TY - JOUR A1 - Garapati, Prashanth A1 - Xue, Gang-Ping A1 - Munne-Bosch, Sergi A1 - Balazadeh, Salma T1 - Transcription Factor ATAF1 in Arabidopsis Promotes Senescence by Direct Regulation of Key Chloroplast Maintenance and Senescence Transcriptional Cascades JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Senescence represents a fundamental process of late leaf development. Transcription factors (TFs) play an important role for expression reprogramming during senescence; however, the gene regulatory networks through which they exert their functions, and their physiological integration, are still largely unknown. Here, we identify the Arabidopsis (Arabidopsis thaliana) abscisic acid (ABA)- and hydrogen peroxide-activated TF Arabidopsis thaliana ACTIVATING FACTOR1 (ATAF1) as a novel upstream regulator of senescence. ATAF1 executes its physiological role by affecting both key chloroplast maintenance and senescence-promoting TFs, namely GOLDEN2-LIKE1 (GLK1) and ORESARA1 (ARABIDOPSIS NAC092), respectively. Notably, while ATAF1 activates ORESARA1, it represses GLK1 expression by directly binding to their promoters, thereby generating a transcriptional output that shifts the physiological balance toward the progression of senescence. We furthermore demonstrate a key role of ATAF1 for ABA- and hydrogen peroxide-induced senescence, in accordance with a direct regulatory effect on ABA homeostasis genes, including NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3 involved in ABA biosynthesis and ABC TRANSPORTER G FAMILY MEMBER40, encoding an ABA transport protein. Thus, ATAF1 serves as a core transcriptional activator of senescence by coupling stress-related signaling with photosynthesis- and senescence-related transcriptional cascades. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00567 SN - 0032-0889 SN - 1532-2548 VL - 168 IS - 3 SP - 1122 EP - + PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Garapati, Prashanth A1 - Feil, Regina A1 - Lunn, John Edward A1 - Van Dijck, Patrick A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - Transcription Factor Arabidopsis Activating Factor1 Integrates Carbon Starvation Responses with Trehalose Metabolism JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Plants respond to low carbon supply by massive reprogramming of the transcriptome and metabolome. We show here that the carbon starvation-induced NAC (for NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON) transcription factor Arabidopsis (Arabidopsis thaliana) Transcription Activation Factor1 (ATAF1) plays an important role in this physiological process. We identified TREHALASE1, the only trehalase-encoding gene in Arabidopsis, as a direct downstream target of ATAF1. Overexpression of ATAF1 activates TREHALASE1 expression and leads to reduced trehalose-6-phosphate levels and a sugar starvation metabolome. In accordance with changes in expression of starch biosynthesis-and breakdown-related genes, starch levels are generally reduced in ATAF1 overexpressors but elevated in ataf1 knockout plants. At the global transcriptome level, genes affected by ATAF1 are broadly associated with energy and carbon starvation responses. Furthermore, transcriptional responses triggered by ATAF1 largely overlap with expression patterns observed in plants starved for carbon or energy supply. Collectively, our data highlight the existence of a positively acting feedforward loop between ATAF1 expression, which is induced by carbon starvation, and the depletion of cellular carbon/energy pools that is triggered by the transcriptional regulation of downstream gene regulatory networks by ATAF1. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00917 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 1 SP - 379 EP - 390 PB - American Society of Plant Physiologists CY - Rockville ER - TY - INPR A1 - Müller-Röber, Bernd T1 - That "crispert" in Plant Cultivation T2 - Journal für Verbraucherschutz und Lebensmittelsicherheit = Journal of consumer protection and food safety Y1 - 2015 U6 - https://doi.org/10.1007/s00003-015-0985-1 SN - 1661-5751 SN - 1661-5867 VL - 10 IS - 4 SP - 305 EP - 306 PB - Springer CY - Basel ER - TY - THES A1 - Kamranfar, Iman T1 - Functional analysis of gene regulatory networks controlled by stress responsive transcription factors in Arabidopsis thaliana Y1 - 2015 ER - TY - THES A1 - Zhao, Liming T1 - Characterization genes involved in leaf development and senescence of arabidopsis Y1 - 2015 ER - TY - THES A1 - Balazadeh, Salma T1 - New insights into the molecular mechanisms of leaf senescence Y1 - 2015 ER - TY - THES A1 - Herde, Antje T1 - Individual differences and seasonal variation in behaviour BT - Studies on common voles Y1 - 2015 ER - TY - JOUR A1 - Imholt, Christian A1 - Reil, Daniela A1 - Eccard, Jana A1 - Jacob, Daniela A1 - Hempelmann, Nils A1 - Jacob, Jens T1 - Quantifying the past and future impact of climate on outbreak patterns of bank voles (Myodes glareolus) JF - Pest management science N2 - BACKGROUND Central European outbreak populations of the bank vole (Myodes glareolus Schreber) are known to cause damage in forestry and to transmit the most common type of Hantavirus (Puumala virus, PUUV) to humans. A sound estimation of potential effects of future climate scenarios on population dynamics is a prerequisite for long-term management strategies. Historic abundance time series were used to identify the key weather conditions associated with bank vole abundance, and were extrapolated to future climate scenarios to derive potential long-term changes in bank vole abundance dynamics. RESULTS Classification and regression tree analysis revealed the most relevant weather parameters associated with high and low bank vole abundances. Summer temperatures 2 years prior to trapping had the highest impact on abundance fluctuation. Extrapolation of the identified parameters to future climate conditions revealed an increase in years with high vole abundance. CONCLUSION Key weather patterns associated with vole abundance reflect the importance of superabundant food supply through masting to the occurrence of bank vole outbreaks. Owing to changing climate, these outbreaks are predicted potentially to increase in frequency 3-4-fold by the end of this century. This may negatively affect damage patterns in forestry and the risk of human PUUV infection in the long term. (c) 2014 Society of Chemical Industry KW - climate change KW - population dynamics KW - bank vole KW - regression tree KW - outbreak Y1 - 2015 U6 - https://doi.org/10.1002/ps.3838 SN - 1526-498X SN - 1526-4998 VL - 71 IS - 2 SP - 166 EP - 172 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Weiß, Lina A1 - Jeltsch, Florian T1 - The response of simulated grassland communities to the cessation of grazing JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Changes in land-use are supposed to be among the severest prospective threats to plant diversity worldwide. In semi-natural temperate grasslands, the cessation of traditional land use like livestock grazing is considered to be one of the most important drivers of the diversity loss witnessed within the last decades. Despite of the enormous number of studies on successional pathways following grazing abandonment there is no general pattern of how grassland communities are affected in terms of diversity, trait composition and pace of succession. To gain a comprehensive picture is difficult given the heterogeneity of environments and the time and effort needed for long-term investigations. We here use a proven individual- and trait-based grassland community model to analyze short- and long-term consequences of grazing abandonment under different assumptions of resource availability, pre-abandonment grazing intensity and regional isolation of communities. Grazing abandonment led to a decrease of plant functional type (PFT) diversity in all but two scenarios in the long-term. In short-term we also found an increase or no change in Shannon diversity for several scenarios. With grazing abandonment we overall found an increase in maximum plant mass, clonal integration and longer lateral spread, a decrease in rosette plant types and in stress tolerant plants, as well as an increase in grazing tolerant and a decrease in grazing avoiding plant types. Observed changes were highly dependent on the regional configuration of communities, prevalent resource conditions and land use intensity before abandonment. While long-term changes took around 10-20 years in resource rich conditions, new equilibria established in resource poor conditions only after 30-40 years. Our results confirm the potential threats caused by recent land-use changes and the assumption that oligotrophic communities are more resistant than mesotrophic communities also for long-term abandonment. Moreover, results revealed that species-rich systems are not per se more resistant than species-poor grasslands. (C) 2015 Elsevier B.V. All rights reserved. KW - Diversity KW - Individual-based model KW - Land use intensity KW - Seed immigration KW - Abandonment KW - Resistance Y1 - 2015 U6 - https://doi.org/10.1016/j.ecolmodel.2015.02.002 SN - 0304-3800 SN - 1872-7026 VL - 303 SP - 1 EP - 11 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bergholz, Kolja A1 - Jeltsch, Florian A1 - Weiß, Lina A1 - Pottek, Janine A1 - Geißler, Katja A1 - Ristow, Michael T1 - Fertilization affects the establishment ability of species differing in seed mass via direct nutrient addition and indirect competition effects JF - Oikos N2 - Fertilization causes species loss and species dominance changes in plant communities worldwide. However, it still remains unclear how fertilization acts upon species functional traits, e.g. seed mass. Seed mass is a key trait of the regeneration strategy of plants, which influences a range of processes during the seedling establishment phase. Fertilization may select upon seed mass, either directly by increased nutrient availability or indirectly by increased competition. Since previous research has mainly analyzed the indirect effects of fertilization, we disentangled the direct and indirect effects to examine how nutrient availability and competition influence the seed mass relationships on four key components during seedling establishment: seedling emergence, time of seedling emergence, seedling survival