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51. Longitudinal Changes of Fixation Location and Stability Within 12 Months in Stargardt Disease: ProgStar Report No. 12

Author

Schönbach, Etienne M., primary, Strauss, Rupert W., additional, Kong, Xiangrong, additional, Muñoz, Beatriz, additional, Ibrahim, Mohamed A., additional, Sunness, Janet S., additional, Birch, David G., additional, Hahn, Gesa-Astrid, additional, Nasser, Fadi, additional, Zrenner, Eberhart, additional, Sadda, SriniVas R., additional, West, Sheila K., additional, Scholl, Hendrik P.N., additional, Wolfson, Yulia, additional, Bittencourt, Millena, additional, Shah, Syed Mahmood, additional, Ahmed, Mohamed, additional, Schönbach, Etienne, additional, Fujinami, Kaoru, additional, Traboulsi, Elias, additional, Ehlers, Justis, additional, Marino, Meghan, additional, Crowe, Susan, additional, Briggs, Rachael, additional, Borer, Angela, additional, Pinter, Anne, additional, Fecko, Tami, additional, Burgnoni, Nikki, additional, Applegate, Carol, additional, Russell, Leslie, additional, Michaelides, Michel, additional, Esposti, Simona Degli, additional, Moore, Anthony, additional, Webster, Andrew, additional, Connor, Sophie, additional, Barnfield, Jade, additional, Salchi, Zaid, additional, Alfageme, Clara, additional, McCudden, Victoria, additional, Pefkianaki, Maria, additional, Aboshiha, Jonathan, additional, Liew, Gerald, additional, Holder, Graham, additional, Robson, Anthony, additional, King, Alexa, additional, Narvaez, Daniela Ivanova Cajas, additional, Barnard, Katy, additional, Grigg, Catherine, additional, Dunbar, Hannah, additional, Obadeyi, Yetunde, additional, Girard-Claudon, Karine, additional, Swann, Hilary, additional, Rughani, Avani, additional, Amoah, Charles, additional, Carrington, Dominic, additional, Bibi, Kanom, additional, Co, Emerson Ting, additional, Illiyas, Mohamed Nafaz, additional, Begum, Hamida, additional, Carter, Andrew, additional, Georgiou, Anne, additional, Lewism, Selma, additional, Shaheen, Saddaf, additional, Shinmar, Harpreet, additional, Burton, Linda, additional, Bernstein, Paul, additional, Wegner, Kimberley, additional, Sawyer, Briana Lauren, additional, Carlstrom, Bonnie, additional, Farnsworth, Kellian, additional, Fry, Cyrie, additional, Chandler, Melissa, additional, Jenkins, Glen, additional, Creel, Donnel, additional, Birch, David, additional, Wang, Yi-Zhong, additional, Rodriguez, Luis, additional, Locke, Kirsten, additional, Klein, Martin, additional, Mejia, Paulina, additional, Cideciyan, Artur V., additional, Jacobson, Samuel G., additional, Schwartz, Sharon B., additional, Matsui, Rodrigo, additional, Gruzensky, Michaela, additional, Charng, Jason, additional, Roman, Alejandro J., additional, Hahn, Gesa