilization quantities in agriculture exceed the physiological tolerance of common Lepidoptera species. Our results suggest that (1) the negative effect of plant fertilization on Lepidoptera has previously been underestimated and (2) that it contributes to the range-wide decline of Lepidoptera. KW - Agricultural fertilization KW - Global change KW - Host-plant quality KW - Nitrogen-limitation hypothesis KW - Rearing experiment Y1 - 2018 U6 - https://doi.org/10.1007/s00442-018-4266-4 SN - 0029-8549 SN - 1432-1939 VL - 188 IS - 4 SP - 1227 EP - 1237 PB - Springer CY - New York ER - TY - JOUR A1 - Scheffler, Christiane A1 - Kruetzfeldt, Louisa-Marie A1 - Dasgupta, Parasmani A1 - Hermanussen, Michael T1 - No association between fat tissue and height in 5019 children and adolescents, measured between 1982 and 2011 in Kolkata/India JF - Journal of biological and clinical anthropology JF - Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - Body height has traditionally been looked upon as a mirror of the condition of society, short height being an indicator of poor nutritional status, poor education, and low social status and income. This view has recently been questioned. We aimed to quantify the effects of nutrition, education, sibship size, and household income, factors that are conventionally considered to be related to child growth, on body height of children and adolescents raised under urban Indian conditions. Sample and methods: We re-analyzed several anthropometric measurements and questionnaires with questions on sibship size, fathers’ and mother’s education, and monthly family expenditure, from two cross-sectional growth studies performed in Kolkata, India. The first Kolkata Growth Study (KG1) took place in 1982-1983, with data on 825 Bengali boys aged 7 to 16 years; and the second Kolkata Growth Study (KG2) between 1999 and 2011 with data of 1999 boys aged 7 to 21 years from Bengali Hindu families, and data of 2195 girls obtained between 2005 and 2011. Results: Indian children showed positive insignificant secular trends in height and a significant secular trend in weight and BMI between between 1982 and 2011. Yet, multiple regression analysis failed to detect an association between nutritional status (expressed in terms of skinfold thickness), monthly family expenditure and sibship size with body height of these children. The analysis only revealed an influence of parental education on female, but not on male height. Conclusion: We failed to detect influences of nutrition, sibship size, and monthly family expenditure on body height in a large sample of children and adolescents raised in Kolkata, India, between 1982 and 2011. We found a mild positive association between parental education and girls’ height. The data question current concepts regarding the impact of nutrition, and household and economic factors on growth, but instead underscore the effect of parental education. KW - body height KW - nutrition KW - social growth adjustment Y1 - 2018 U6 - https://doi.org/10.1127/anthranz/2018/0827 SN - 0003-5548 VL - 74 IS - 5 SP - 403 EP - 411 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Ehrlich, Elias A1 - Gaedke, Ursula T1 - Not attackable or not crackable BT - How pre-and post-attack defenses with different competition costs affect prey coexistence and population dynamics JF - Ecology and Evolution N2 - It is well-known that prey species often face trade-offs between defense against predation and competitiveness, enabling predator-mediated coexistence. However, we lack an understanding of how the large variety of different defense traits with different competition costs affects coexistence and population dynamics. Our study focusses on two general defense mechanisms, that is, pre-attack (e.g., camouflage)and post-attack defenses (e.g., weaponry) that act at different phases of the predator—prey interaction. We consider a food web model with one predator, two prey types and one resource. One prey type is undefended, while the other one is pre-or post-attack defended paying costs either by a higher half-saturation constant for resource uptake or a lower maximum growth rate. We show that post-attack defenses promote prey coexistence and stabilize the population dynamics more strongly than pre-attack defenses by interfering with the predator’s functional response: Because the predator spends time handling “noncrackable” prey, the undefended prey is indirectly facilitated. A high half-saturation constant as defense costs promotes coexistence more and stabilizes the dynamics less than a low maximum growth rate. The former imposes high costs at low resource concentrations but allows for temporally high growth rates at predator-induced resource peaks preventing the extinction of the defended prey. We evaluate the effects of the different defense mechanisms and costs on coexistence under different enrichment levels in order to vary the importance of bottom-up and top-down control of the prey community. KW - coexistence KW - competition–defense trade‐off KW - defense against predation KW - functional response KW - indirect facilitation KW - predator–prey cycles Y1 - 2018 U6 - https://doi.org/10.1002/ece3.4145 SN - 2045-7758 VL - 8 IS - 13 SP - 6625 EP - 6637 PB - Wiley ER - TY - JOUR A1 - Hilgers, Leon A1 - Hartmann, Stefanie A1 - Hofreiter, Michael A1 - von Rintelen, Thomas T1 - Novel Genes, Ancient Genes, and Gene Co-Option Contributed o the Genetic Basis of the Radula, a Molluscan Innovation JF - Molecular biology and evolution N2 - The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations. KW - chitin synthase KW - novelty KW - radula KW - RNAseq KW - shell KW - Tylomelania sarasinorum Y1 - 2018 U6 - https://doi.org/10.1093/molbev/msy052 SN - 0737-4038 SN - 1537-1719 VL - 35 IS - 7 SP - 1638 EP - 1652 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Schibalski, Anett A1 - Körner, Katrin A1 - Maier, Martin A1 - Jeltsch, Florian A1 - Schröder, Boris T1 - Novel model coupling approach for resilience analysis of coastal plant communities JF - Ecological applications : a publication of the Ecological Society of America N2 - Resilience is a major research focus covering a wide range of topics from biodiversity conservation to ecosystem (service) management. Model simulations can assess the resilience of, for example, plant species, measured as the return time to conditions prior to a disturbance. This requires process-based models (PBM) that implement relevant processes such as regeneration and reproduction and thus successfully reproduce transient dynamics after disturbances. Such models are often complex and thus limited to either short-term or small-scale applications, whereas many research questions require species predictions across larger spatial and temporal scales. We suggest a framework to couple a PBM and a statistical species distribution model (SDM), which transfers the results of a resilience analysis by the PBM to SDM predictions. The resulting hybrid model combines the advantages of both approaches: the convenient applicability of SDMs and the relevant process detail of PBMs in abrupt environmental change situations. First, we simulate dynamic responses of species communities to a disturbance event with a PBM. We aggregate the response behavior in two resilience metrics: return time and amplitude of the response peak. These metrics are then used to complement long-term SDM projections with dynamic short-term responses to disturbance. To illustrate our framework, we investigate the effect of abrupt short-term groundwater level and salinity changes on coastal vegetation at the German Baltic Sea. We found two example species to be largely resilient, and, consequently, modifications of SDM predictions consisted mostly of smoothing out peaks in the occurrence probability that were not confirmed by the PBM. Discrepancies between SDM- and PBM-predicted species responses were caused by community dynamics simulated in the PBM and absent from the SDM. Although demonstrated with boosted regression trees (SDM) and an existing individual-based model, IBC-grass (PBM), our flexible framework can easily be applied to other PBM and SDM types, as well as other definitions of short-term disturbances or long-term trends of environmental change. Thus, our framework allows accounting for biological feedbacks in the response to short- and long-term environmental changes as a major advancement in predictive vegetation modeling. KW - Baltic Sea KW - hybrid model KW - Lolium perenne KW - model coupling KW - Scirpus maritimus KW - transient dynamics Y1 - 2018 U6 - https://doi.org/10.1002/eap.1758 SN - 1051-0761 SN - 1939-5582 VL - 28 IS - 6 SP - 1640 EP - 1654 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Fischer, Martin H. A1 - Shaki, Samuel T1 - Number concepts: abstract and embodied JF - Philosophical transactions of the Royal Society of London : B, Biological sciences N2 - Numerical knowledge, including number concepts and arithmetic procedures, seems to be a clear-cut case for abstract symbol manipulation. Yet, evidence from perceptual and motor behaviour reveals that natural number knowledge and simple arithmetic also remain closely associated with modal experiences. Following a review of behavioural, animal and neuroscience studies of number processing, we