and seedling growth. We conducted a common garden experiment with 22 dry grassland species with a two-way full factorial design that simulated additional nutrient supply and increased competition. While we found no evidence that fertilization either directly by additional nutrient supply or indirectly by increased competition alters the relationship between seed mass and (time of) seedling emergence, we revealed that large seed mass is beneficial under nutrient-poor conditions (seedlings have greater chances of survival, particularly in nutrient-poor soils) as well as under competition (large-seeded species produced larger seedlings, which suffered less from competition than small-seeded species). Based on these findings, we argue that both factors, i.e. nutrient availability and competition intensity, ought to be considered to understand how fertilization influences seedling establishment and species composition with respect to seed mass in natural communities. We propose a simple conceptual model, in which seed mass in natural communities is determined by competition intensity and nutrient availability. Here, we hypothesize that seed mass shows a U-shaped pattern along gradients of soil fertility, which may explain the contrasting soil fertility-seed mass relationships found in the recent literature. Y1 - 2015 U6 - https://doi.org/10.1111/oik.02193 SN - 0030-1299 SN - 1600-0706 VL - 124 IS - 11 SP - 1547 EP - 1554 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Reil, Daniela A1 - Imholt, Christian A1 - Eccard, Jana A1 - Jacob, Jens T1 - Beech Fructification and Bank Vole Population Dynamics - Combined Analyses of Promoters of Human Puumala Virus Infections in Germany JF - PLoS one N2 - The transmission of wildlife zoonoses to humans depends, amongst others, on complex interactions of host population ecology and pathogen dynamics within host populations. In Europe, the Puumala virus (PUUV) causes nephropathia epidemica in humans. In this study we investigated complex interrelations within the epidemic system of PUUV and its rodent host, the bank vole (Myodes glareolus). We suggest that beech fructification and bank vole abundance are both decisive factors affecting human PUUV infections. While rodent host dynamics are expected to be directly linked to human PUUV infections, beech fructification is a rather indirect predictor by serving as food source for PUUV rodent hosts. Furthermore, we examined the dependence of bank vole abundance on beech fructification. We analysed a 12-year (2001-2012) time series of the parameters: beech fructification (as food resource for the PUUV host), bank vole abundance and human incidences from 7 Federal States of Germany. For the first time, we could show the direct interrelation between these three parameters involved in human PUUV epidemics and we were able to demonstrate on a large scale that human PUUV infections are highly correlated with bank vole abundance in the present year, as well as beech fructification in the previous year. By using beech fructification and bank vole abundance as predictors in one model we significantly improved the degree of explanation of human PUUV incidence. Federal State was included as random factor because human PUUV incidence varies considerably among states. Surprisingly, the effect of rodent abundance on human PUUV infections is less strong compared to the indirect effect of beech fructification. Our findings are useful to facilitate the development of predictive models for host population dynamics and the related PUUV infection risk for humans and can be used for plant protection and human health protection purposes. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0134124 SN - 1932-6203 VL - 10 IS - 7 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Liesenjohann, Thilo A1 - Liesenjohann, Monique A1 - Trebaticka, Lenka A1 - Sundell, Janne A1 - Haapakoski, Marko A1 - Ylonen, Hannu A1 - Eccard, Jana T1 - State-dependent foraging: lactating voles adjust their foraging behavior according to the presence of a potential nest predator and season JF - Behavioral ecology and sociobiology N2 - Parental care often produces a trade-off between meeting nutritional demands of offspring and the duties of offspring protection, especially in altricial species. Parents have to leave their young unattended for foraging trips, during which nestlings are exposed to predators. We investigated how rodent mothers of altricial young respond to risk of nest predation in their foraging decisions. We studied foraging behavior of lactating bank voles (Myodes glareolus) exposed to a nest predator, the common shrew (Sorex araneus). We conducted the experiment in summer (high resource provisioning for both species) and autumn (less food available) in 12 replicates with fully crossed factors "shrew presence" and "season." We monitored use of feeding stations near and far from the nest as measurement of foraging activity and strategic foraging behavior. Vole mothers adapted their strategies to shrew presence and optimized their foraging behavior according to seasonal constraints, resulting in an interaction of treatment and season. In summer, shrew presence reduced food intake from feeding stations, while it enhanced intake in autumn. Shrew presence decreased the number of visited feeding stations in autumn and concentrated mother's foraging efforts to fewer stations. Independent of shrew presence or season, mothers foraged more in patches further away from the nest than near the nest. Results indicate that females are not investing in nest guarding but try to avoid the accumulation of olfactory cues near the nest leading a predator to the young. Additionally, our study shows how foraging strategies and nest attendance are influenced by seasonal food provision. KW - Myodes glareolus KW - Optimal foraging KW - Sorex araneus KW - Nest protection KW - Seasonality KW - Interference Y1 - 2015 U6 - https://doi.org/10.1007/s00265-015-1889-x SN - 0340-5443 SN - 1432-0762 VL - 69 IS - 5 SP - 747 EP - 754 PB - Springer CY - New York ER - TY - JOUR A1 - Kopyshev, Alexey A1 - Lomadze, Nino A1 - Feldmann, David A1 - Genzer, Jan A1 - Santer, Svetlana T1 - Making polymer brush photosensitive with azobenzene containing surfactants JF - Polymer : the international journal for the science and technology of polymers N2 - We report on rendering polyelectrolyte brushes photosensitive by loading them with azobenzene-containing cationic surfactants. Planar poly( methacrylic acid) (PMAA) brushes are synthesized using the "grafting from" free-radical polymerization scheme followed by exposure to a solution of photosensitive surfactants consisting of positively-charged head groups and hydrophobic tails into which azobenzene moieties are inserted. In this study the length of the hydrophobic methylene spacer connecting the azobenzene and the charged head group ranges from 4 to 10 CH2 groups. Under irradiation with UV light, the photo-isomerization of azobenzene integrated into a surfactant results in a change in size, geometry, dipole moment and free volume of the whole molecule. When the brush loaded with photosensitive surfactants is exposed to irradiation with UV interference patterns, the topography of the brush deforms following the distribution of the light intensity, exhibiting surface relief gratings (SRG). Since SRG formation is accompanied by a local rupturing of polymer chains in areas from which the polymer material is receding, most of the polymer material is removed from the surface during treatment with good solvent, leaving behind characteristic patterns of lines or dots. The azobenzene molecules still integrated within the polymer film can be removed by washing the brush with water. The remaining nano-structured brush can then be re-used for further functionalization. Although the opto-mechanically induced rupturing occurs for all surfactants, larger species do not penetrate deep enough into the brush such that after rupturing a leftover layer of polymer material remains on the substrate. This indicates that rupturing occurs predominantly in regions of high surfactant density. KW - Azobenzene containing cationic surfactants KW - Photosensitive polymer brushes KW - Opto-mechanically induced scission of KW - polymer chains Y1 - 2015 U6 - https://doi.org/10.1016/j.polymer.2015.09.023 SN - 0032-3861 SN - 1873-2291 VL - 79 SP - 65 EP - 72 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Del Campo, Cristian A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Ignatova, Zoya T1 - Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005613 SN - 1553-7404 VL - 11 IS - 10 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Henry, Brian D. A1 - Neill, Daniel R. A1 - Becker, Katrin Anne A1 - Gore, Suzanna A1 - Bricio-Moreno, Laura A1 - Ziobro, Regan A1 - Edwards, Michael J. A1 - Muehlemann, Kathrin A1 - Steinmann, Joerg A1 - Kleuser, Burkhard A1 - Japtok, Lukasz A1 - Luginbuehl, Miriam A1 - Wolfmeier, Heidi A1 - Scherag, Andre A1 - Gulbins, Erich A1 - Kadioglu, Aras A1 - Draeger, Annette A1 - Babiychuk, Eduard B. T1 - Engineered liposomes sequester bacterial exotoxins and protect from severe invasive infections in mice JF - Nature biotechnology : the science and business of biotechnology N2 - Gram-positive bacterial pathogens that secrete cytotoxic pore-forming toxins, such as Staphylococcus aureus and Streptococcus pneumoniae, cause a substantial burden of disease. Inspired by the principles that govern natural toxin-host interactions, we have engineered artificial liposomes that are tailored to effectively compete with host cells for toxin binding. Liposome-bound toxins are unable to lyse mammalian cells in vitro. We use these artificial liposomes as decoy targets to sequester bacterial toxins that are produced during active infection in vivo. Administration of artificial liposomes within 10 h after infection rescues mice from septicemia caused by S. aureus and S. pneumoniae, whereas untreated mice die within 24-33 h. Furthermore, liposomes protect mice against invasive pneumococcal pneumonia. Composed exclusively of naturally occurring lipids, tailored liposomes are not bactericidal and could be used therapeutically either alone or in conjunction with antibiotics to combat bacterial infections and to minimize toxin-induced tissue damage that occurs during bacterial