Astrid, additional, Wilhelm, Barbara, additional, Peters, Tobias, additional, Beier, Benjamin, additional, Koenig, Tilman, additional, Kramer, Susanne, additional, Sahel, José-Alain, additional, Mohand-Said, Saddek, additional, Audo, Isabelle, additional, Laurent-Coriat, Caroline, additional, Sliesoraityte, Ieva, additional, Zeitz, Christina, additional, Boyard, Fiona, additional, Tran, Minh Ha, additional, Chapon, Mathias, additional, Chaumette, Céline, additional, Amaudruz, Juliette, additional, Ganem, Victoria, additional, Sancho, Serge, additional, Girmens, Aurore, additional, Wojciechowski, Robert, additional, Khan, Shazia, additional, Emmert, David G., additional, Cain, Dennis, additional, Herring, Mark, additional, Bassinger, Jennifer, additional, Liberto, Lisa, additional, West, Sheila, additional, Ervin, Ann-Margret, additional, Munoz, Beatriz, additional, Dreger, Kurt, additional, Jones, Jennifer, additional, Sadda, Srinivas, additional, Ip, Michael S., additional, Jha, Anamika, additional, Ho, Alex, additional, Kramer, Brendan, additional, Lam, Ngoc, additional, Tawdros, Rita, additional, Zhou, Yong Dong, additional, Carmona, Johana, additional, Uji, Akihito, additional, Hariri, Amirhossein, additional, Lock, Amy, additional, Elshafei, Anthony, additional, Ganegoda, Anushika, additional, Petrossian, Christine, additional, Jenkins, Dennis, additional, Strnad, Edward, additional, Baghdasaryan, Elmira, additional, Ito, Eric, additional, Samson, Feliz, additional, Blanquel, Gloria, additional, Akil, Handan, additional, Melendez, Jhanisus, additional, Lei, Jianqin, additional, Huang, Jianyan, additional, Chau, Jonathan, additional, Falavarjani, Khalil G., additional, Espino, Kristina, additional, Li, Manfred, additional, Mendoza, Maria, additional, Nittala, Muneeswar Gupta, additional, Roded, Netali, additional, Saleh, Nizar, additional, Huang, Ping, additional, Pitetta, Sean, additional, Balasubramanian, Siva, additional, Leahy, Sophie, additional, Srinivas, Sowmya J., additional, Velaga, Swetha B., additional, Margaryan, Teresa, additional, Tepelus, Tudor, additional, Brown, Tyler, additional, Fan, Wenying, additional, Murillo, Yamileth, additional, Shi, Yue, additional, Aguilar, Katherine, additional, Chan, Cynthia, additional, Santos, Lisa, additional, Seo, Brian, additional, Sison, Christopher, additional, Perez, Silvia, additional, Chao, Stephanie, additional, Miyasato, Kelly, additional, Higgins, Julia, additional, Luna, Zoila, additional, Menchaca, Anita, additional, Gonzalez, Norma, additional, Robledo, Vicky, additional, Carig, Karen, additional, Baker, Kirstie, additional, Ellenbogen, David, additional, Bluemel, Daniel, additional, Sanford, Theo, additional, Linares, Daisy, additional, Tran, Mei, additional, Nava, Lorane, additional, Oberoi, Michelle, additional, Romero, Mark, additional, Chiguil, Vivian, additional, Bynum-Bain, Grantley, additional, Kim, Monica, additional, Mendiguren, Carolina, additional, Huang, Xiwen, additional, Smith, Monika, additional, and Sarreal, Natalie, additional