propose a revised understanding of psychological number concepts as grounded in physical constraints, embodied in experience and situated through task-specific intentions. The idea that number concepts occupy a range of positions on the continuum between abstract and modal conceptual knowledge also accounts for systematic heuristics and biases in mental arithmetic, thus inviting psycho-logical approaches to the study of the mathematical mind. KW - embodied cognition KW - mental arithmetic KW - mental number line KW - numerical cognition KW - SNARC effect Y1 - 2018 U6 - https://doi.org/10.1098/rstb.2017.0125 SN - 0962-8436 SN - 1471-2970 VL - 373 IS - 1752 PB - Royal Society CY - London ER - TY - JOUR A1 - Eccard, Jana A1 - Scheffler, Ingo A1 - Franke, Steffen A1 - Hoffmann, Julia T1 - Off-grid BT - solar powered LED illumination impacts epigeal arthropods JF - Insect conservation and diversity N2 - 1. Advances in LED technology combined with solar, storable energy bring light to places remote from electricity grids. Worldwide more than 1.3 billion of people are living off-grid, often in developing regions of high insect biodiversity. In developed countries, dark refuges for wildlife are threatened by ornamental garden lights. Solar powered LEDs (SPLEDs) are cheaply available, dim, and often used to illuminate foot paths, but little is known on their effects on ground living (epigeal) arthropods. 2. We used off-the-shelf garden lamps with a single ‘white’ LED (colour temperature 7250 K) to experimentally investigate effects on attraction and nocturnal activity of ground beetles (Carabidae). 3. We found two disparate and species-specific effects of SPLEDs. (i) Some nocturnal, phototactic species were not reducing activity under illumination and were strongly attracted to lamps (>20-fold increase in captures compared to dark controls). Such species aggregate in lit areas and SPLEDs may become ecological traps, while the species is drawn from nearby, unlit assemblages. (ii) Other nocturnal species were reducing mobility and activity under illumination without being attracted to light, which may cause fitness reduction in lit areas. 4. Both reactions offer mechanistic explanations on how outdoor illumination can change population densities of specific predatory arthropods, which may have cascading effects on epigeal arthropod assemblages. The technology may thus increase the area of artificial light at night (ALAN) impacting insect biodiversity. 5. Measures are needed to mitigate effects, such as adjustment of light colour temperature and automated switch-offs. KW - Artificial light at night (ALAN) KW - Carabidae KW - illuminance KW - light pollution KW - light spectrum KW - nocturnal epigeal insect KW - phototaxis KW - solar powered light-emitting diode KW - spectral irradiance KW - white light Y1 - 2018 U6 - https://doi.org/10.1111/icad.12303 SN - 1752-458X SN - 1752-4598 VL - 11 IS - 6 SP - 600 EP - 607 PB - Wiley CY - Hoboken ER - TY - GEN A1 - Luckner, Madlen A1 - Dunsing, Valentin A1 - Chiantia, Salvatore A1 - Hermann, Andreas T1 - Oligomerization and nuclear shuttling dynamics of viral proteins studied by quantitative molecular brightness analysis using fluorescence correlation spectroscopy T2 - Biophysical journal Y1 - 2018 U6 - https://doi.org/10.1016/j.bpj.2017.11.1951 SN - 0006-3495 SN - 1542-0086 VL - 114 IS - 3 SP - 350A EP - 350A PB - Cell Press CY - Cambridge ER - TY - GEN A1 - Barlow, Axel A1 - Sheng, Gui-Lian A1 - Lai, Xu-Long A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. T1 - Once lost, twice found: Combined analysis of ancient giant panda sequences characterises extinct clade T2 - Journal of biogeography Y1 - 2018 U6 - https://doi.org/10.1111/jbi.13486 SN - 0305-0270 SN - 1365-2699 VL - 46 IS - 1 SP - 251 EP - 253 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Dunsing, Valentin A1 - Luckner, Madlen A1 - Zuehlke, Boris A1 - Petazzi, Roberto Arturo A1 - Herrmann, Andreas A1 - Chiantia, Salvatore T1 - Optimal fluorescent protein tags for quantifying protein oligomerization in living cells JF - Scientific reports N2 - Fluorescence fluctuation spectroscopy has become a popular toolbox for non-disruptive analysis of molecular interactions in living cells. The quantification of protein oligomerization in the native cellular environment is highly relevant for a detailed understanding of complex biological processes. An important parameter in this context is the molecular brightness, which serves as a direct measure of oligomerization and can be easily extracted from temporal or spatial fluorescence fluctuations. However, fluorescent proteins (FPs) typically used in such studies suffer from complex photophysical transitions and limited maturation, inducing non-fluorescent states. Here, we show how these processes strongly affect molecular brightness measurements. We perform a systematic characterization of non-fluorescent states for commonly used FPs and provide a simple guideline for accurate, unbiased oligomerization measurements in living cells. Further, we focus on novel red FPs and demonstrate that mCherry2, an mCherry variant, possesses superior properties with regards to precise quantification of oligomerization. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-28858-0 SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Alberti, Federica A1 - Gonzalez, Javier A1 - Paijmans, Johanna L. A. A1 - Basler, Nikolas A1 - Preick, Michaela A1 - Henneberger, Kirstin A1 - Trinks, Alexandra A1 - Rabeder, Gernot A1 - Conard, Nicholas J. A1 - Muenzel, Susanne C. A1 - Joger, Ulrich A1 - Fritsch, Guido A1 - Hildebrandt, Thomas A1 - Hofreiter, Michael A1 - Barlow, Axel T1 - Optimized DNA sampling of ancient bones using Computed Tomography scans JF - Molecular ecology resources N2 - The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era. KW - ancient DNA KW - computer tomography KW - palaeogenomics KW - paleogenetics KW - petrous bone Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12911 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1196 EP - 1208 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Bizic-Ionescu, Mina A1 - Ionescu, Danny A1 - Grossart, Hans-Peter T1 - Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems JF - Frontiers in microbiology N2 - The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3–4 particles of identical source and age and further evaluated the consequences of averaging 10–1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as “the bottle-effect.” In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn’t change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems. KW - particle-associated bacteria KW - microbial communities KW - inter- and intra-species interactions KW - antagonism KW - phage KW - transcriptome Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.02569 SN - 1664-302X VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - GEN A1 - Messerschmidt, Katrin A1 - Machens, Fabian A1 - Hochrein, Lena A1 - Naseri, Gita T1 - Orthogonal, light-inducible protein expression platform in yeast Sacchararomyces cerevisiae T2 - New biotechnology Y1 - 2018 U6 - https://doi.org/10.1016/j.nbt.2018.05.153 SN - 1871-6784 SN - 1876-4347 VL - 44 SP - S19 EP - S19 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Krstic, Jelena A1 - Reinisch, Isabel A1 - Schupp, Michael A1 - Schulz, Tim Julius A1 - Prokesch, Andreas T1 - p53 functions in adipose tissue metabolism and homeostasis JF - International journal of molecular sciences N2 - As a tumor suppressor and the most frequently mutated gene in cancer, p53 is among the best-described molecules in medical research. As cancer is in most cases an age-related disease, it seems paradoxical that p53 is so strongly conserved from early multicellular organisms to humans. A function not directly related to tumor suppression, such as the regulation of metabolism in nontransformed cells, could explain this selective pressure. While this role of p53 in cellular metabolism is gradually emerging, it is imperative to dissect the tissue-and cell-specific actions of p53 and its downstream signaling pathways. In this review, we focus on studies reporting p53's impact on adipocyte development, function, and maintenance, as well as the causes and consequences of altered p53 levels in white and brown adipose tissue (AT) with respect to systemic energy homeostasis. While whole body p53 knockout mice gain less weight and fat mass under a high-fat diet owing to increased energy expenditure, modifying p53 expression specifically in adipocytes yields more refined insights: (1) p53 is a negative regulator of in vitro adipogenesis; (2) p53 levels in white AT are increased in diet-induced and genetic obesity mouse models and in obese humans; (3) functionally, elevated p53 in white AT increases senescence and chronic inflammation, aggravating systemic insulin resistance; (4) p53 is not required for normal development of brown AT; and (5) when p53 is activated in brown AT in mice fed a high-fat diet, it increases brown AT temperature and brown AT marker gene expression, thereby contributing to reduced fat mass accumulation. In addition, p53 is increasingly being recognized as crucial player in nutrient sensing pathways. Hence, despite existence of contradictory findings and a varying