clearance. Y1 - 2015 U6 - https://doi.org/10.1038/nbt.3037 SN - 1087-0156 SN - 1546-1696 VL - 33 IS - 1 SP - 81 EP - U295 PB - Nature Publ. Group CY - New York ER - TY - THES A1 - Liebrich, Marietta T1 - Einfluss von Prozessoptimierungen auf die mikrobielle Diversität und die Effizienz der Gasbildung in Co-Vergärungsanlagen der Abfallwirtschaft T1 - Influence of process optimizations on the microbial diversity and the efficiency of the gas production in co-fermentation plants of waste management N2 - Im Hinblick auf die Problematik der Umweltverschmutzung durch die Nutzung fossiler Brennstoffe ist es nötig, eine langfristig stabile und umweltfreundliche Energieversorgung zu gewährleisten. Eine Möglichkeit, den Energiebedarf CO2-neutral zu decken, ist die Nutzung von Biogas. Hierbei spielt der Einsatz von biogenen Reststoffen, die durch einen hohen Anteil an Kohlenhydraten, Fetten und Proteinen gekennzeichnet sind und daher ein hohes Biogaspotential besitzen, eine wichtige Rolle. Voraussetzung für die Effizienz und Rentabilität solcher Anlagen ist u. a. ein stabiler Gasbildungsprozess. Da bisher noch nicht alle Aspekte der Biogasbildung vollständig verstanden sind, werden die Anlagen oft nicht optimal ausgelastet, um Prozessstörungen wie z. B. Übersäuerung zu vermeiden. Um dennoch auftretende Prozessstörungen zu beheben, können unterschiedliche Maßnahmen durchgeführt werden. Neben der Senkung der Raumbelastung, ist es möglich, den pH-Wert durch die Zugabe von Natronlauge oder Calciumoxid anzuheben. In der vorliegenden Arbeit wurden sowohl Prozessstörungen als auch Prozessregenerierungen an einer großtechnischen Biogasanlage und in Laborversuchen untersucht. Dabei galt es, neben den physikalischen und chemischen Parametern, die mikrobielle Biozönose mit Hilfe des genetischen Fingerprintings zu charakterisieren und Änderungen zu detektieren. Während der Prozessregenerierungen wurden nach der Zugabe von CaO Veränderungen des Gärrestes beobachtet. Es bildeten sich Pellets, die im Hinblick auf ihre Funktion für die Prozessregenerierung und die Prozessstabilität molekularbiologisch und mikroskopisch untersucht wurden. Es wurde weiterhin der Frage nachgegangen, welche Rolle die Mikroorganismen bei der Entstehung der Pellets spielen. Die vor allem aus Calcium und Fettsäuren bestehenden Pellets dienten als Aufwuchsflächen für verschiedene Mikroorganismen. Die Bildung von Biofilmen, wie sie auf und in den Pellets nachgewiesen wurde, bot für Mikroorganismen einen Schutz vor negativen Umwelteinflüssen wie z. B. hohe Propionsäurekonzentrationen. Unter diesen günstigen Bedingungen war die Bildung von Biogas auch unter hohen Wasserstoffpartialdrücken, die den Abbau von Propionsäure hemmten, möglich. Als Indikator für bessere Lebensbedingungen wurde im Laborversuch ein Methanoculleus receptaculi-verwandter Organismus identifiziert. Dieses methanogene Archaeon wurde im Pellet nachgewiesen, während es im Gärrest erst nach der Prozessregenerierung detektiert wurde. Der Nachweis eines im Vergleich zum umgebenden Gärrest höheren Anteils an Archaeen im Kern der Pellets sowie von Biofilmen/EPS, verschiedenen Phosphatsalzen und schwerlöslichen Calciumsalzen zeigte, dass sowohl Präzipitation und Adsorption als auch Degradation von LCFA dazu führen, dass deren Konzentration im flüssigen Gärrest gesenkt wird. Dadurch nimmt die Hemmung auf die Biozönose ab und die Biogasbildungsrate steigt. Daher ist der Abbau der Fettsäuren auch bei einem niedrigen pH-Wert und unter hohen Wasserstoffpartialdrücken möglich und der Biogasbildungsprozess ist langfristig stabil. Die Bildung von Pellets unterstützt die Prozessstabilität, sofern diese nicht zu groß werden und dann u. a. die Durchmischung behindern und den Ablauf verstopfen. Nach erfolgreicher Prozessstabilisierung wurden keine Pellets im Gärrest beobachtet. Der Abbau des organischen Materials wurde sowohl durch die steigende Calciumkonzentration als auch die steigende Gasproduktion angezeigt. N2 - In regard to the problems of the environmental pollution with the use of fossil fuels it is necessary to guarantee a long term stable and environment-friendly energy supply. The production of biogas of such organic substances as waste or renewable raw materials is an economically and ecologically interesting option, intended to reduce the effects of climate change, due to increased CO2 emissions and to replace traditional fossil fuels. The use of biogenic residues plays an important role, as they are characterised by a high amount of carbohydrates, fats and proteins and therefore have a high biogas potential. To optimise the efficiency and reliability of biogas plants, it is important to ensure a process of stable gas production. However, many aspects of the biogas production process are still unknown. Thus, biogas plants are often run below their maximum loading rate to prevent process failures. To solve occurring process failures different counter measures can be performed such as decrease of the organic loading rate or raise the pH by adding sodium hydroxide or calcium oxide. In this work, both process failures and process recovery were studied in a large-scale biogas plant and in laboratory experiments. Physical and chemical parameters were examined, and using genetic fingerprinting the microbial biocenosis was characterised and changes were detected. During the deacidification process with CaO, the structure of the digestate changed, and pellets were observed. These were examined by molecular biology and microscopy, in terms of their function for the process recovery and process stability. Furthermore the role of microorganisms in the formation of these pellets was investigated. The pellets consisted predominantly of calcium and fatty acids and were providing a large surface for microbial growth. The detected biofilms out and inside the pellets were offering a protection from environmental influences, such as high propionic acid concentrations. These favourable conditions enabled the formation of biogas in the pellets, despite a hydrogen partial pressure in the digestate that was far too high for an energy gaining degradation of propionic acid. As an indicator of better living conditions, a Methanoculleus receptaculi-related organism was identified in laboratory studies. This methanogenic archaea was detected in the pellet during overacidification but only after process recovery in the digestate. The proof of higher abundance of archaea in the core of the pellets as well as the detection of biofilms/EPS, different phosphate minerals and sparingly soluble calcium salts indicates that both precipitation and adsorption and degradation of LCFA cause their decreasing concentration in the liquid digestate. This decreases the inhibition of the microbial biocenosis, and the biogas production rate increases. Therefore, the degradation of fatty acids is also possible with a low pH and high hydrogen partial pressures and the biogas production process is long-term stable. The formation of pellets supports process stability, providing that these are not too big and hamper the mixing or clog the drain. After successful process recovery no pellets were observed in the digestate. The degradation of organic material was evidenced by both the increasing calcium concentration and increasing gas production rate. KW - Biogas KW - biogas KW - Übersäuerung KW - overacidification KW - Prozessregenerierung KW - process recovery KW - Phosphat akkumulierende Organismen KW - phosphate accumulating organisms KW - Pelletbildung KW - granule formation Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-91066 ER - TY - THES A1 - Reim, Tina T1 - Biogene Aminrezeptoren bei der Honigbiene Apis mellifera T1 - Biogenic amine receptors in the honey bee Apis mellifera BT - Charakterisierung des Tyramin 2-Rezeptors und die Beteiligung der Octopamin- und Tyraminrezeptoren an der Steuerung der altersabhängigen Arbeitsteilung N2 - Die Honigbiene Apis mellifera zeigt innerhalb einer Kolonie eine an das Alter gekoppelte Arbeitsteilung. Junge Honigbienen versorgen die Brut (Ammenbienen), während ältere Honigbienen (Sammlerinnen) außerhalb des Stocks Pollen und Nektar eintragen. Die biogenen Amine Octopamin und Tyramin sind an der Steuerung der Arbeitsteilung maßgeblich beteiligt. Sie interagieren mit Zielzellen über die Bindung an G Protein gekoppelte Rezeptoren. A. mellifera besitzt fünf charakterisierte Octopaminrezeptoren (AmOctαR1, AmOctβR1-4), einen charakterisierten Tyraminrezeptor (AmTyr1) sowie einen weiteren putativen Tyraminrezeptor. In der vorliegenden Arbeit wurde dieser putative Aminrezeptor als zweiter Tyraminrezeptor (AmTyr2) identifiziert, lokalisiert und pharmakologisch charakterisiert. Die von der cDNA abgeleitete Aminosäuresequenz weist strukturelle Eigenschaften und konservierte Motive von G Protein gekoppelten Rezeptoren auf. Phylogenetisch ordnet sich der AmTyr2 Rezeptor bei den Tyramin 2 Rezeptoren anderer Insekten ein. Die funktionelle und pharmakologische Charakterisierung des putativen Tyraminrezeptors erfolgte in modifizierten HEK293 Zellen, die mit der Rezeptor cDNA transfiziert wurden. Die Applikation von Tyramin aktiviert Adenylylcyclasen in diesen Zellen und resultiert in einem Anstieg des intrazellulären cAMP Gehalts. Der AmTyr2 Rezeptor kann durch Tyramin in nanomolaren Konzentrationen halbmaximal aktiviert werden. Während es sich bei Octopamin um einen wirkungsvollen Agonisten des Rezeptors handelt, sind Mianserin und Yohimbin effektive Antagonisten. Für die Lokalisierung des Rezeptorproteins wurde ein polyklonaler Antikörper generiert. Eine AmTyr2-ähnliche Immunreaktivität zeigt sich im Gehirn in den optischen Loben, den Antennalloben, dem Zentralkomplex und in den Kenyon Zellen der Pilzkörper. Des Weiteren wurde die Rolle der Octopamin- und Tyraminrezeptoren bei der Steuerung der altersabhängigen Arbeitsteilung analysiert. Die Genexpression des AmOctαR1 in verschiedenen Gehirnteilen korreliert unabhängig vom Alter mit der sozialen Rolle, während sich die Genexpression von AmOctβR3/4 und den Tyraminrezeptoren AmTyr1 und AmTyr2 maximal mit dem Alter aber nicht der sozialen Rolle ändert. Sammlerinnen weisen einen höheren Octopamingehalt im Gesamtgehirn auf als Ammenbienen; bei Tyramin zeigen sich keine Unterschiede. Während Tyramin offensichtlich keine direkte Rolle spielt, werden durch Octopamin