Published
2018
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52. Carbon budgets of top- and subsoil food webs in an arable system

Author

Pausch, Johanna, primary, Hünninghaus, Maike, additional, Kramer, Susanne, additional, Scharroba, Anika, additional, Scheunemann, Nicole, additional, Butenschoen, Olaf, additional, Marhan, Sven, additional, Bonkowski, Michael, additional, Kandeler, Ellen, additional, Scheu, Stefan, additional, Kuzyakov, Yakov, additional, and Ruess, Liliane, additional

Published
2018
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54. Changes in bacterial community composition and soil respiration indicate rapid successions of protist grazers during mineralization of maize crop residues

Author

Huenninghaus, Maike, Koller, Robert, Kramer, Susanne, Marhan, Sven, Kandeler, Ellen, Bonkowski, Michael, Huenninghaus, Maike, Koller, Robert, Kramer, Susanne, Marhan, Sven, Kandeler, Ellen, and Bonkowski, Michael

Abstract

Decomposition of organic matter is crucial for ecosystem functioning. Microorganisms, which are responsible for the mineralization of organic matter, are usually treated as a homogeneous functional guild, despite mineralization capacity can differ profoundly between taxa. In addition, a significant part of the microbial community is top-down controlled by microbial grazers, such as protist. Since protist grazing is selective, and selectivity differs among species, we hypothesized that protist taxa complement each other in grazing intensity and thereby affect bacterial community structure and mineralization rate. In a laboratory experiment the species richness of protist communities was manipulated in an arable field soil and the mineralization rate of maize litter residues followed during the decomposition of the labile (4 days) and recalcitrant (3 weeks) carbon (C) fractions. Mineralization rate overall increased in the presence of protists. Changes in microbial function could be related to changes in microbial community composition (measured by phospholipid fatty acids pattern). During microbial decomposition, different protist grazers gained influence on mineralization rates over consecutive time intervals, indicating that a succession of protists caused an enhanced bacterial C-mineralization of plant detritus. Protist identity and species richness affected the microbial community composition, but not the magnitude of its mineralization function. In general, protist identity appeared to be more relevant for the composition of the microbial communities at the beginning of decomposition while the protist species richness appeared to be more critical in the later, slow phase of decomposition. This study provides an example that the overall outcome of ecosystem processes, such as mineralization rate is regulated by the sum of positive and negative effects of complex species interactions operating at a very fine spatial and temporal scales. (C) 2017 Elsevier GmbH. All

Published
2017

55. Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution

Author

Kramer, Susanne

Subjects
Cell Nucleus, Cytoplasm, Mice, Transcription, Genetic, RNA Stability, ddc:570, Trypanosoma brucei brucei, NIH 3T3 Cells, Methods Online, Animals, RNA, Messenger, In Situ Hybridization, Fluorescence
Abstract

The detection of mRNAs undergoing transcription or decay is challenging, because both processes are fast. However, the relative proportion of an mRNA in synthesis or decay increases with mRNA size and decreases with mRNA half-life. Based on this rationale, I have exploited a 22 200 nucleotide-long, short-lived endogenous mRNA as a reporter for mRNA metabolism in trypanosomes. The extreme 5΄ and 3΄ ends were labeled with red- and green-fluorescent Affymetrix® single mRNA FISH probes, respectively. In the resulting fluorescence images, yellow spots represent intact mRNAs; red spots are mRNAs in transcription or 3΄-5΄ decay, and green spots are mRNAs in 5΄-3΄ degradation. Most red spots were nuclear and insensitive to transcriptional inhibition and thus likely transcription intermediates. Most green spots were cytoplasmic, confirming that the majority of cytoplasmic decay in trypanosomes is 5΄-3΄. The system showed the expected changes at inhibition of transcription or translation and RNAi depletion of the trypanosome homologue to the 5΄-3΄ exoribonuclease Xrn1. The method allows to monitor changes in mRNA metabolism both on cellular and on population/tissue wide levels, but also to study the subcellular localization of mRNA transcription and decay pathways. I show that the system is applicable to mammalian cells.

Published
2016

56. Polycistronic trypanosome mRNAs are a target for the exosome

Author

Kramer, Susanne, Piper, Sophie, Estevez, Antonio, Carrington, Mark, German Research Foundation, Wellcome Trust, Ministerio de Economía y Competitividad (España), Estévez, Antonio M., Carrington, Mark, Carrington, Mark [0000-0002-6435-7266], Apollo - University of Cambridge Repository, and Estévez, Antonio M. [0000-0002-8272-5405]

Subjects
Cell Nucleus, trans-splicing, Exosome Multienzyme Ribonuclease Complex, Short Communication, Trypanosoma brucei brucei, Exosome, ddc:570, Trypanosomes, Polycistronic mRNA, NMD, Parasitology, Trypanosoma brucei, RNA, Messenger, Molecular Biology, RNA, Protozoan, ComputingMethodologies_COMPUTERGRAPHICS
Abstract