density of evidence, several functions of p53 in adipocytes and ATs have been emerging, positioning p53 as an essential regulatory hub in ATs. Future studies need to make use of more sophisticated in vivo model systems and should identify an AT-specific set of p53 target genes and downstream pathways upon different (nutrient) challenges to identify novel therapeutic targets to curb metabolic diseases KW - p53 KW - adipose tissue KW - metabolic syndrome KW - obesity KW - adipogenesis KW - insulin resistance Y1 - 2018 U6 - https://doi.org/10.3390/ijms19092622 SN - 1422-0067 VL - 19 IS - 9 PB - MDPI CY - Basel ER - TY - GEN A1 - Dammhahn, Melanie A1 - Dingemanse, Niels J. A1 - Niemelae, Petri T. A1 - Reale, Denis T1 - Pace-of-life syndromes BT - a framework for the adaptive integration of behaviour, physiology and life history T2 - Behavioral ecology and sociobiology N2 - This introduction to the topical collection on Pace-of-life syndromes: a framework for the adaptive integration of behaviour, physiology, and life history provides an overview of conceptual, theoretical, methodological, and empirical progress in research on pace-of-life syndromes (POLSs) over the last decade. The topical collection has two main goals. First, we briefly describe the history of POLS research and provide a refined definition of POLS that is applicable to various key levels of variation (genetic, individual, population, species). Second, we summarise the main lessons learned from current POLS research included in this topical collection. Based on an assessment of the current state of the theoretical foundations and the empirical support of the POLS hypothesis, we propose (i) conceptual refinements of theory, particularly with respect to the role of ecology in the evolution of (sexual dimorphism in) POLS, and (ii) methodological and statistical approaches to the study of POLS at all major levels of variation. This topical collection further holds (iii) key empirical examples demonstrating how POLS structures may be studied in wild populations of (non) human animals, and (iv) a modelling paper predicting POLS under various ecological conditions. Future POLS research will profit from the development of more explicit theoretical models and stringent empirical tests of model assumptions and predictions, increased focus on how ecology shapes (sex-specific) POLS structures at multiple hierarchical levels, and the usage of appropriate statistical tests and study designs. Significance statement As an introduction to the topical collection, we summarise current conceptual, theoretical, methodological and empirical progress in research on pace-of-life syndromes (POLSs), a framework for the adaptive integration of behaviour, physiology and life history at multiple hierarchical levels of variation (genetic, individual, population, species). Mixed empirical support of POLSs, particularly at the within-species level, calls for an evaluation and refinement of the hypothesis. We provide a refined definition of POLSs facilitating testable predictions. Future research on POLSs will profit from the development of more explicit theoretical models and stringent empirical tests of model assumptions and predictions, increased focus on how ecology shapes (sex-specific) POLSs structures at multiple hierarchical levels and the usage of appropriate statistical tests and study designs. Y1 - 2018 U6 - https://doi.org/10.1007/s00265-018-2473-y SN - 0340-5443 SN - 1432-0762 VL - 72 IS - 3 PB - Springer CY - New York ER - TY - THES A1 - Bibi, Faysal T1 - Paleoecology and evolution in the Afro-Arabian neogene T1 - Paläoökologie und Evolution im afro-arabischen Neogen N2 - This cumulative habilitation thesis presents new work on the systematics, paleoecology, and evolution of antelopes and other large mammals, focusing mainly on the late Miocene to Pleistocene terrestrial fossil record of Africa and Arabia. The studies included here range from descriptions of new species to broad-scale analyses of diversification and community evolution in large mammals over millions of years. A uniting theme is the evolution, across both temporal and spatial scales, of the environments and faunas that characterize modern African savannas today. One conclusion of this work is that macroevolutionary changes in large mammals are best characterized at regional (subcontinental to continental) and long-term temporal scales. General views of evolution developed on records that are too restricted in spatial and temporal extent are likely to ascribe too much influence to local or short-lived events. While this distinction in the scale of analysis and interpretation may seem trivial, it is challenging to implement given the geographically and temporally uneven nature of the fossil record, and the difficulties of synthesizing spatially and temporally dispersed datasets. This work attempts to do just that, bringing together primary fossil discoveries from eastern Africa to Arabia, from the Miocene to the Pleistocene, and across a wide range of (mainly large mammal) taxa. The end result is support for hypotheses stressing the impact of both climatic and biotic factors on long-term faunal change, and a more geographically integrated view of evolution in the African fossil record. N2 - Die vorliegende kumulative Habilitationsarbeit beschäftigt sich mit der Systematik, Paläoökologie und Evolution von Antilopen und anderen Großsäugetieren mit Schwerpunkt auf dem spätmiozänen bis pleistozänen Fossilbericht Arabiens und Afrikas. Die Untersuchungen reichen dabei von der Beschreibung neuer Arten bis hin zu großmaßstäblichen Analysen zur Diversifikation und Community-Evolution von Großsäugern über mehrere Millionen Jahre, mit besonderem Augenmerk auf der zeitlichen und räumlichen Evolution der für die heutigen afrikanischen Savannen charakteristischen Fauna und Umwelt. Eine der Schlussfolgerungen der vorliegenden Arbeit lautet, dass makroevolutionärer Wandel bei Großsäugetieren am besten auf der regionalen (subkontinental bis kontinentalen) Ebene sowie über lange zeitliche Skalen hinweg sichtbar wird. Umgekehrt scheinen davon abweichende Ergebnisse früherer Studien, welche häufig auf zeitlich und räumlich eingeschränkter Basis durchgeführt wurden, übermäßig von kurzfristigen Ereignissen beeinflusst worden zu sein. Ein besseres Verständnis für die methodischen Ursachen dieser unterschiedlichen Bewertungen ist von großer Bedeutung in Anbetracht der variablen Qualität des Fossilberichts und den Schwierigkeiten, derartige zeitlich und räumlich oftmals heterogenen Datensätze adäquat zu synthetisieren – letzteres war ein erklärtes Ziel der vorliegenden Arbeit. Schlussendlich unterstützen die hier dargelegten Untersuchungen die Hypothese eines Einflusses von sowohl klimatischen wie biotischen Faktoren auf langzeitlichen Faunenwandel und bieten eine neue, integrierte Perspektive auf die Evolution der afrikanischen Großsäuger-Faunen. KW - Africa KW - Arabia KW - neogene KW - paleontology KW - mammals KW - Afrika KW - Arabien KW - Neogen KW - Paläontologie KW - Säugetiere Y1 - 2018 ER - TY - JOUR A1 - Malinova, Irina A1 - Qasim, Hadeel M. A1 - Brust, Henrike A1 - Fettke, Jörg T1 - Parameters of Starch Granule Genesis in Chloroplasts of Arabidopsis thaliana JF - Frontiers in Plant Science N2 - Starch is the primary storage carbohydrate in most photosynthetic organisms and allows the accumulation of carbon and energy in form of an insoluble and semi-crystalline particle. In the last decades large progress, especially in the model plant Arabidopsis thaliana, was made in understanding the structure and metabolism of starch and its conjunction. The process underlying the initiation of starch granules remains obscure, although this is a fundamental process and seems to be strongly regulated, as in Arabidopsis leaves the starch granule number per chloroplast is fixed with 5-7. Several single, double, and triple mutants were reported in the last years that showed massively alterations in the starch granule number per chloroplast and allowed further insights in this important process. This mini review provides an overview of the current knowledge of processes involved in the initiation and formation of starch granules. We discuss the central role of starch synthase 4 and further proteins for starch genesis and affecting metabolic factors. KW - starch biosynthesis KW - starch granule biogenesis KW - starch synthase KW - plastidial phosphorylase KW - maltooligosaccharides Y1 - 2018 U6 - https://doi.org/10.3389/fpls.2018.00761 SN - 1664-462X VL - 9 SP - 1 EP - 7 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Barlow, Axel A1 - Cahill, James A. A1 - Hartmann, Stefanie A1 - Theunert, Christoph A1 - Xenikoudakis, Georgios A1 - Gonzalez-Fortes, Gloria M. A1 - Paijmans, Johanna L. A. A1 - Rabeder, Gernot A1 - Frischauf, Christine A1 - Garcia-Vazquez, Ana A1 - Murtskhvaladze, Marine A1 - Saarma, Urmas A1 - Anijalg, Peeter A1 - Skrbinsek, Tomaz A1 - Bertorelle, Giorgio A1 - Gasparian, Boris A1 - Bar-Oz, Guy A1 - Pinhasi, Ron A1 - Slatkin, Montgomery A1 - Dalen, Love A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Partial genomic survival of cave bears in living brown bears JF - Nature Ecology & Evolution N2 - Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species. Y1 - 2018 U6 - https://doi.org/10.1038/s41559-018-0654-8 SN - 2397-334X VL - 2 IS - 10 SP - 1563 EP - 1570 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Tejos, Ricardo A1 - Rodriguez-Furlan, Cecilia A1 - Adamowski, Maciej A1 - Sauer, Michael A1 - Norambuena, Lorena A1 - Friml, Jiri T1 - PATELLINS are regulators of auxin-mediated PIN1 relocation and plant development in Arabidopsis thaliana JF - Journal of cell science N2 - Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We used a microarray-based approach to find regulators of the auxin-induced PIN relocation in Arabidopsis thaliana root, and identified a subset of a family of phosphatidylinositol transfer proteins (PITPs), the PATELLINs (PATLs). Here, we show that PATLs are expressed in partially overlapping cell types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests that PATLs play a redundant and crucial role in polarity and patterning in Arabidopsis. KW - PATELLIN KW - Auxin KW - Arabidopsis thaliana KW - Auxin transport KW - Canalization Y1 - 2018 U6 - https://doi.org/10.1242/jcs.204198 SN - 0021-9533 SN - 1477-9137 VL - 131 IS - 2 PB - Company of Biologists Limited CY - Cambridge ER - TY - GEN A1 - Hermanussen, Michael A1 - Scheffler, Christiane A1 - Groth, Detlef A1 - Bogin, Barry T1 - Perceiving stunting - Student research and the "Lieschen Muller effect" in nutrition science T2 - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie KW - stunting KW - undernutrition KW - strategic growth adjustments KW - competitive growth KW - community effect on height Y1 - 2018 U6 - https://doi.org/10.1127/anthranz/2018/0858 SN - 0003-5548 VL - 74 IS - 5 SP - 355 EP - 358 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Tischew, Sabine A1 - Dierschke, Hartmut A1 - Schwabe, Angelika A1 - Garve, Eckhard A1 - Heinken, Thilo A1 - Holzel, Norbert A1 - Bergmeier, Erwin A1 - Remy, Dominique A1 - Haerdtle, Werner T1 - Pflanzengesellschaft des Jahres 2019: Die Glatthaferwiese T1 - Plant Community of the Year 2019: Oatgras Meadow JF - Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft N2 - Um Themen des Schutzes von Pflanzengemeinschaften wirksamer in der breiten Öffentlichkeit zu kommunizieren wird der Vorstand der „Floristisch-Soziologischen Arbeitsgemeinschaft (FlorSoz)“ ab 2019 eine „Pflanzengesellschaft des Jahres“ ausrufen. Damit sollen politische und administrative Entscheidungs- und Umsetzungsprozesse zur Erhaltung der Vielfalt von Ökosystemen und Pflanzengesellschaften in Deutschlands gezielt unterstützt werden. Für das Jahr 2019 wurde die Glatthaferwiese ausgewählt. Sie zählt aktuell zu den durch Artenverarmung und Flächenrückgang besonders bedrohten Pflanzengesellschaften Deutschlands. Es sind deshalb dringend Maßnahmen zum Schutz und zur Wiederherstellung notwendig. Dieser Artikel gibt einen kurzen Überblick zur naturschutzfachlichen Bedeutung von Glatthaferwiesen und deren Ökosystemleistungen sowie zur floristisch-soziologischen Erforschung, zu Ursachen ihres Rückgangs und zu geeigneten Gegenmaßnahmen. N2 - Aiming at a better promotion of topics related to the conservation of ecosystems and plant communities, the board of the Floristisch-Soziologische Arbeitsgemeinschaft (FlorSoz)" has launched the initiative to announce a "Plant Community of the Year". Therewith we hope to raise awareness and stimulate civil society and politics in promoting more efficient conservation strategies. For the forthcoming year, we choose the oatgras meadow as Plant Community of the Year 2019. These lowland hay meadows belong to the most threatened plant communities in Germany. Concepts and schemes aiming at the conservation and restoration of lowland hay meadows are urgently needed. This article provides a short overview of the high nature-conservation value of lowland hay meadows and their ecosystem services as well as of the floristic-phytosociological research, reasons for their sharp decline and appropriate countermeasures. Y1 - 2018 U6 - https://doi.org/10.14471/2018.38.011 SN - 0722-494X IS - 38 SP - 287 EP - 295 PB - Floristisch-Soziologische Arbeitsgemeinschaft CY - Göttingen ER - TY - JOUR A1 - Zhao, Liming A1 - Xia, Yan A1 - Wu, Xiao-Yuan A1 - Schippers, Jos H. M. A1 - Jing, Hai-Chun T1 - Phenotypic analysis and molecular markers of leaf senescence JF - Plant Senescence: Methods and Protocols N2 - The process of leaf senescence consists of the final stage of leaf development. It has evolved as a mechanism to degrade macromolecules and micronutrients and remobilize them to other developing parts of the plant; hence it plays a central role for the survival of plants and crop production. During senescence, a range of physiological, morphological, cellular, and molecular events occur, which are generally referred to as the senescence syndrome that includes several hallmarks such as visible yellowing, loss of chlorophyll and water content, increase of ion leakage and cell death, deformation of chloroplast and cell structure, as well as the upregulation of thousands of so-called senescence-associated genes (SAGs) and downregulation of photosynthesis-associated genes (PAGs). This chapter is devoted to methods characterizing the onset and progression of leaf senescence at the morphological, physiological, cellular, and molecular levels. Leaf senescence normally progresses in an age-dependent manner but is also induced prematurely by a variety of environmental stresses in plants. Focused on the hallmarks of the senescence syndrome, a series of protocols is described to asses quantitatively the senescence process caused by developmental cues or environmental perturbations. We first briefly describe the senescence process, the events associated with the senescence syndrome, and the theories and methods to phenotype senescence. Detailed protocols for monitoring senescence in planta and in vitro, using the whole plant and the detached leaf, respectively, are presented. For convenience, most of the protocols use the model plant species Arabidopsis and rice, but they can be easily extended to other plants. KW - Leaf senescence KW - Visible yellowing KW - Chlorophyll KW - Ion leakage KW - Cell death KW - Senescence-associated genes (SAGs) KW - Arabidopsis KW - Rice Y1 - 2018 SN - 978-1-4939-7672-0 SN - 978-1-4939-7670-6 U6 - https://doi.org/10.1007/978-1-4939-7672-0_3 SN - 1064-3745 SN - 1940-6029 VL - 1744 SP - 35 EP - 48 PB - Humana Press Inc. CY - Totowa ER - TY - JOUR A1 - Horreo, Jose L. A1 - Pelaez, Maria L. A1 - Suarez, Teresa A1 - Breedveld, Merel Cathelijne A1 - Heulin, Benoit A1 - Surget-Groba, Yann A1 - Oksanen, Tuula A. A1 - Fitze, Patrick S. T1 - Phylogeography, evolutionary history and effects of glaciations in a species (Zootoca vivipara) inhabiting multiple biogeographic regions JF - Journal of biogeography N2 - Location Eurasia. Methods We generated the largest molecular dataset to date of Z. vivipara, ran phylogenetic analyses, reconstructed its evolutionary history, determined the location of glacial refuges and reconstructed ancestral biogeographic regions. Results The phylogenetic analyses revealed a complex evolutionary history, driven by expansions and contractions of the distribution due to glacials and interglacials, and the colonization of new biogeographic regions by all lineages of Z. vivipara. Many glacial refugia were detected, most were located close to the southern limit of the Last Glacial Maximum. Two subclades recolonized large areas covered by permafrost during the last glaciation: namely, Western and Northern Europe and North-Eastern Europe and Asia. KW - ancestral area reconstruction KW - ancestral biogeographic region reconstruction KW - biogeography KW - glacial refuges KW - last glacial maxima KW - molecular diversity KW - phylogeny KW - post-glacial recolonization Y1 - 2018 U6 - https://doi.org/10.1111/jbi.13349 SN - 0305-0270 SN - 1365-2699 VL - 45 IS - 7 SP - 1616 EP - 1627 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Lämke, Jörn. S. A1 - Unsicker, Sybille Barbara T1 - Phytochemical variation in treetops BT - causes and consequences for tree-insect herbivore interactions JF - Oecologia N2 - The interaction of plants and their herbivorous opponents has shaped the evolution of an intricate network of defences and counter-defences for millions of years. The result is an astounding diversity of phytochemicals and plant strategies to fight and survive. Trees are specifically challenged to resist the plethora of abiotic and biotic stresses due to their dimension and longevity. Here, we review the recent literature on the consequences of phytochemical variation in trees on insect-tree-herbivore interactions. We discuss the importance of genotypic and phenotypic variation in tree defence against insects and suggest some molecular mechanisms that might bring about phytochemical diversity in crowns of individual trees. KW - Chromatin-based mechanisms KW - Genotypic variation KW - Insect herbivore KW - Phenotypic plasticity KW - Tree defence Y1 - 2018 U6 - https://doi.org/10.1007/s00442-018-4087-5 SN - 0029-8549 SN - 1432-1939 VL - 187 IS - 2 SP - 377 EP - 388 PB - Springer CY - New York ER - TY - JOUR A1 - Möser, Christin A1 - Lorenz, Jessica S. A1 - Sajfutdinow, Martin A1 - Smith, David M. T1 - Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence JF - International journal of molecular sciences N2 - DNA nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL, an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner. Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover, Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison to one of EphA2’s natural ligands ephrin-A1, which is known to bind promiscuously to multiple receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling peptides through oligovalent presentation and serve as potential tools for examination of complex signaling pathways. KW - DNA nanostructure KW - ephrin KW - EphA2 KW - SWL KW - PC-3 cells KW - multivalence Y1 - 2018 U6 - https://doi.org/10.3390/ijms19113482 SN - 1422-0067 VL - 19 IS - 11 PB - MDPI CY - Basel ER - TY - JOUR A1 - Lukan, Tjaša A1 - Machens, Fabian A1 - Coll, Anna A1 - Baebler, Špela A1 - Messerschmidt, Katrin A1 - Gruden, Kristina T1 - Plant X-tender BT - an extension of the AssemblX system for the assembly and expression of multigene constructs in plants JF - PLOS ONE N2 - Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0190526 SN - 1932-6203 VL - 13 IS - 1 PB - Public Library of Science CY - San Fransisco ER - TY - JOUR A1 - Cisek, Richard A1 - Tokarz, Danielle A1 - Kontenis, Lukas A1 - Barzda, Virginijus A1 - Steup, Martin T1 - Polarimetric second harmonic generation microscopy BT - an analytical tool for starch bioengineering JF - Starch-Starke N2 - Second harmonic generation (SHG) is a nonlinear optical process that inherently generates signal in non-centrosymmetric materials, such as starch granules, and therefore can be used for label-free imaging. Both intensity and polarization of SHG are determined by material properties that are characterized by the nonlinear susceptibility tensor, ((2)). Examination of the tensor is performed for each focal volume of the image by measuring the outgoing polarization state of the SHG signal for a set of incoming laser beam polarizations. Mapping of nonlinear properties expressed as the susceptibility ratio reveals structural features including the organization of crystalline material within a single starch granule, and the distribution of structural properties in a population of granules. Isolated granules, as well as in situ starch, can be analyzed using polarimetric SHG microscopy. Due to the fast sample preparation and short imaging times, polarimetric SHG microscopy allows for a quick assessment of starch structure and permits rapid feedback for bioengineering applications. This article presents the basics of SHG theory and microscopy applications for starch-containing materials. Quantification of ultrastructural features within individual starch granules is described. New results obtained by polarization resolved SHG microscopy of starch granules are presented for various maize genotypes revealing heterogeneity within a single starch particle and between various granules. KW - Determination of crystallinity KW - Determination of hydration KW - Label-free imaging KW - Nonlinear optical microscopy KW - Structural determination Y1 - 2017 U6 - https://doi.org/10.1002/star.201700031 SN - 0038-9056 SN - 1521-379X VL - 70 IS - 1-2 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Wen, Xi A1 - Unger, Viktoria A1 - Jurasinski, Gerald A1 - Koebsch, Franziska A1 - Horn, Fabian A1 - Rehder, Gregor A1 - Sachs, Torsten A1 - Zak, Dominik A1 - Lischeid, Gunnar A1 - Knorr, Klaus-Holger A1 - Boettcher, Michael E. A1 - Winkel, Matthias A1 - Bodelier, Paul L. E. A1 - Liebner, Susanne T1 - Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions JF - Biogeosciences N2 - The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rRNA high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity (EC) was more than 3 times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5 mS cm(-1), respectively. Porewater concentrations of terminal electron acceptors (TEAs) varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid (re) establishment of methanogens and slow (re) establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting. Y1 - 2018 U6 - https://doi.org/10.5194/bg-15-6519-2018 SN - 1726-4170 SN - 1726-4189 VL - 15 IS - 21 SP - 6519 EP - 6536 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Stoessel, Daniel A1 - Schulte, Claudia A1 - dos Santos, Marcia C. Teixeira A1 - Scheller, Dieter A1 - Rebollo-Mesa, Irene A1 - Deuschle, Christian A1 - Walther, Dirk A1 - Schauer, Nicolas A1 - Berg, Daniela A1 - da Costa, Andre Nogueira A1 - Maetzler, Walter T1 - Promising Metabolite Profiles in the Plasma and CSF of Early Clinical JF - Frontiers in Aging Neuroscience N2 - Parkinson's disease (PD) shows high heterogeneity with regard to the underlying molecular pathogenesis involving multiple pathways and mechanisms. Diagnosis is still challenging and rests entirely on clinical features. Thus, there is an urgent need for robust diagnostic biofluid markers. Untargeted metabolomics allows establishing low-molecular compound biomarkers in a wide range of complex diseases by the measurement of various molecular classes in biofluids such as blood plasma, serum, and cerebrospinal fluid (CSF). Here, we applied untargeted high-resolution mass spectrometry to determine plasma and CSF metabolite profiles. We semiquantitatively determined small-molecule levels (<= 1.5 kDa) in the plasma and CSF from early PD patients (disease duration 0-4 years; n = 80 and 40, respectively), and sex-and age-matched controls (n = 76 and 38, respectively). We performed statistical analyses utilizing partial least square and random forest analysis with a 70/30 training and testing split approach, leading to the identification of 20 promising plasma and 14 CSF metabolites. The semetabolites differentiated the test set with an AUC of 0.8 (plasma) and 0.9 (CSF). Characteristics of the metabolites indicate perturbations in the glycerophospholipid, sphingolipid, and amino acid metabolism in PD, which underscores the high power of metabolomic approaches. Further studies will enable to develop a potential metabolite-based biomarker panel specific for PD KW - biomarker KW - untargeted metabolomics KW - neurodegeneration KW - plasma KW - CSF KW - machinelearning Y1 - 2018 U6 - https://doi.org/10.3389/fnagi.2018.00051 SN - 1663-4365 VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - GEN A1 - Autenrieth, Marijke A1 - Ernst, Anja A1 - Deaville, Rob A1 - Demaret, Fabien A1 - Ijsseldijk, Lonneke L. A1 - Siebert, Ursula A1 - Tiedemann, Ralph T1 - Putative origin and maternal relatedness of male sperm whales (Physeter macrocephalus) recently stranded in the North Sea T2 - Mammalian biology = Zeitschrift für Säugetierkunde N2 - The globally distributed sperm whale (Physeter macrocephalus) has a partly matrilineal social structure with predominant male dispersal. At the beginning of 2016, a total of 30 male sperm whales stranded in five different countries bordering the southern North Sea. It has been postulated that these individuals were on a migration route from the north to warmer temperate and tropical waters where females live in social groups. By including samples from four countries (n = 27), this event provided a unique chance to genetically investigate the maternal relatedness and the putative origin of these temporally and spatially co-occuring male sperm whales. To utilize existing genetic resources, we sequenced 422 bp of the mitochondrial control region, a molecular marker for which sperm whale data are readily available from the entire distribution range. Based on four single nucleotide polymorphisms (SNPs) within the mitochondrial control region, five matrilines could be distinguished within the stranded specimens, four of which matched published haplotypes previously described in the Atlantic. Among these male sperm whales, multiple matrilineal lineages co-occur. We analyzed the population differentiation and could show that the genetic diversity of these male sperm whales is comparable to the genetic diversity in sperm whales from the entire Atlantic Ocean. We confirm that within this stranding event, males do not comprise maternally related individuals and apparently include assemblages of individuals from different geographic regions. (c) 2017 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved. KW - Mitochondrial DNA KW - Maternal relationships KW - Population genetics KW - Migration KW - Marine mammals Y1 - 2018 U6 - https://doi.org/10.1016/j.mambio.2017.09.003 SN - 1616-5047 SN - 1618-1476 VL - 88 SP - 156 EP - 160 PB - Elsevier CY - München ER - TY - JOUR A1 - Käch, Heidi A1 - Mathe-Hubert, Hugo A1 - Dennis, Alice B. A1 - Vorburger, Christoph T1 - Rapid evolution of symbiont-mediated resistance compromises biological control of aphids by parasitoids JF - Evolutionary applications N2 - There is growing interest in biological control as a sustainable and environmentally friendly way to control pest insects. Aphids are among the most detrimental agricultural pests worldwide, and parasitoid wasps are frequently employed for their control. The use of asexual parasitoids may improve the effectiveness of biological control because only females kill hosts and because asexual populations have a higher growth rate than sexuals. However, asexuals may have a reduced capacity to track evolutionary change in their host populations. We used a factorial experiment to compare