gesteuerte Prozesse der altersabhängigen Arbeitsteilung bei der Honigbiene vermutlich über den AmOctαR1 vermittelt. Die Ergebnisse der vorliegenden Arbeit zeigen die wichtige Rolle von biogenen Aminen, insbesondere Octopamin bei der sozialen Organisation von Insektenstaaten. N2 - The honey bee Apis mellifera exhibits an age-dependent division of labour. Young bees take care of the brood (nurse bees), while older honey bees (foragers) leave the hive to provide the colony with pollen and nectar. The biogenic amines octopamine and tyramine are significantly involved in regulating the division of labour. They interact with target cells via binding to G protein-coupled receptors. A. mellifera has five characterised octopamine receptors (AmOctαR1, AmOctβR1-4), one characterised tyramine receptor (AmTyr1) and an additional putative tyramine receptor. In the present study, the putative amine receptor was identified as a second tyramine receptor (AmTyr2), was localized and characterised pharmacologically. The deduced amino acid sequence shows structural properties and conserved motifs of G protein-coupled receptors. Phylogenetically the AmTyr2 receptor clusters with tyramine 2 receptors from other insect species. Functional and pharmacological characterisation of the putative tyramine receptor was carried out using modified HEK293 cells trans¬fected with the receptor cDNA. Application of tyramine activates adenylyl cyclases in these cells, which leads to an elevated intracellular cAMP level. Half maximal activation can be achieved by applying tyramine with concentrations in the nanomolar range. While octopa¬mine is an effective agonist of the receptor, mianserin and yohimbine are the most effective antagonists. A polyclonal antibody was generated for the localisation of the receptor protein. AmTyr2 like immunoreactivity can be observed in the optic lobes, the Kenyon cells of the mushroom bodies, the antennal lobes and the central complex of the brain. Furthermore, the role of the octopamine and tyramine receptors in regulating the age-dependent division of labour was analysed. The gene expression of the AmOctαR1 in different brain neuropiles correlates with the social role of the honey bee, while the gene expression of AmOctβR3/4, AmTyr1 and AmTyr2 mostly changes with age but not social role. Additionally, foragers have higher octopamine brain titres than nurse bees. No differences can be observed for the titre of tyramine. Octopamine-regulated processes in age-dependent division of labour are probably mediated via the AmOctαR1. Tyramine has obviously no direct impact on the age-dependent division of labour. The present study shows the important role of biogenic amines, particularly octopamine in the social organisation of insect societies. KW - Apis mellifera KW - honey bee KW - Honigbiene KW - biogene Amine KW - biogenic amines KW - Octopamin KW - octopamine KW - Tyramin KW - tyramine KW - Arbeitsteilung KW - division of labor Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-80982 ER - TY - JOUR A1 - Lamanna, Francesco A1 - Kirschbaum, Frank A1 - Waurick, Isabelle A1 - Dieterich, Christoph A1 - Tiedemann, Ralph T1 - Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae) JF - BMC Genomics N2 - Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ’s transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO. Y1 - 2015 U6 - https://doi.org/10.1186/s12864-015-1858-9 SN - 1471-2164 VL - 16 IS - 668 PB - Biomed Central CY - London ER - TY - JOUR A1 - Mossbrucker, Alexander Markus A1 - Apriyana, Isabella A1 - Fickel, Jörns A1 - Imron, Muhammad Ali A1 - Pudyatmoko, Satyawan A1 - Sumardi, A1 - Suryadi, Helena T1 - Non-invasive genotyping of Sumatran elephants: implications for conservation JF - Tropical conservation science N2 - Reliable baseline information necessary for the monitoring and conservation of Sumatran elephants is scarce. We here combine non-invasive molecular genetics methods and capture-recapture modeling to estimate elephant population size, distribution, sex ratio, and age structure for the Bukit Tigapuluh landscape in Sumatra, Indonesia. Two separate subpopulations were found, for which we estimated a population size of 99 (95% CI = [86, 125], PCCL = 38.59%) and 44 elephants (95% CI = [37, 56], PCCL = 43.18%), respectively. Low elephant densities are likely the result of patchy habitat usage and anthropogenically increased mortality, the latter assumption being supported by strong skews in both sex ratio and age structure as well as direct evidence of elephant killing. Still, the Bukit Tigapuluh landscape currently holds the largest known population of elephants in central Sumatra, representing one of the most important areas for their conservation in Indonesia. Conservation of both the elephant population and their habitat in this region should thus be of high priority. We identified several threats to the population, including (i) the risk of inbreeding and subsequent loss of genetic diversity, (ii) illegal elephant killing, and (iii) the lack of protected habitat. In order to overcome these challenges we suggest: (i) the implementation of a meta-population management program, (ii) monitoring and safeguarding elephants and improving law enforcement, and (iii) providing sufficient safe habitat to mitigate human-elephant-conflict (HEC) and ensure elephant survival. KW - Elephas maximus sumatranus KW - capture-recapture modeling KW - abundance estimation KW - sex ratio KW - age structure KW - Bukit Tigapuluh Landscape Y1 - 2015 SN - 1940-0829 VL - 8 IS - 3 SP - 745 EP - 759 PB - Mongabay.com CY - Menlo Park ER - TY - THES A1 - Schirmack, Janosch T1 - Activity of methanogenic archaea under simulated Mars analog conditions T1 - Aktivität methanogener Archaeen unter simulierten Marsanalogen Bedingungen N2 - Assumed comparable environmental conditions of early Mars and early Earth in 3.7 Ga ago – at a time when first fossil records of life on Earth could be found – suggest the possibility of life emerging on both planets in parallel. As conditions changed, the hypothetical life on Mars either became extinct or was able to adapt and might still exist in biological niches. The controversial discussed detection of methane on Mars led to the assumption, that it must have a recent origin – either abiotic through active volcanism or chemical processes, or through biogenic production. Spatial and seasonal variations in the detected methane concentrations and correlations between the presence of water vapor and geological features such as subsurface hydrogen, which are occurring together with locally increased detected concentrations of methane, gave fuel to the hypothesis of a possible biological source of the methane on Mars. Therefore the phylogenetically old methanogenic archaea, which have evolved under early Earth conditions, are often used as model-organisms in astrobiological studies to investigate the potential of life to exist in possible extraterrestrial habitats on our neighboring planet. In this thesis methanogenic archaea originating from two extreme environments on Earth were investigated to test their ability to be active under simulated Mars analog conditions. These extreme environments – the Siberian permafrost-affected soil and the chemoautotrophically based terrestrial ecosystem of Movile cave, Romania – are regarded as analogs for possible Martian (subsurface) habitats. Two novel species of methanogenic archaea isolated from these environments were described within the frame of this thesis. It could be shown that concentrations up to 1 wt% of Mars regolith analogs added to the growth media had a positive influence on the methane production rates of the tested methanogenic archaea, whereas higher concentrations resulted in decreasing rates. Nevertheless it was possible for the organisms to metabolize when incubated on water-saturated soil matrixes made of Mars regolith analogs without any additional nutrients. Long-term desiccation resistance of more than 400 days was proven with reincubation and indirect counting of viable cells through a combined treatment with propidium monoazide (to inactivate DNA of destroyed cells) and quantitative PCR. Phyllosilicate rich regolith analogs seem to be the best soil mixtures for the tested methanogenic archaea to be active under Mars analog conditions. Furthermore, in a simulation chamber experiment the activity of the permafrost methanogen strain Methanosarcina soligelidi SMA-21 under Mars subsurface analog conditions could be proven. Through real-time wavelength modulation spectroscopy measurements the increase in the methane concentration at temperatures down to -5 °C could be detected. The results presented in this thesis contribute to the understanding of the activity potential of methanogenic archaea under Mars analog conditions and therefore provide insights to the possible habitability of present-day Mars (near) subsurface environments. Thus, it contributes also to the data interpretation of future life detection missions on that planet. For example the ExoMars mission of the European Space Agency (ESA) and Roscosmos which is planned to be launched in 2018 and is aiming to drill in the Martian subsurface. N2 - Die Vermutung vergleichbarer Umweltbedingungen des frühen Mars und der frühen Erde vor 3,7 Mrd. Jahren – der Zeitpunkt, zu dem die ersten fossilen Spuren des Lebens auf der Erde gefunden werden konnten – weisen auf die Möglichkeit hin, dass das Leben auf beiden Planeten parallel entstanden sein könnte. Als die Bedingungen auf dem Mars schlechter wurden, ist das hypothetische Leben dort entweder ausgestorben, oder es war in der Lage sich anzupassen und könnte noch heute in biologischen Nischen auf dem Planeten existieren. Die kontrovers diskutierte Detektion von Methan auf dem Mars führte zu der Annahme, dass dieses einen rezenten Ursprung haben muss – entweder abiotisch durch aktiven Vulkanismus oder chemische Prozesse oder aber durch biogene Produktion. Räumliche und saisonale Schwankungen der durch Fernerkundung gemessenen Methankonzentrationen, sowie die Korrelation zwischen dem Auftreten von Wasserdampf und im Untergrund detektiertem Wasserstoff zusammen mit lokal erhöhten Konzentrationen von Methan, befürworten die Hypothese einer biologischen Methanquelle auf dem Mars. Daher werden methanogene Archaeen, welche sich unter den Bedingungen der frühen Erde entwickelt haben, oft als Modellorganismen in astrobiologischen Studien zu potentiellem Leben auf unserem benachbarten Planeten Mars verwendet. In dieser Dissertation wurden methanogene Archaeen aus zwei extremen Habitaten auf der Erde auf ihre Fähigkeiten hin untersucht, unter simulierten Mars-analogen Bedingungen aktiven Metabolismus zu zeigen. Die beiden extremen Habitate – der active layer des sibirischen Permafrosts und das auf Chemoautotrophie basierende terrestrische Ökosystem der Movile Höhle in Rumänien – gelten als Analoga für mögliche Habitate auf dem Mars. Im Rahmen dieser Arbeit wurden zwei neue Arten von methanogenen Archaeen beschrieben, die aus den beiden genannten extremen Habitaten isoliert worden sind. In dieser Studie konnte gezeigt werden, dass Mars-Regolith-Analoga, in Konzentrationen bis zu 1 Gew.