Eukaryotic cells have several mRNA quality control checkpoints to avoid the production of aberrant proteins. Intron-containing mRNAs are actively degraded by the nuclear exosome, prevented from nuclear exit and, if these systems fail, degraded by the cytoplasmic NMD machinery. Trypanosomes have only two introns. However, they process mRNA5 from long polycistronic precursors by trans-splicing and polycistronic mRNA molecules frequently arise from any missed splice site. Here, we show that RNAi depletion of the trypanosome exosome, but not of the cytoplasmic 5'-3' exoribonuclease XRNA or the NMD helicase UPF1, causes accumulation of oligocistronic mRNA5. We have also revisited the localization of the trypanosome exosome by expressing eYFP-fusion proteins of the exosome subunits RRP44 and RRP6. Both proteins are significantly enriched in the nucleus. Together with published data, our data suggest a major nuclear function of the trypanosome exosome in rRNA, snoRNA and mRNA quality control. (C) 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.orgilicensesiby/4.0/)., This work was funded by the DFG (Kr4017/1-1 and Kr4017/1-2 to SK), by the Wellcome trust (grant number 085956/Z/08/Z to MC) and by the Spanish Ministerio de Economia e Innovacion (BFU2014-55193-P to AE). Markus Engstler (University of Wurzburg) is acknowledged for mentoring and providing lab space and research infrastructure. Anti-BiP was kindly provided by Jay Bangs (University of Wisconsin-Madison, Madison, US).

Published
2016

63. Novel insights into RNP granules by employing the trypanosome's microtubule skeleton as a molecular sieve

Author

Fritz, Melanie, Vanselow, Jens, Sauer, Nadja, Lamer, Stephanie, Goos, Carina, Siegel, T. Nicolai, Subota, Ines, Schlosser, Andreas, Carrington, Mark, and Kramer, Susanne

Subjects
ddc:610
Abstract

RNP granules are ribonucleoprotein assemblies that regulate the post-transcriptional fate of mRNAs in all eukaryotes. Their exact function remains poorly understood, one reason for this is that RNP granule purification has not yet been achieved. We have exploited a unique feature of trypanosomes to prepare a cellular fraction highly enriched in starvation stress granules. First, granules remain trapped within the cage-like, subpellicular microtubule array of the trypanosome cytoskeleton while soluble proteins are washed away. Second, the microtubules are depolymerized and the granules are released. RNA sequencing combined with single molecule mRNA FISH identified the short and highly abundant mRNAs encoding ribosomal mRNAs as being excluded from granules. By mass spectrometry we have identified 463 stress granule candidate proteins. For 17/49 proteins tested by eYFP tagging we have confirmed the localization to granules, including one phosphatase, one methyltransferase and two proteins with a function in trypanosome life-cycle regulation. The novel method presented here enables the unbiased identification of novel RNP granule components, paving the way towards an understanding of RNP granule function.

Published
2015

65. Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil

Author

Kramer, Susanne, Dibbern, Dorte, Moll, Julia, Huenninghaus, Maike, Koller, Robert, Krueger, Dirk, Marhan, Sven, Urich, Tim, Wubet, Tesfaye, Bonkowski, Michael, Buscot, Francois, Lueders, Tillmann, Kandeler, Ellen, Kramer, Susanne, Dibbern, Dorte, Moll, Julia, Huenninghaus, Maike, Koller, Robert, Krueger, Dirk, Marhan, Sven, Urich, Tim, Wubet, Tesfaye, Bonkowski, Michael, Buscot, Francois, Lueders, Tillmann, and Kandeler, Ellen

Abstract

The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the Actinobacteria, Bacteroidetes, Gammaproteobacteria, Basidiomycota, Ascomycota as well as Peronosporomycetes were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere.

Published
2016

66. Polycistronic trypanosome mRNAs are a target for the exosome

Author

German Research Foundation, Wellcome Trust, Ministerio de Economía y Competitividad (España), Estévez, Antonio M. [0000-0002-8272-5405], Carrington, Mark [0000-0002-6435-7266], Kramer, Susanne, Piper, Sophie, Estévez, Antonio M., Carrington, Mark, German Research Foundation, Wellcome Trust, Ministerio de Economía y Competitividad (España), Estévez, Antonio M. [0000-0002-8272-5405], Carrington, Mark [0000-0002-6435-7266], Kramer, Susanne, Piper, Sophie, Estévez, Antonio M., and Carrington, Mark