the ability of sexual and asexual populations of the parasitoid Lysiphlebus fabarum to control caged populations of black bean aphids (Aphis fabae) of high and low clonal diversity. The aphids came from a natural population, and one-third of the aphid clones harbored Hamiltonella defensa, a heritable bacterial endosymbiont that increases resistance to parasitoids. We followed aphid and parasitoid population dynamics for 3months but found no evidence that the reproductive mode of parasitoids affected their effectiveness as biocontrol agents, independent of host clonal diversity. Parasitoids failed to control aphids in most cases, because their introduction resulted in strong selection for clones protected by H.defensa. The increasingly resistant aphid populations escaped control by parasitoids, and we even observed parasitoid extinctions in many cages. The rapid evolution of symbiont-conferred resistance in turn imposed selection on parasitoids. In cages where asexual parasitoids persisted until the end of the experiment, they became dominated by a single genotype able to overcome the protection provided by H.defensa. Thus, there was evidence for parasitoid counteradaptation, but it was generally too slow for parasitoids to regain control over aphid populations. It appears that when pest aphids possess defensive symbionts, the presence of parasitoid genotypes able to overcome symbiont-conferred resistance is more important for biocontrol success than their reproductive mode. KW - aphids KW - Aphis fabae KW - biological control KW - defensive symbiosis KW - Hamiltonella defensa KW - Lysiphlebus fabarum KW - parasitoid KW - resistance Y1 - 2018 U6 - https://doi.org/10.1111/eva.12532 SN - 1752-4571 VL - 11 IS - 2 SP - 220 EP - 230 PB - Wiley CY - Hoboken ER - TY - GEN A1 - Uhlig, Katja A1 - Gehre, Christian P. A1 - Kammerer, Sarah A1 - Küpper, Jan-Heiner A1 - Coleman, Charles Dominic A1 - Püschel, Gerhard Paul A1 - Duschl, Claus T1 - Real-time monitoring of oxygen consumption of hepatocytes in a microbioreactor T2 - Toxicology letters Y1 - 2018 U6 - https://doi.org/10.1016/j.toxlet.2018.06.652 SN - 0378-4274 SN - 1879-3169 VL - 295 SP - S115 EP - S115 PB - Elsevier CY - Clare ER - TY - JOUR A1 - Cuadrat, Rafael R. C. A1 - Ionescu, Danny A1 - Davila, Alberto M. R. A1 - Grossart, Hans-Peter T1 - Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics JF - Frontiers in microbiology N2 - Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem. KW - metagenomics 2.0 KW - PKS KW - NRPS KW - freshwater KW - environmental genomics Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.00251 SN - 1664-302X VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - de Abreu e Lima, Francisco Anastacio A1 - Leifels, Lydia A1 - Nikoloski, Zoran T1 - Regression-based modeling of complex plant traits based on metabolomics data JF - Plant Metabolomics N2 - Bridging metabolomics with plant phenotypic responses is challenging. Multivariate analyses account for the existing dependencies among metabolites, and regression models in particular capture such dependencies in search for association with a given trait. However, special care should be undertaken with metabolomics data. Here we propose a modeling workflow that considers all caveats imposed by such large data sets. KW - Metabolomics KW - Plants KW - Trait KW - Regression KW - Prediction KW - Modeling KW - R programing language KW - R software packages Y1 - 2018 SN - 978-1-4939-7819-9 SN - 978-1-4939-7818-2 U6 - https://doi.org/10.1007/978-1-4939-7819-9_23 SN - 1064-3745 SN - 1940-6029 VL - 1778 SP - 321 EP - 327 PB - Humana Press Inc. CY - New York ER - TY - THES A1 - Mubeen, Umarah T1 - Regulation of central carbon and nitrogen metabolism by Target of Rapamycin (TOR) kinase in Chlamydomonas reinhardtii T1 - Regulation des zentralen Kohlen- und Stickstoff Stoffwechsels durch die Target of Rapamycin Kinase in der Grünalge Chlamydomonas reinhardtii N2 - The highly conserved protein complex containing the Target of Rapamycin (TOR) kinase is known to integrate intra- and extra-cellular stimuli controlling nutrient allocation and cellular growth. This thesis describes three studies aimed to understand how TOR signaling pathway influences carbon and nitrogen metabolism in Chlamydomonas reinhardtii. The first study presents a time-resolved analysis of the molecular and physiological features across the diurnal cycle. The inhibition of TOR leads to 50% reduction in growth followed by nonlinear delays in the cell cycle progression. The metabolomics analysis showed that the growth repression is mainly driven by differential carbon partitioning between anabolic and catabolic processes. Furthermore, the high accumulation of nitrogen-containing compounds indicated that TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression. In the second study the cause of the high accumulation of amino acids is explained. For this purpose, the effect of TOR inhibition on Chlamydomonas was examined under different growth regimes using stable 13C- and 15N-isotope labeling. The data clearly showed that an increased nitrogen uptake is induced within minutes after the inhibition of TOR. Interestingly, this increased N-influx is accompanied by increased activities of nitrogen assimilating enzymes. Accordingly, it was concluded that TOR inhibition induces de-novo amino acid synthesis in Chlamydomonas. The recognition of this novel process opened an array of questions regarding potential links between central metabolism and TOR signaling. Therefore a detailed phosphoproteomics study was conducted to identify the potential substrates of TOR pathway regulating central metabolism. Interestingly, some of the key enzymes involved in carbon metabolism as well as amino acid synthesis exhibited significant changes in the phosphosite intensities immediately after TOR inhibition. Altogether, these studies provide a) detailed insights to metabolic response of Chlamydomonas to TOR inhibition, b) identification of a novel process causing rapid upshifts in amino acid levels upon TOR inhibition and c) finally highlight potential targets of TOR signaling regulating changes in central metabolism. Further biochemical and molecular investigations could confirm these observations and advance the understanding of growth signaling in microalgae. N2 - Target of Rapamycin (TOR) ist das Zentralprotein eines hochkonservierten Proteinkomplexes, welcher Nährstoff- und Energie Ressourcen für zelluläre Wachstumsprozesse kontengiert. Diese Doktorarbeit beschreibt anhand dreier Studien, wie TOR zu diesem Zweck, in der Grünalge Chlamydomonas reinhardtii, den zentralen Stoffwechsel reguliert. Die erste Studie untersucht dazu das zeitaufgelöste Verhalten von Biomolekülen im Tagesverlauf synchronisiert wachsender Algen. Dabei konnte gezeigt werden, das der TOR Inhibitor Rapamycin das Wachstum um 50% reduziert und den Zellzyklus verzögert. Die Zellzyklus Verzögerung scheint dabei hauptsächlich durch veränderte Stoffwechselprozesse erklärt zu sein. Hierbei konnte gezeigt werden, dass TOR vor allem stickstoffhaltige Stoffwechselprodukte (z.B. Aminosäuren) kontrolliert, welche die Grundlage für Biomasseproduktion, Wachstum und den Zellzyklus bilden. Im Rahmen der zweiten Studie konnte dann der molekulare Mechanismus der Akkumulation der zellulären Aminosäuren aufgeklärt werden. Zu diesem Zweck wurden Fütterungsstudien mit 13C- und 15N-Isotopen durchgeführt. Die Ergebnisse dieser Fütterung konnten klar zeigen, dass die Inhibition von TOR zur verstärkten Aufnahme von Stickstoff in die Zelle und dessen Assimilierung in Aminosäuren führt. Die Aufdeckung dieses neuen, von TOR gesteuerten Prozesses eröffnete somit die Frage, wie die Signalkaskade von TOR zu den Enzymen der Aminosäuresynthese verläuft. Detaillierte phosphoproteomische Studien sollten dieser Frage nachgehen und Zielprotein der TOR Kinase zu identifizieren und regulierte Stoffwechselprozesses zu finden. Dabei stellte sich heraus, dass sowohl verschiedene Enzyme der Aminosäuresynthese als auch Enzyme des zentralen Stoffwechsels innerhalb weniger Minuten stark verändert wurden. Zusammenfassend kann man festhalten das die vorliegende Arbeit detaillierte Stoffwechselanalysen des Stoffwechsels nach einer TOR Inhibition aufdeckt. Hierbei ein neuer Mechanismus zur Regulation der Aminosäuresynthese, nach TOR Inhibition gezeigt werden konnte, welche durch systemische Regulation der Phosphorylierungsmuster zellulärer Proteine kontrolliert wird. Zusätzliche molekulare und biochemische Studien konnten weiterhin zeigen, dass wie TOR das zelluläre Wachstum der photosynthetischen Grünalge kontrolliert und somit steuert. KW - Target of Rapamycin kinase KW - Growth signaling KW - metabolism KW - phosphoproteomics KW - Chlamydomonas KW - Target of Rapamycin kinase KW - Wachstumssignale KW - Stoffwechsel KW - Phosphoproteomik KW - Chlamydomonas Y1 - 2018 ER - TY - GEN A1 - Synodinos, Alexios D. A1 - Eldridge, David A1 - Geißler, Katja A1 - Jeltsch, Florian A1 - Lohmann, Dirk A1 - Midgley, Guy A1 - Blaum, Niels T1 - Remotely sensed canopy height reveals three pantropical ecosystem states BT - a comment T2 - Ecology : a publication of the Ecological Society of America Y1 - 2017 U6 - https://doi.org/10.1002/ecy.1997 SN - 0012-9658 SN - 1939-9170 VL - 99 IS - 1 SP - 231 EP - 234 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Muhl, Rika M. W. A1 - Roelke, Daniel L. A1 - Zohary, Tamar A1 - Moustaka-Gouni, Maria A1 - Sommer, Ulrich A1 - Borics, Gabor A1 - Gaedke, Ursula A1 - Withrow, Frances G. A1 - Bhattacharyya, Joydeb T1 - Resisting annihilation BT - relationships between functional trait dissimilarity, assemblage competitive power and allelopathy JF - Ecology letters N2 - Allelopathic species can alter biodiversity. Using simulated assemblages that are characterised by neutrality, lumpy coexistence and intransitivity, we explore relationships between within-assemblage competitive dissimilarities and resistance to allelopathic species. An emergent behaviour from our models is that assemblages are more resistant to allelopathy when members strongly compete exploitatively (high competitive power). We found that neutral assemblages were the most vulnerable to allelopathic species, followed by lumpy and then by intransitive assemblages. We find support for our modeling in real-world time-series data from eight lakes of varied morphometry and trophic state. Our analysis of this data shows that a lake's history of allelopathic phytoplankton species biovolume density and dominance is related to the number of species clusters occurring in the plankton assemblages of those lakes, an emergent trend similar to that of our modeling. We suggest that an assemblage's competitive power determines its allelopathy resistance. KW - Allelopathy KW - exploitative competition KW - interference competition KW - intransitivity KW - lumpy coexistence KW - neutrality KW - species supersaturated assemblages Y1 - 2018 U6 - https://doi.org/10.1111/ele.13109 SN - 1461-023X SN - 1461-0248 VL - 21 IS - 9 SP - 1390 EP - 1400 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - De Lombaerde, Emiel A1 - Verheyen, Kris A1 - Perring, Michael P. A1 - Bernhardt-Roemermann, Markus A1 - Van Calster, Hans A1 - Brunet, Jorg A1 - Chudomelova, Marketa A1 - Decocq, Guillaume A1 - Diekmann, Martin A1 - Durak, Tomasz A1 - Hedl, Radim A1 - Heinken, Thilo A1 - Hommel, Patrick A1 - Jaroszewicz, Bogdan A1 - Kopecky, Martin A1 - Lenoir, Jonathan A1 - Macek, Martin A1 - Máliš, František A1 - Mitchell, Fraser J. G. A1 - Naaf, Tobias A1 - Newman, Miles A1 - Petřík, Petr A1 - Reczyńska, Kamila A1 - Schmidt, Wolfgang A1 - Swierkosz, Krzysztof A1 - Vild, Ondrej A1 - Wulf, Monika A1 - Baetena, Lander T1 - Responses of competitive understorey species to spatial environmental gradients inaccurately explain temporal changes JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - Understorey plant communities play a key role in the functioning of forest ecosystems. Under favourable environmental conditions, competitive understorey species may develop high abundances and influence important ecosystem processes such as tree regeneration. Thus, understanding and predicting the response of competitive understorey species as a function of changing environmental conditions is important for forest managers. In the absence of sufficient temporal data to quantify actual vegetation changes, space-for-time (SFT) substitution is often used, i.e. studies that use environmental gradients across space to infer vegetation responses to environmental change over time. Here we assess the validity of such SFT approaches and analysed 36 resurvey studies from ancient forests with low levels of recent disturbances across temperate Europe to assess how six competitive understorey plant species respond to gradients of overstorey cover, soil conditions, atmospheric N deposition and climatic conditions over space and time. The combination of historical and contemporary surveys allows (i) to test if observed contemporary patterns across space are consistent at the time of the historical survey, and, crucially, (ii) to assess whether changes in abundance over time given recorded environmental change match expectations from patterns recorded along environmental gradients in space. We found consistent spatial relationships at the two periods: local variation in soil variables and overstorey cover were the best predictors of individual species’ cover while interregional variation in coarse-scale variables, i.e. N deposition and climate, was less important. However, we found that our SFT approach could not accurately explain the large variation in abundance changes over time. We thus recommend to be cautious when using SFT substitution to infer species responses to temporal changes. KW - Temperate forest KW - Herb layer KW - Tree regeneration KW - Global change KW - Nitrogen deposition KW - Canopy KW - Spatiotemporal resurvey data KW - Cover abundance KW - Chronosequence KW - forestREplot Y1 - 2018 U6 - https://doi.org/10.1016/j.baae.2018.05.013 SN - 1439-1791 SN - 1618-0089 VL - 30 SP - 52 EP - 64 PB - Elsevier GMBH CY - München ER - TY - JOUR A1 - Göritz, Anna A1 - Berger, Stella A. A1 - Gege, Peter A1 - Grossart, Hans-Peter A1 - Nejstgaard, Jens C. A1 - Riedel, Sebastian A1 - Röttgers, Rüdiger A1 - Utschig, Christian T1 - Retrieval of water constituents from hyperspectral in-situ measurements under variable cloud cover BT - a case study at Lake Stechlin (Germany) JF - Remote sensing / Molecular Diversity Preservation International (MDPI) N2 - Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring. KW - remote sensing KW - inland water KW - hyperspectral measurements KW - in-situ KW - cloud KW - surface reflection KW - inversion KW - bio-optical modeling Y1 - 2018 U6 - https://doi.org/10.3390/rs10020181 SN - 2072-4292 VL - 10 IS - 2 PB - MDPI CY - Basel ER - TY - JOUR A1 - van Velzen, Ellen A1 - Gaedke, Ursula T1 - Reversed predator BT - prey cycles are driven by the amplitude of prey oscillations JF - Ecology and Evolution N2 - Ecoevolutionary feedbacks in predator–prey systems have been shown to qualitatively alter predator–prey dynamics. As a striking example, defense–offense coevolution can reverse predator–prey cycles, so predator peaks precede prey peaks rather than vice versa. However, this has only rarely been shown in either model studies or empirical systems. Here, we investigate whether this rarity is a fundamental feature of reversed cycles by exploring under which conditions they should be found. For this, we first identify potential conditions and parameter ranges most likely to result in reversed cycles by developing a new measure, the effective prey biomass, which combines prey biomass with prey and predator traits, and represents the prey biomass as perceived by the predator. We show that predator dynamics always follow the dynamics of the effective prey biomass with a classic ¼‐phase lag. From this key insight, it follows that in reversed cycles (i.e., ¾‐lag), the dynamics of the actual and the effective prey biomass must be in antiphase with each other, that is, the effective prey biomass must be highest when actual prey biomass is lowest, and vice versa. Based on this, we predict that reversed cycles should be found mainly when oscillations in actual prey biomass are small and thus have limited impact on the dynamics of the effective prey biomass, which are mainly driven by trait changes. We then confirm this prediction using numerical simulations of a coevolutionary predator–prey system, varying the amplitude of the oscillations in prey biomass: Reversed cycles are consistently associated with regions of parameter space leading to small‐amplitude prey oscillations, offering a specific and highly testable prediction for conditions under which reversed cycles should occur in natural systems. KW - coevolution KW - ecoevolutionary dynamics KW - predator-prey dynamics KW - top-down control Y1 - 2018 U6 - https://doi.org/10.1002/ece3.4184 SN - 2045-7758 SP - 1 EP - 13 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - van Velzen, Ellen A1 - Gaedke, Ursula T1 - Reversed predator-prey cycles are driven by the amplitude of prey oscillations JF - Ecology and evolution N2 - Ecoevolutionary feedbacks in predator-prey systems have been shown to qualitatively alter predator-prey dynamics. As a striking example, defense-offense coevolution can reverse predator-prey cycles, so predator peaks precede prey peaks rather than vice versa. However, this has only rarely been shown in either model studies or empirical systems. Here, we investigate whether this rarity is a fundamental feature of reversed cycles by exploring under which conditions they should be found. For this, we first identify potential conditions and parameter ranges most likely to result in reversed cycles by developing a new measure, the effective prey biomass, which combines prey biomass with prey and predator traits, and represents the prey biomass as perceived by the predator. We show that predator dynamics always follow the dynamics of the effective prey biomass with a classic 1/4-phase lag. From this key insight, it follows that in reversed cycles (i.e., -lag), the dynamics of the actual and the effective prey biomass must be in antiphase with each other, that is, the effective prey biomass must be highest when actual prey biomass is lowest, and vice versa. Based on this, we predict that reversed cycles should be found mainly when oscillations in actual prey biomass are small and thus have limited impact on the dynamics of the effective prey