-% zum Wachstumsmedium hinzugefügt, einen positiven Einfluss auf die Methanbildungsraten der getesteten Archaeen hatten, während höhere zugefügte Konzentrationen sinkende Raten verursachten. Dennoch war es den Organismen möglich, auf wassergesättigten künstlichen Böden aus Mars-Regolith-Analoga Methan zu produzieren, auch ohne Zugabe jeglicher weiterer Nährstoffe. Die Resistenz gegenüber Langzeit-Austrocknung von mehr als 400 Tagen wurde mittels Reinkubation sowie indirekter Zellzahlbestimmung von lebensfähigen Zellen nachgewiesen. Dies erfolgte durch eine Kombinationsbehandlung mit Propidium-Monoazide (zur Inaktivierung der DNA aus Zellen mit zerstörter Membran) und quantitativer PCR. Regolith-Analoga mit einem hohen Anteil an Phyllosilikaten schienen die besten Bodenmischungen für die metabolische Aktivität der getesteten methanogenen Archaeen unter Marsanalogen Bedingungen zu liefern. Des Weiteren konnte mittels einer Simulationskammer für den Permafrost-Stamm Methanosarcina soligelidi SMA-21 Methanbildung unter Bedingungen analog zum Marsuntergrund nachgewiesen werden. Durch Wellenlängen-Modulations-Spektroskopie konnte die Zunahme der Methankonzentration bei Temperaturen bis zu -5 °C gemessen werden. Die in dieser Arbeit vorgestellten Ergebnisse erweitern das Verständnis des Potenzials der methanogenen Archaeen, unter Mars-analogen Bedingungen aktiv sein zu können und vermitteln Einblicke in die mögliche Habitabilität vom heutigen Marsuntergrund. Außerdem tragen sie zur Interpretation der Daten von zukünftigen Marsmissionen zur Erkundung von möglichem Leben auf dem Planeten bei. Ein Beispiel hierfür könnte die ExoMars-Mission der Europäischen Weltraumorganisation (ESA) und Roskosmos sein, welche im Jahr 2018 gestartet werden soll und bestrebt ist, in den Marsuntergrund zu bohren. KW - methanogenic archaea KW - Mars KW - simulation experiments KW - long-term desiccation KW - Martian regolith analogs KW - methanogene Archaeen KW - Mars KW - Marsanaloge Regolithe KW - Simulationsexperimente KW - Langzeitaustrocknung Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-73010 ER - TY - JOUR A1 - van Kleunen, Mark A1 - Dawson, Wayne A1 - Essl, Franz A1 - Pergl, Jan A1 - Winter, Marten A1 - Weber, Ewald A1 - Kreft, Holger A1 - Weigelt, Patrick A1 - Kartesz, John A1 - Nishino, Misako A1 - Antonova, Liubov A. A1 - Barcelona, Julie F. A1 - Cabezas, Francisco J. A1 - Cardenas, Dairon A1 - Cardenas-Toro, Juliana A1 - Castano, Nicolas A1 - Chacon, Eduardo A1 - Chatelain, Cyrille A1 - Ebel, Aleksandr L. A1 - Figueiredo, Estrela A1 - Fuentes, Nicol A1 - Groom, Quentin J. A1 - Henderson, Lesley A1 - Inderjit, A1 - Kupriyanov, Andrey A1 - Masciadri, Silvana A1 - Meerman, Jan A1 - Morozova, Olga A1 - Moser, Dietmar A1 - Nickrent, Daniel L. A1 - Patzelt, Annette A1 - Pelser, Pieter B. A1 - Baptiste, Maria P. A1 - Poopath, Manop A1 - Schulze, Maria A1 - Seebens, Hanno A1 - Shu, Wen-sheng A1 - Thomas, Jacob A1 - Velayos, Mauricio A1 - Wieringa, Jan J. A1 - Pysek, Petr T1 - Global exchange and accumulation of non-native plants JF - Nature : the international weekly journal of science N2 - All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch(1,2) is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage(3). So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species. Y1 - 2015 U6 - https://doi.org/10.1038/nature14910 SN - 0028-0836 SN - 1476-4687 VL - 525 IS - 7567 SP - 100 EP - + PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Apelt, Federico A1 - Breuer, David A1 - Nikoloski, Zoran A1 - Stitt, Mark A1 - Kragler, Friedrich T1 - Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth JF - The plant journal N2 - Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D), we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants. Significance Statement Phytotyping(4D) is a non-invasive and accurate imaging system that combines a 3D light-field camera with an automated pipeline, which provides validated measurements of growth, movement, and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping(4D) is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge. KW - plant growth KW - hyponasty KW - 3D imaging KW - light-field camera KW - Arabidopsis thaliana KW - pgm KW - technical advance Y1 - 2015 U6 - https://doi.org/10.1111/tpj.12833 SN - 0960-7412 SN - 1365-313X VL - 82 IS - 4 SP - 693 EP - 706 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Cui, Xiao A1 - Lv, Yang A1 - Chen, Miaolin A1 - Nikoloski, Zoran A1 - Twell, David A1 - Zhang, Dabing T1 - Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome JF - Molecular plant N2 - The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens. KW - pollen KW - evolution KW - young genes KW - transcriptome Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2014.12.008 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 6 SP - 935 EP - 945 PB - Cell Press CY - Cambridge ER - TY - GEN A1 - Üstün, Suayib A1 - Bartetzko, Verena A1 - Börnke, Frederik T1 - The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid T2 - Frontiers in plant science N2 - XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 432 KW - Xanthomonas KW - type-III effector KW - XopJ KW - avirulence KW - salicylic acid Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-406537 ER - TY - JOUR A1 - Üstün, Suayib A1 - Bartetzko, Verena A1 - Börnke, Frederik T1 - The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid JF - Frontiers in plant science N2 - XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana. KW - Xanthomonas KW - type-III effector KW - XopJ KW - avirulence KW - salicylic acid Y1 - 2015 U6 - https://doi.org/10.3389/fpls.2015.00599 SN - 1664-462X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Herzschuh, Ulrike A1 - Pestryakova, Luidmila Agafyevna A1 - Klemm, Juliane A1 - Epp, Laura Saskia A1 - Tiedemann, Ralph T1 - Genetic data from algae sedimentary DNA reflect the influence of environment over geography JF - Scientific reports N2 - Genetic investigations on eukaryotic plankton confirmed the existence of modern biogeographic patterns, but analyses of palaeoecological data exploring the temporal variability of these patterns have rarely been presented. Ancient sedimentary DNA proved suitable for investigations of past assemblage turnover in the course of environmental change, but genetic relatedness of the identified lineages has not yet been undertaken. Here, we investigate the relatedness of diatom lineages in Siberian lakes along environmental gradients (i.e. across treeline transects), over geographic distance and through time (i.e. the last 7000 years) using modern and ancient sedimentary DNA. Our results indicate that closely-related Staurosira lineages occur in similar environments and less-related lineages in dissimilar environments, in our case different vegetation and co-varying climatic and limnic variables across treeline transects. Thus our study reveals that environmental conditions rather than geographic distance is reflected by diatom-relatedness patterns in space and time. We tentatively speculate that the detected relatedness pattern in Staurosira across the treeline could be a result of adaptation to diverse environmental conditions across the arctic boreal treeline, however, a geographically-driven divergence and subsequent repopulation of ecologically different habitats might also be a potential explanation for the observed pattern. Y1 - 2015 U6 - https://doi.org/10.1038/srep12924 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER - TY - GEN A1 - Kappel, Christian A1 - Trost, Gerda A1 - Czesnick, Hjördis A1 - Ramming, Anna A1 - Kolbe, Benjamin A1 - Vi, Song Lang A1 - Bispo, Cláudia A1 - Becker, Jörg D. A1 - de Moor, Cornelia A1 - Lenhard, Michael T1 - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana N2 - The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 259 KW - comprehensive analysis KW - cytoplasmic polyadenylation KW - differential expression analysis KW - gene-expression KW - mammalian-cells KW - messenger-rna polyadenylation KW - poly(a)-binding protein KW - specificity factor KW - tail-length KW - translational control Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-96400 SP - 1 EP - 30 ER - TY - JOUR A1 - Manning, Pete A1 - Gossner, Martin M. A1 - Bossdorf, Oliver A1 - Allan, Eric A1 - Zhang, Yuan-Ye A1 - Prati, Daniel A1 - Blüthgen, Nico A1 - Boch, Steffen A1 - Böhm, Stefan A1 - Börschig, Carmen A1 - Hölzel, Norbert A1 - Jung, Kirsten A1 - Klaus, Valentin H. A1 - Klein, Alexandra-Maria A1 - Kleinebecker, Till A1 - Krauss, Jochen A1 - Lange, Markus A1 - Müller, Jörg A1 - Pasalic, Esther A1 - Socher, Stephanie A. A1 - Tschapka, Marco A1 - Türke, Manfred A1 - Weiner, Christiane A1 - Werner, Michael A1 - Gockel, Sonja A1 - Hemp, Andreas A1 - Renner, Swen C. A1 - Wells, Konstans A1 - Buscot, Francois A1 - Kalko, Elisabeth K. V. A1 - Linsenmair, Karl Eduard A1 - Weisser, Wolfgang W. A1 - Fischer, Markus T1 - Grassland management intensification weakens the associations among the diversities of multiple plant and animal taxa JF - Ecology : a publication of the Ecological Society of America N2 - Land-use intensification is a key driver of biodiversity change. However, little is known about how it alters relationships between the diversities of different taxonomic groups, which are often correlated due to shared environmental drivers and trophic interactions. Using data from 150 grassland sites, we examined how land-use intensification (increased fertilization, higher livestock