Abstract

Eukaryotic cells have several mRNA quality control checkpoints to avoid the production of aberrant proteins. Intron-containing mRNAs are actively degraded by the nuclear exosome, prevented from nuclear exit and, if these systems fail, degraded by the cytoplasmic NMD machinery. Trypanosomes have only two introns. However, they process mRNA5 from long polycistronic precursors by trans-splicing and polycistronic mRNA molecules frequently arise from any missed splice site. Here, we show that RNAi depletion of the trypanosome exosome, but not of the cytoplasmic 5'-3' exoribonuclease XRNA or the NMD helicase UPF1, causes accumulation of oligocistronic mRNA5. We have also revisited the localization of the trypanosome exosome by expressing eYFP-fusion proteins of the exosome subunits RRP44 and RRP6. Both proteins are significantly enriched in the nucleus. Together with published data, our data suggest a major nuclear function of the trypanosome exosome in rRNA, snoRNA and mRNA quality control. (C) 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.orgilicensesiby/4.0/).

Published
2016

67. Phosphorus Pools in Tree and Intercanopy Microsites of a Juniper--Grass Ecosystem

Author

Kramer, Susanne and Green, Douglas M.

Subjects
Soils -- Phosphorus content, Biotic communities -- Research, Earth sciences
Abstract

Gradients of soil-nutrient distribution between trees and intercanopy areas are common in many semiarid woodland ecosystems. To test if microsites under and between canopies influenced P pool distribution in a semiarid woodland dominated by one-seed juniper [Juniperus monosperma (Engelm.) Sarg.] and galleta grass [Hilaria jamesii (Torr.) Benth.], we compared inorganic, organic, and microbial P pools under trees and intercanopy areas of two Aridisols. Soils collected (5-15 cm depth) under eight tree canopies and in eight intercanopy areas from a Calciorthid and a Camborthid were subjected to a sequential P fractionation scheme. Soils and microsites were significant independent factors determining total soil P, which ranged from 814 [micro]g P [g.sup.-1] soil (SE = 25) to 1123 [micro]g P [g.sup.-1] soil (SE = 21). Resin P was significantly influenced by the interaction of soils with microsite. Organic hydroxide P was the largest organic P fraction and exceeded or equaled the amount of resin P. It differed significantly between the Calciorthid at 10.1 [micro]g P [g.sup.-1] soil (SE = 1.0) and the Camborthid at 22.1 [micro]g P [g.sup.-1] soil (SE = 1.6). Microsite and soil did not significantly affect microbial P, which ranged from 12.9 [micro]g P [g.sup.-1] soil (SE = 2.1) to 17.0 [micro]g P [g.sup.-1] soil (SE = 0.7). Nutrients and microbial activity are usually concentrated under canopies in semiarid and arid ecosystems. This research shows that P pools distribution in the studied ecosystem did not follow this general pattern, and that soils may be more important in determining P pool distribution than microsites.

Published
1999

68. Effects of resource availability and quality on soil microorganisms and their carbon assimilation

Author

Kramer, Susanne

Subjects
arable field, Kohlenstoffkreislauf, Nahrungsnetze, Pilze, Stabile Isotope, Wurzel, food webs, ddc:630, stable isotopes, Agrarfläche, Agriculture, Streu, Bakterien
Abstract