biomass, which are mainly driven by trait changes. We then confirm this prediction using numerical simulations of a coevolutionary predator-prey system, varying the amplitude of the oscillations in prey biomass: Reversed cycles are consistently associated with regions of parameter space leading to small-amplitude prey oscillations, offering a specific and highly testable prediction for conditions under which reversed cycles should occur in natural systems. KW - coevolution KW - ecoevolutionary dynamics KW - predator-prey dynamics KW - top-down control Y1 - 2018 U6 - https://doi.org/10.1002/ece3.4184 SN - 2045-7758 VL - 8 IS - 12 SP - 6317 EP - 6329 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Manzoni, Stefano A1 - Capek, Petr A1 - Porada, Philipp A1 - Thurner, Martin A1 - Winterdahl, Mattias A1 - Beer, Christian A1 - Bruchert, Volker A1 - Frouz, Jan A1 - Herrmann, Anke M. A1 - Lindahl, Bjorn D. A1 - Lyon, Steve W. A1 - Šantrůčková, Hana A1 - Vico, Giulia A1 - Way, Danielle T1 - Reviews and syntheses BT - Carbon use efficiency from organisms to ecosystems - definitions, theories, and empirical evidence JF - Biogeosciences N2 - The cycling of carbon (C) between the Earth surface and the atmosphere is controlled by biological and abiotic processes that regulate C storage in biogeochemical compartments and release to the atmosphere. This partitioning is quantified using various forms of C-use efficiency (CUE) - the ratio of C remaining in a system to C entering that system. Biological CUE is the fraction of C taken up allocated to biosynthesis. In soils and sediments, C storage depends also on abiotic processes, so the term C-storage efficiency (CSE) can be used. Here we first review and reconcile CUE and CSE definitions proposed for autotrophic and heterotrophic organisms and communities, food webs, whole ecosystems and watersheds, and soils and sediments using a common mathematical framework. Second, we identify general CUE patterns; for example, the actual CUE increases with improving growth conditions, and apparent CUE decreases with increasing turnover. We then synthesize > 5000CUE estimates showing that CUE decreases with increasing biological and ecological organization - from uni-cellular to multicellular organisms and from individuals to ecosystems. We conclude that CUE is an emergent property of coupled biological-abiotic systems, and it should be regarded as a flexible and scale-dependent index of the capacity of a given system to effectively retain C. Y1 - 2018 U6 - https://doi.org/10.5194/bg-15-5929-2018 SN - 1726-4170 SN - 1726-4189 VL - 15 IS - 19 SP - 5929 EP - 5949 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - He, Hai A1 - Edlich-Muth, Christian A1 - Lindner, Steffen N. A1 - Bar-Even, Arren T1 - Ribulose Monophosphate Shunt Provides Nearly All Biomass and Energy Required for Growth of E. coli JF - ACS Synthetic Biology N2 - The ribulose monophosphate (RuMP) cycle is a highly efficient route for the assimilation of reduced one-carbon compounds. Despite considerable research, the RuMP cycle has not been fully implemented in model biotechnological organisms such as Escherichia coli, mainly since the heterologous establishment of the pathway requires addressing multiple challenges: sufficient formaldehyde production, efficient formaldehyde assimilation, and sufficient regeneration of the formaldehyde acceptor, ribulose 5-phosphate. Here, by efficiently producing formaldehyde from sarcosine oxidation and ribulose 5-phosphate from exogenous xylose, we set aside two of these concerns, allowing us to focus on the particular challenge of establishing efficient formaldehyde assimilation via the RuMP shunt, the linear variant of the RuMP cycle. We have generated deletion strains whose growth depends, to different extents, on the activity of the RuMP shunt, thus incrementally increasing the selection pressure for the activity of the synthetic pathway. Our final strain depends on the activity of the RuMP shunt for providing the cell with almost all biomass and energy needs, presenting an absolute coupling between growth and activity of key RuMP cycle components. This study shows the value of a stepwise problem solving approach when establishing a difficult but promising pathway, and is a strong basis for future engineering, selection, and evolution of model organisms for growth via the RuMP cycle. KW - ribulose monophosphate cycle KW - methylotrophy KW - metabolic engineering KW - growth selection KW - carbon labeling KW - flux modeling KW - formaldehyde assimilation Y1 - 2018 U6 - https://doi.org/10.1021/acssynbio.8b00093 SN - 2161-5063 VL - 7 IS - 6 SP - 1601 EP - 1611 PB - ACS CY - Washington, DC ER - TY - JOUR A1 - Schwanhold, Nadine A1 - Iobbi-Nivol, Chantal A1 - Lehmann, Angelika A1 - Leimkühler, Silke T1 - Same but different BT - Comparison of two system-specific molecular chaperones for the maturation of formate dehydrogenases JF - PLoS one N2 - The maturation of bacterial molybdoenzymes is a complex process leading to the insertion of the bulky bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor into the apoenzyme. Most molybdoenzymes were shown to contain a specific chaperone for the insertion of the bis-MGD cofactor. Formate dehydrogenases (FDH) together with their molecular chaperone partner seem to display an exception to this specificity rule, since the chaperone FdhD has been proven to be involved in the maturation of all three FDH enzymes present in Escherichia colt. Multiple roles have been suggested for FdhD-like chaperones in the past, including the involvement in a sulfur transfer reaction from the L-cysteine desulfurase IscS to bis-MGD by the action of two cysteine residues present in a conserved CXXC motif of the chaperones. However, in this study we show by phylogenetic analyses that the CXXC motif is not conserved among FdhD-like chaperones. We compared in detail the FdhD-like homologues from Rhodobacter capsulatus and E. colt and show that their roles in the maturation of FDH enzymes from different subgroups can be exchanged. We reveal that bis-MGDbinding is a common characteristic of FdhD-like proteins and that the cofactor is bound with a sulfido-ligand at the molybdenum atom to the chaperone. Generally, we reveal that the cysteine residues in the motif CXXC of the chaperone are not essential for the production of active FDH enzymes. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0201935 SN - 1932-6203 VL - 13 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Yannelli, Florencia A. A1 - Karrer, Gerhard A1 - Hall, Rea A1 - Kollmann, Johannes A1 - Heger, Tina T1 - Seed density is more effective than multi-trait limiting similarity in controlling grassland resistance against plant invasions in mesocosms JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - QuestionDisturbed areas offer great opportunities for restoring native biodiversity, but they are also prone to invasion by alien plants. Following the limiting similarity hypothesis, we address the question of whether or not similarity of plant functional traits helps developing seed mixtures of native communities with high resistance to invasive species at an early stage of restoration. LocationCentre of Greenhouses and Laboratories Durnast, Technische Universitat Munchen, Freising, Germany. MethodsUsing a system of linear equations, we designed native communities maximizing the similarity between the native and two invasive species according to ten functional traits. We used native grassland plants, two invasive alien species that are often problematic in disturbed areas (i.e., Ambrosia artemisiifolia and Solidago gigantea) and trait information obtained from databases. The two communities were then tested for resistance against establishment of the two invaders separately in a greenhouse experiment. We measured height of the invasive species and above-ground biomass, along with leaf area index, 4 and 8months after sowing respectively. ResultsBoth invasive species were successfully reduced by the native community designed to suppress S. gigantea dominated by small-seeded species. These results could be considered as partial support for the limiting similarity hypothesis. However, given the success of this mixture against both invasive species, suppression was better explained by a seed density effect resulting from the smaller seed mass of the native species included in this mixture. Further, the dominance of a fast-developing competitive species could also contribute to its success. ConclusionsThere was no unequivocal support for the limiting similarity hypothesis in terms of the traits selected. Instead we found that increasing seeding density of native species and selecting species with a fast vegetative development is an effective way to suppress invasive plants during early stages of restoration. If limiting similarity is used to design communities for restoration, early life-history traits should be taken into account. KW - Achillea millefolium KW - Ambrosia artemisiifolia KW - biotic resistance KW - competition KW - density-driven suppression KW - disturbed areas KW - restoration KW - seed mixtures KW - Solidago gigantea Y1 - 2018 U6 - https://doi.org/10.1111/avsc.12373 SN - 1402-2001 SN - 1654-109X VL - 21 IS - 3 SP - 411 EP - 418 PB - Wiley CY - Hoboken ER -