densities, and increased mowing frequency) altered correlations between the species richness of 15 plant, invertebrate, and vertebrate taxa. We found that 54% of pairwise correlations between taxonomic groups were significant and positive among all grasslands, while only one was negative. Higher land-use intensity substantially weakened these correlations(35% decrease in rand 43% fewer significant pairwise correlations at high intensity), a pattern which may emerge as a result of biodiversity declines and the breakdown of specialized relationships in these conditions. Nevertheless, some groups (Coleoptera, Heteroptera, Hymenoptera and Orthoptera) were consistently correlated with multidiversity, an aggregate measure of total biodiversity comprised of the standardized diversities of multiple taxa, at both high and lowland-use intensity. The form of intensification was also important; increased fertilization and mowing frequency typically weakened plant-plant and plant-primary consumer correlations, whereas grazing intensification did not. This may reflect decreased habitat heterogeneity under mowing and fertilization and increased habitat heterogeneity under grazing. While these results urge caution in using certain taxonomic groups to monitor impacts of agricultural management on biodiversity, they also suggest that the diversities of some groups are reasonably robust indicators of total biodiversity across a range of conditions. KW - Biodiversity indicators KW - correlation KW - fertilization KW - grassland management KW - grazing KW - land-use change KW - land-use intensity KW - mowing KW - multidiversity KW - multitrophic interactions Y1 - 2015 U6 - https://doi.org/10.1890/14-1307.1 SN - 0012-9658 SN - 1939-9170 VL - 96 IS - 6 SP - 1492 EP - 1501 PB - Wiley CY - Washington ER - TY - INPR A1 - Ensslin, Andreas A1 - Tschoepe, Okka A1 - Burkart, Michael A1 - Joshi, Jasmin Radha T1 - Fitness decline and adaptation to novel environments in ex situ plant collections: Current knowledge and future perspectives T2 - : an international journal N2 - The conservation of rare plant species as living collections in botanic gardens and arboreta has become an established tool in the battle against worldwide species' extinctions. However, the establishment of ex situ collections with a high conservation value requires a sound understanding of the evolutionary processes that may reduce the suitability of these collections for future reintroductions. Particularly, risks such as fitness decline of cultivated plants over time, trait shifts and loss of adaptation to the original habitat due to changes in selection regimes have rarely been addressed so far. Based on a literature review and results of our own project we show that genetic drift can lead to fitness decline in ex situ cultivated plants, but these drift effects strongly depend on the conditions and cultivation history in the ex situ facility. Furthermore, we provide evidence that shifts in traits such as germination and flowering time, and a decrease in stress tolerance to drought and competition can reduce the conservation value of ex situ collections. These threats associated with ex situ conditions require more attention by researchers, curators and conservationists. We need to increase knowledge on traits that are subject to novel selection pressures in ex situ collections, and to define population sizes that prevent genetic drift. Establishing conservation networks with replicated collections across gardens and balancing the seed contribution of mother plants to the next generation within a collection are suggested as first steps to increase the conservation value of ex situ plant collections. (C) 2015 Elsevier Ltd. All rights reserved. KW - Ex situ conservation KW - Botanic gardens KW - Artificial selection KW - Genetic drift KW - Adaptive evolution Y1 - 2015 U6 - https://doi.org/10.1016/j.biocon.2015.10.012 SN - 0006-3207 SN - 1873-2917 VL - 192 SP - 394 EP - 401 PB - Elsevier CY - Oxford ER - TY - THES A1 - Schmidt, Andreas T1 - Charakterisierung der Lipopolysaccharid-Bindungseigenschaften von Adhäsionsproteinen aus Salmonella-Bakteriophagen T1 - Characterization of lipopolysaccharide-binding properties of adhesion proteins from Salmonella-bacteriophages N2 - Die Interaktionen von komplexen Kohlenhydraten und Proteinen sind ubiquitär. Sie spielen wichtige Rollen in vielen physiologischen Prozessen wie Zelladhäsion, Signaltransduktion sowie bei viralen Infektionen. Die molekularen Grundlagen der Interaktion sind noch nicht komplett verstanden. Ein Modellsystem für Kohlenhydrat-Protein-Interaktionen besteht aus Adhäsionsproteinen (Tailspikes) von Bakteriophagen, die komplexe Kohlenhydrate auf bakteriellen Oberflächen (O-Antigen) erkennen. Das Tailspike-Protein (TSP), das in dieser Arbeit betrachtet wurde, stammt aus dem Bakteriophagen 9NA (9NATSP). 9NATSP weist eine hohe strukturelle Homologie zum gut charakterisierten TSP des Phagen P22 (P22TSP) auf, bei einer niedriger sequenzieller Ähnlichkeit. Die Substratspezifitäten beider Tailspikes sind ähnlich mit Ausnahme der Toleranz gegenüber den glucosylierten Formen des O-Antigens. Die Struktur der beiden Tailspikes ist bekannt, sodass sie ein geeignetes System für vergleichende Bindungsstudien darstellen, um die strukturellen Grundlagen für die Unterschiede der Spezifität zu untersuchen. Im Rahmen dieser Arbeit wurde der ELISA-like tailspike adsorption assay (ELITA) etabliert, um Binderpaare aus TSPs und O-Antigen zu identifizieren. Dabei wurden 9NATSP und P22TSP als Sonden eingesetzt, deren Bindung an die intakten, an die Mikrotiterplatte adsorbierten Bakterien getestet wurde. Beim Test einer Sammlung aus 44 Salmonella-Stämmen wurden Stämme identifiziert, die bindendes O-Antigen exprimieren. Gleichzeitig wurden Unterschiede in der Bindung der beiden TSPs an Salmonella-Stämme mit gleichem O-Serotyp beobachtet. Die Ergebnisse der ELITA-Messung wurden qualitativ durch eine FACS-basierte Bindungsmessung bestätigt. Zusätzlich ermöglichte die FACS-Messung bei Stämmen, die teilweise modifizierte O-Antigene herstellen, den Anteil an Zellen mit und ohne Modifikation zu erfassen. Die Oberflächenplasmonresonanz (SPR)-basierten Interaktionsmessungen wurden eingesetzt, um Bindungsaffinitäten für eine TSP-O-Antigen Kombination zu quantifizieren. Dafür wurden zwei Methoden getestet, um die Oligosaccharide auf einem SPR-Chip zu immobilisieren. Zum einen wurden die enzymatisch hergestellten O-Antigenfragmente mit einem bifunktionalen Oxaminadapter derivatisiert, der eine primäre Aminogruppe für die Immobilisierung bereitstellt. Ein Versuch, diese Oligosaccharidfragmente zu immobilisieren, war jedoch nicht erfolgreich. Dagegen wurde das nicht derivatisierte Polysaccharid, bestehend aus repetitivem O-Antigen und einem konservierten Kernsaccharid, erfolgreich auf einem SPR-Chip immobilisiert. Die Immobilisierung wurde durch Interaktionsmessungen mit P22TSP bestätigt. Durch die Immobilisierung des Polysaccharids sind somit quantitative SPR-Bindungsmessungen mit einem polydispersen Interaktionspartner möglich. Eine Auswahl von Salmonella-Stämmen mit einer ausgeprägt unterschiedlichen Bindung von 9NATSP und P22TSP im ELITA-Testsystem wurde hinsichtlich der Zusammensetzung des O-Antigens mittels HPLC, Kapillargelelektrophorese und MALDI-MS analysiert. Dabei wurden nicht-stöchiometrische Modifikationen der O-Antigene wie Acetylierung und Glucosylierung detektiert. Das Ausmaß der Glucosylierung korrelierte negativ mit der Effizienz der Bindung und des Verdaus durch die beiden TSPs, wobei der negative Effekt bei 9NATSP weniger stark ausgeprägt war als bei P22TSP. Dies stimmt mit den Literaturdaten zu Infektivitätsstudien mit 9NA und P22 überein, die mit Stämmen mit vergleichbaren O-Antigenvarianten durchgeführt wurden. Die Korrelation zwischen der Glucosylierung und Bindungseffizienz konnte strukturell interpretiert werden. Auf Grundlage der O-Antigenanalysen sowie der Ergebnisse der ELITA- und FACS-Bindungstests wurden die Salmonella-Stämme Brancaster und Kalamu identifiziert, die annähernd quantitativ glucosyliertes O-Antigen exprimieren. Damit eignen sich diese Stämme für weiterführende Studien, um die Zusammenhänge zwischen der Spezifität und der Organisation der Bindestellen der beiden TSPs zu untersuchen. N2 - Interactions between complex carbohydrates and proteins are ubiquitous. They play a major role in plenty of physiological processes as cell adhesion, signal transduction, as well as viral infections. The molecular details of the interaction are not completely understood. A model system for protein-carbohydrate interactions consists of adhesion proteins (Tailspikes) of bacteriophages, which recognize complex carbohydrates on the bacterial surface (O-antigen). A Tailspike primary used in this work originates from the bacteriophage 9NA (9NATSP). 9NATSP shows a remarkable structural similarity to the extensively studied TSP of the bacteriophage P22 (P22TSP), showing a low sequential similarity. Since structures of both TSP's are known, they provide an appropriate system for comparative interaction studies. An ELISA-like Tailspike-adsorbtion assay (ELITA) was established in this work which allows identification of binding pairs consisting of TSP's and O-antigens. In this approach 9NATSP and P22TSP were used as probes. Their binding to intact bacteria adsorbed to a multi-well plate was tested. In a collection of 44 Salmonella-strains a set of strains was identified which express a binding O-antigen. Additionally different binding efficiencies were observed among the strains of the same O-serotype. Binding data of the ELITA were qualitatively resembled in a FACS-based binding test. Additionally FACS-measurements allowed estimation of the extent of non-stoichiometric modifications of the O-antigens in strains expressing modified O-antigen variants. The surface plasmone resonance (SPR) interaction-measurements were used to quantify affinities of TSP-O-antigen binding. For this, two carbohydrate immobilization strategies were tested. An O-antigen fragment, produced by enzymatic digestion, was derivatized by a bi-functional Oxamine-spacer. The spacer provides a primary amine-functionality for the immobilization. Despite the successful derivatization, sufficient amount of the O-antigen fragment could not be immobilized. Oppositely, the non-derivatized whole polysaccharide was successfully immobilized. The immobilization was confirmed by SPR-measurements with P22TSP. This approach allows quantitative measurements with polysaccharide as ligand, despite of its polydisperse characteristics. A set of Salmonella-strains with a distinctively different binding to 9NATSP and P22TSP in ELITA were characterized in terms of the content of their O-antigen by HPLC, capillary gel electrophoresis and MALDI-MS. Non-stoichiometric modifications of the O-antigens as acetylation and glucosylation were identified. The extent of glucosylation correlated negatively with the binding efficiencies to both TSP's, identifying 9NATSP as more susceptible to the glucosylation. That finding resembles with published data from early studies on the infectivity of bacteriophages 9NA and P22. Observed data could be interpreted in a structural context. The results of the O-antigen analysis as well as the results of ELITA and FACS-based interaction tests two Salmonella-strains, were identified, which produce almost completely glucosylated O-antigen: Salmonella Brancaster and Salmonella Kalamu. These strains are suitable for further studies to investigate the interdependence of the specificity and the structure of the binding sites of both TSP's. KW - Lipopolysaccharid KW - O-Antigen KW - nicht-stöchiometrische Modifikationen KW - Glycosylierung KW - Bakteriophagen KW - Adhäsionsproteine KW - Tailspike KW - Protein-Kohlenhydrat Interaktionen KW - lipopolysaccharide KW - O-antigen KW - non-stoichiometric modifications KW - glycosylation KW - bacteriophages KW - adhesion proteins KW - Tailspikes KW - protein-carbohydrate interactions Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-79529 ER - TY - JOUR A1 - Kappel, Christian A1 - Trost, Gerda A1 - Czesnick, Hjördis A1 - Ramming, Anna A1 - Kolbe, Benjamin A1 - Vi, Son Lang A1 - Bispo, Cláudia A1 - Becker, Jörg D. A1 - de Moor, Cornelia A1 - Lenhard, Michael T1 - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. KW - messenger-rna polyadenylation KW - differential expression analysis KW - gene-expression KW - tail-length KW - cytoplasmic polyadenylation KW - poly(a)-binding protein KW - translational control KW - comprehensive analysis KW - specificity factor KW - mammalian-cells Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005474 SN - 1553-7390 SN - 1553-7404 VL - 11 IS - 8 PB - Public Library of Science CY - San Francisco ER - TY - GEN A1 - Sicard, Adrien A1 - Kappel, Christian A1 - Josephs, Emily B. A1 - Wha Lee, Young A1 - Marona, Cindy A1 - Stinchcombe, John R. A1 - Wright, Stephen I. A1 - Lenhard, Michael T1 - Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella N2 - In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 231 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-93568 ER - TY - THES A1 - Kreibich, Christoph T1 - Erucasäure in Brassica napus L. - ein phänotypisches Merkmal im Genetikunterricht und ihr Nachweis mit Hilfe von Papierchromatographie T1 - Erucic acid in Brassica napus L. - a phenotypic trait in genetics and their detection by paper chromatography N2 - Erucic acid is a mono-unsaturated fatty acid that is naturally found in large quantities in seeds of rapeseed (Brassica napus L.) and other Brassica species. Erucic acid represents an important resource in the industry, however, due to its injurious effects on the heart muscle, this fatty acid is considered to be nutritionally harmful. Therefore, new high quality rapeseed cultivars were bred in order to eliminate the content of erucic acid in rapeseed oil at the end of the 20th century. In the breeding process, paper chromatography was used for the distinction between seeds with high and low content of erucic acid. Here, this outdated method was revised and optimized for educational purposes. By means of paper chromatography the qualitative content of erucic acid and four other unsaturated fatty acids was analyzed in rapeseed and linseed. The character ‘erucic acid content’, determined by two additive genes, can be used as a practical example of a phenotypic marker in school lessons, for instance, in the course 'achievement of plant breeding'. Thus, this qualitative analysis of erucic acid content enables the teacher to connect classical genetics with modern methods of plant genetics. N2 - Erucasäure ist eine einfach ungesättigte Fettsäure, die sich in großer Menge im Samen von Raps und anderen Kreuzblütlern findet. Ernährungsphysiologisch gilt sie als problematisch, da sie eine nachweislich schädliche Wirkung auf die Herzmuskulatur hat. Daher wurde sie im Laufe des 20. Jahrhunderts zum größten Teil aus dem Deutschen Winterraps durch Züchtung fast vollständig eliminiert. In einigen Zweigen der Industrie ist sie jedoch weiterhin ein bedeutender Rohstoff. In dieser Arbeit wird die Papierchromatographie als kostengünstige Methode zur Trennung von Fettsäuren vorgestellt, welche auch im Schulunterricht angewendet werden kann. Diese veraltete Methode wurde reaktiviert und für die vorliegenden Zwecke optimiert. Mit Hilfe der hier beschriebenen Papierchromatographie lassen sich sowohl Rapssamen auf ihren qualitativen Gehalt an Erucasäure untersuchen, als auch eine Vielzahl von ungesättigten Fettsäuren in Raps- und auch Leinsamen qualitativ nachweisen. Es ist so möglich erucasäurefreie und erucasäurehaltige Rapssamen auf dem Papier zu unterscheiden. Der Gehalt an Erucasäure, welcher von nur zwei additiv wirkenden Genen gesteuert wird, kann im Schulunterricht z.B. im Themenbereich „Errungenschaften der Pflanzenzüchtung“ als praktisches Beispiels herangezogen werden. Durch die hier beschriebene Methode können die Mendelschen Regeln anhand dieses phänotypischen Merkmals erarbeitet oder vertieft werden. Zudem ermöglicht die praktische Untersuchung von Erucasäure themenübergreifendes Arbeiten im Biologieunterricht, da sie klassische Genetik mit moderner Pflanzenzüchtung verbindet. KW - Erucasäure KW - Genetik KW - Fettsäure KW - Papierchromatographie KW - Brassica napus L. KW - Rapssamen KW - erucic acid KW - genetic KW - fatty acid KW - paper chromatography KW - Brassica napus L. KW - rape seed Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-93341 ER - TY - JOUR A1 - Alseekh, Saleh A1 - Tohge, Takayuki A1 - Wendenberg, Regina A1 - Scossa, Federico A1 - Omranian, Nooshin A1 - Li, Jie A1 - Kleessen, Sabrina A1 - Giavalisco, Patrick A1 - Pleban, Tzili A1 - Müller-Röber, Bernd A1 - Zamir, Dani A1 - Nikoloski, Zoran A1 - Fernie, Alisdair R. T1 - Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato JF - The plant cell N2 - A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism. Y1 - 2015 U6 - https://doi.org/10.1105/tpc.114.132266 SN - 1040-4651 SN - 1532-298X VL - 27 IS - 3 SP - 485 EP - 512 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Omranian, Nooshin A1 - Kleessen, Sabrina A1 - Tohge, Takayuki A1 - Klie, Sebastian A1 - Basler, Georg A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran T1 - Differential metabolic and coexpression networks of plant metabolism JF - Trends in plant science N2 - Recent analyses have demonstrated that plant metabolic networks do not differ in their structural properties and that genes involved in basic metabolic processes show smaller coexpression than genes involved in specialized metabolism. By contrast, our analysis reveals differences in the structure of plant metabolic networks and patterns of coexpression for genes in (non)specialized metabolism. Here we caution that conclusions concerning the organization of plant metabolism based on network-driven analyses strongly depend on the computational approaches used. KW - plant specialized metabolism KW - metabolic networks KW - gene coexpression KW - differential network analysis Y1 - 2015 U6 - https://doi.org/10.1016/j.tplants.2015.02.002 SN - 1360-1385 VL - 20 IS - 5 SP - 266 EP - 268 PB - Elsevier CY - London ER - TY - JOUR A1 - Geissler, Peter A1 - Poyarkov, Nikolay A. A1 - Grismer, Lee A1 - Nguyen, Truong Q. A1 - An, Hang T. A1 - Neang, Thy A1 - Kupfer, Alexander A1 - Ziegler, Thomas A1 - Böhme, Wolfgang A1 - Müller, Hendrik T1 - New Ichthyophis species from Indochina (Gymnophiona, Ichthyophiidae): 1. The unstriped forms with descriptions of three new species and the redescriptions of I-acuminatus Taylor, 1960, I-youngorum Taylor, 1960 and I-laosensis Taylor, 1969 JF - Organisms, diversity & evolution : official journal of the Gesellschaft für Biologische Systematik N2 - Caecilians of the genus Ichthyophis Fitzinger, 1826 are among the most poorly known amphibian taxa within Southeast Asia. Populations of Ichthyophis from the Indochina region (comprising Cambodia, Laos, and Vietnam) have been assigned to five taxa: Ichthyophis acuminatus, Ichthyophis bannanicus, Ichthyophis kohtaoensis, Ichthyophis laosensis, and Ichthyophis nguyenorum. Barcoding of recently collected specimens indicates that Indochinese congeners form a clade that includes several morphologically and genetically distinct but yet undescribed species. Although body coloration is supported by the molecular analyses as a diagnostic character at species level, unstriped forms are paraphyletic with respect to striped Ichthyophis. Based on our morphological and molecular analyses, three distinct unstriped ichthyophiid species, Ichthyophis cardamomensis sp. nov. from western Cambodia, Ichthyophis catlocensis sp. nov. from southern Vietnam, and Ichthyophis chaloensis sp. nov. from central Vietnam are described as new herein, almost doubling the number of Ichthyophis species known from the Indochinese region. All three new species differ from their unstriped congeners in a combination of morphological and molecular traits. In addition, redescriptions of three unstriped Ichthyophis species (Ichthyophis acuminatus, I. laosensis, I. youngorum) from Indochina and adjacent Thailand are provided. KW - Biogeography KW - Caecilians KW - Indochina KW - Cambodia KW - Laos KW - Thailand KW - Vietnam KW - mtDNA KW - Barcoding KW - COI KW - cyt b KW - Phylogeny KW - Integrative taxonomy Y1 - 2015 U6 - https://doi.org/10.1007/s13127-014-0190-6 SN - 1439-6092 SN - 1618-1077 VL - 15 IS - 1 SP - 143 EP - 174 PB - Springer CY - Heidelberg ER - TY - THES A1 - Alseekh, Saleh T1 - Identification and mode of inheritance of quantitative trait loci (QTL) for metabolite abundance in tomato Y1 - 2015 ER - TY - JOUR A1 - Lotkowska, Magda E. A1 - Tohge, Takayuki A1 - Fernie, Alisdair R. A1 - Xue, Gang-Ping A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00605 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 3 SP - 1862 EP - 1880 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Wang, Ting A1 - Tohge, Takayuki A1 - Ivakov, Alexander A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Mutwil, Marek A1 - Schippers, Jos H. M. A1 - Persson, Staffan T1 - Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00962 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 2 SP - 1027 EP - + PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Fettke, Jörg A1 - Fernie, Alisdair R. T1 - Intracellular and cell-to-apoplast compartmentation of carbohydrate metabolism JF - Trends in plant science N2 - In most plants, carbohydrates represent the major energy store as well as providing the building blocks for essential structural polymers. Although the major pathways for carbohydrate biosynthesis, degradation, and transport are well characterized, several key steps have only recently been discovered. In addition, several novel minor metabolic routes have been uncovered in the past few years. Here we review current studies of plant carbohydrate metabolism detailing the expanding compendium of functionally characterized transport proteins as well as our deeper comprehension of more minor and conditionally activated metabolic pathways. We additionally explore the pertinent questions that will allow us to enhance our understanding of the response of both major and minor carbohydrate fluxes to changing cellular circumstances. Y1 - 2015 U6 - https://doi.org/10.1016/j.tplants.2015.04.012 SN - 1360-1385 VL - 20 IS - 8 SP - 490 EP - 497 PB - Elsevier CY - London ER - TY - JOUR A1 - Hartmann, Stefanie A1 - Hasenkamp, Natascha A1 - Mayer, Jens A1 - Michaux, Johan A1 - Morand, Serge A1 - Mazzoni, Camila J. A1 - Roca, Alfred L. A1 - Greenwood, Alex D. T1 - Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse JF - BMC genomics N2 - Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection. KW - Murine leukemia virus KW - Endogenous retrovirus KW - Xpr1 KW - XMRV KW - Genomic evolution KW - Markov cluster algorithm Y1 - 2015 U6 - https://doi.org/10.1186/s12864-015-1766-z SN - 1471-2164 VL - 16 PB - BioMed Central CY - London ER - TY - JOUR A1 - Sicard, Adrien A1 - Kappel, Christian A1 - Josephs, Emily B. A1 - Wha Lee, Young A1 - Marona, Cindy A1 - Stinchcombe, John R. A1 - Wright, Stephen I. A1 - Lenhard, Michael T1 - Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella JF - Nature Communications N2 - In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms8960 SN - 2041-1723 VL - 6 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Kappel, Christian A1 - Trost, Gerda A1 - Czesnick, Hjördis A1 - Ramming, Anna A1 - Kolbe, Benjamin A1 - Vi, Son Lang A1 - Bispo, Claudia A1 - Becker, Jörg D. A1 - de Moor, Cornelia A1 - Lenhard, Michael T1 - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005474 SN - 1553-7390 SN - 1553-7404 VL - 11 IS - 8 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Zhang, Houbin A1 - Hanke-Gogokhia, Christin A1 - Jiang, Li A1 - Li, Xiaobo A1 - Wang, Pu A1 - Gerstner, Cecilia D. A1 - Frederick, Jeanne M. A1 - Yang, Zhenglin A1 - Baehr, Wolfgang T1 - Mistrafficking of prenylated proteins causes retinitis pigmentosa 2 JF - The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology N2 - The retinitis pigmentosa 2 polypeptide (RP2) functions as a GTPase-activating protein (GAP) for ARL3 (Arf-like protein 3), a small GTPase. ARL3 is an effector of phosphodiesterase 6 Delta (PDE6D), a prenyl-binding protein and chaperone of prenylated protein in photoreceptors. Mutations in the human RP2 gene cause X-linked retinitis pigmentosa (XLRP) and cone-rod dystrophy (XL-CORD). To study mechanisms causing XLRP, we generated an RP2 knockout mouse. The RP2h(-/-) mice exhibited a slowly progressing rod-cone dystrophy simulating the human disease. RP2h(-/-) scotopic a-wave and photopic b-wave amplitudes declined at 1 mo of age and continued to decline over the next 6 mo. Prenylated PDE6 subunits and G-protein coupled receptor kinase 1 (GRK1) were unable to traffic effectively to the RP2h(-/-) outer segments. Mechanistically, absence of RP2 GAP activity increases ARL3-GTP levels, forcing PDE6D to assume a predominantly "closed" conformation that impedes binding of lipids. Lack of interaction disrupts trafficking of PDE6 and GRK1 to their destination, the photoreceptor outer segments. We propose that hyperactivity of ARL3-GTP in RP2 knockout mice and human patients with RP2 null alleles leads to XLRP resembling recessive rod-cone dystrophy. KW - rod-cone dystrophy KW - ARL3 KW - PDE6D KW - RP2 KW - XLRP Y1 - 2015 U6 - https://doi.org/10.1096/fj.14-257915 SN - 0892-6638 SN - 1530-6860 VL - 29 IS - 3 SP - 932 EP - 942 PB - Federation of American Societies for Experimental Biology CY - Bethesda ER - TY - JOUR A1 - Nowak, Michael D. A1 - Russo, Giancarlo A1 - Schlapbach, Ralph A1 - Cuong Nguyen Huu, A1 - Lenhard, Michael A1 - Conti, Elena T1 - The draft genome of Primula veris yields insights into the molecular basis of heterostyly JF - Genome biology : biology for the post-genomic era N2 - Background: The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources. Results: We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers. Conclusions: The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole. Y1 - 2015 U6 - https://doi.org/10.1186/s13059-014-0567-z SN - 1465-6906 SN - 1474-760X VL - 16 PB - BioMed Central CY - London ER - TY - JOUR A1 - Johnson, Kim L. A1 - Ramm, Sascha A1 - Kappel, Christian A1 - Ward, Sally A1 - Leyser, Ottoline A1 - Sakamoto, Tomoaki A1 - Kurata, Tetsuya A1 - Bevan, Michael W. A1 - Lenhard, Michael T1 - The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis JF - PLoS one N2 - Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0131103 SN - 1932-6203 VL - 10 IS - 7 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Sicard, Adrien A1 - Kappel, Christian A1 - Josephs, Emily B. A1 - Lee, Young Wha A1 - Marona, Cindy A1 - Stinchcombe, John R. A1 - Wright, Stephen I. A1 - Lenhard, Michael T1 - Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella JF - Nature Communications N2 - In the Bateson-Dobzhansky-Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms8960 SN - 2041-1723 VL - 6 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Czesnick, Hjördis A1 - Lenhard, Michael T1 - Size Control in Plants-Lessons from Leaves and Flowers JF - Cold Spring Harbor perspectives in biology N2 - To achieve optimal functionality, plant organs like leaves and petals have to grow to a certain size. Beginning with a limited number of undifferentiated cells, the final size of an organ is attained by a complex interplay of cell proliferation and subsequent cell expansion. Regulatory mechanisms that integrate intrinsic growth signals and environmental cues are required to enable optimal leaf and flower development. This review focuses on plant-specific principles of growth reaching from the cellular to the organ level. The currently known genetic pathways underlying these principles are summarized and network connections are highlighted. Putative non-cell autonomously acting mechanisms that might coordinate plant-cell growth are discussed. Y1 - 2015 U6 - https://doi.org/10.1101/cshperspect.a019190 SN - 1943-0264 VL - 7 IS - 8 PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, NY ER - TY - GEN A1 - Hartmann, Stefanie A1 - Hasenkamp, Natascha A1 - Mayer, Jens A1 - Michaux, Johan A1 - Morand, Serge A1 - Mazzoni, Camila J. A1 - Roca, Alfred L. A1 - Greenwood, Alex D. T1 - Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1329 KW - murine leukemia virus KW - endogenous retrovirus KW - Xpr1 KW - XMRV KW - genomic evolution KW - Markov cluster algorithm Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431200 SN - 1866-8372 IS - 1329 ER - TY - JOUR A1 - Engqvist, Martin K. M. A1 - Schmitz, Jessica A1 - Gertzmann, Anke A1 - Florian, Alexandra A1 - Jaspert, Nils A1 - Arif, Muhammad A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Maurino, Veronica G. T1 - GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast L-Lactate Cytochrome c Oxidoreductase, Supports L-Lactate Oxidation in Roots of Arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - In roots of Arabidopsis (Arabidopsis thaliana), L-lactate is generated by the reduction of pyruvate via L-lactate dehydrogenase, but this enzyme does not efficiently catalyze the reverse reaction. Here, we identify the Arabidopsis glycolate oxidase (GOX) paralogs GOX1, GOX2, and GOX3 as putative L-lactate-metabolizing enzymes based on their homology to CYB2, the L-lactate cytochrome c oxidoreductase from the yeast Saccharomyces cerevisiae. We found that GOX3 uses L-lactate with a similar efficiency to glycolate; in contrast, the photorespiratory isoforms GOX1 and GOX2, which share similar enzymatic properties, use glycolate with much higher efficiencies than L-lactate. The key factor making GOX3 more efficient with L-lactate than GOX1 and GOX2 is a 5- to 10-fold lower Km for the substrate. Consequently, only GOX3 can efficiently metabolize L-lactate at low intracellular concentrations. Isotope tracer experiments as well as substrate toxicity tests using GOX3 loss-of-function and overexpressor plants indicate that L-lactate is metabolized in vivo by GOX3. Moreover, GOX3 rescues the lethal growth phenotype of a yeast strain lacking CYB2, which cannot grow on L-lactate as a sole carbon source. GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves, indicating that it plays a role predominantly in heterotrophic rather than autotrophic tissues, at least under standard growth conditions. In roots of plants grown under normoxic conditions, loss of function of GOX3 induces metabolic rearrangements that mirror wild-type responses under hypoxia. Thus, we identified GOX3 as the enzyme that metabolizes L-lactate to pyruvate in vivo and hypothesize that it may ensure the sustainment of low levels of L-lactate after its formation under normoxia. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.01003 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 2 SP - 1042 EP - 1061 PB - American Society of Plant Physiologists CY - Rockville ER -