Soil microorganisms play a pivotal role in decomposition processes and therefore influence nutrient cycling and ecosystem function. Availability and quality of resources determines activity, growth and identity of substrate users. In agricultural systems, availability of resources is dependent on, for example, crop type, management, season, and depth. At depth substrate availability and microbial biomass decrease. However, there remain gaps in our understanding of C turnover in subsoil and how processes in the topsoil may influence abundance, activity, and function of microorganisms in deeper soil layers. With respect to substrate quality it is thought that bacteria are the dominant users of high quality substrates and more labile components whereas fungi are more important for the degradation of low quality and more recalcitrant substrates (i.e. cellulose, lignin). Therefore, this thesis was designed to increase our understanding of C turnover and the influence of both availability and quality of substrates on microorganisms in an agricultural soil. In the first and second studies, a recently established C3-C4 plant exchange field experiment was used to investigate the C flow from belowground (root) and aboveground (shoot litter) resources into the belowground food web. Maize plants were cultivated to introduce a C4 signal into the soil both by plant growth (belowground / root channel) and also by applying shoot litter (aboveground litter channel). To separate C flow from the shoot litter versus the root channel, maize litter was applied on wheat cultivated plots, while on half of the maize planted plots no maize litter was returned. Wheat cultivated plots without additional maize litter application served as a reference for the calculation of incorporated maize-C into different soil pools. Soil samplings took place in two consecutive years in summer, autumn and winter. Three depths were considered (0-10 cm: topsoil, 40-50 cm: rooted zone beneath the plough layer, 60-70 cm: unrooted zone). In the third study a microcosm experiment with substrates of different recalcitrance and complexity was carried out to identify primary decomposers of different plant litter materials (leaves and roots) during early stages of decomposition (duration of 32 days) and to follow the C flow into the next higher trophic level (protozoa). Bodenmikroorganismen spielen eine zentrale Rolle im Abbau von organischer Substanz und beeinflussen somit Nährstoffkreisläufe und die Funktion von Ökosystemen. Die Verfügbarkeit und Qualität von Ressourcen bestimmt die Aktivität, das Wachstum und die Identität der entsprechenden Substratnutzer. In Agrarökosystemen ist die Verfügbarkeit von Ressourcen zum Beispiel abhängig von Kulturpflanzenart, Bodenbearbeitung, Jahreszeit und Bodentiefe. In der Tiefe ist die Substratverfügbarkeit und somit auch die mikrobielle Biomasse verringert. Aber es ist immer noch wenig bekannt über den C-Umsatz im Unterboden und wie und ob Prozesse im Oberboden die Abundanz, Aktivität und Funktion von Mikroorganismen im Unterboden beeinflussen. In Bezug auf die Substratqualität wird davon ausgegangen, dass Bakterien vor allem am Abbau hoch qualitativer und leicht abzubauender Substrate beteiligt sind, während Pilze eine wichtigere Rolle beim Abbau von qualitativ minderwertigeren und schwerer abzubauenden Substraten (z.B. Cellulose, Lignin) spielen. Die vorliegende Arbeit wurde durchgeführt, um das Verständnis des C-Umsatzes und den Einfluss von Verfügbarkeit und Qualität von Substraten auf Mikroorganismen in einer Agrarfläche zu verbessern. In der ersten und zweiten Studie wurde ein Feldversuch genutzt, der angelegt wurde, um mit Hilfe eines C3-C4 Pflanzenwechsels den C-Fluss von unterirdischen (Wurzel) und oberirdischen (Streu) Ressourcen ins unterirdische Nahrungsnetz zu untersuchen. Maispflanzen wurden angebaut, um das C4-bürtige Signal in den Boden einzuführen. Dies geschah einerseits durch Pflanzenwachstum (unterirdisch / Wurzelkanal) und andererseits durch das Rückführen von Streu auf die Flächen (oberirdischer Streukanal). Um den C-Fluss des Wurzel- und Streu-Kanals zu trennen, wurde Streu auf Flächen aufgebracht, auf denen Weizen angebaut wurde, während auf der Hälfte der Flächen, auf denen Mais angebaut wurde, keine Streu zurückgeführt wurde. Weizenflächen auf denen keine zusätzliche Maisstreu aufgebracht wurde, wurden als Referenz für die Berechnung des C-Eintrags in die unterschiedlichen Bodenpools genutzt. Bodenproben wurden in 2 aufeinanderfolgenden Jahren im Sommer, Herbst und Winter genommen. Es wurden 3 unterschiedliche Bodentiefen betrachtet (0-10 cm: Oberboden, 40-50 cm: durchwurzelte Zone unter dem Pflughorizont, 60-70 cm: nicht durchwurzelte Zone). In der dritten Studie wurde ein Mikrokosmenexperiment mit Substraten unterschiedlicher Qualität und Komplexität durchgeführt, um primäre Nutzer von unterschiedlichem Pflanzenmaterial (Blätter und Wurzeln) während der frühen Abbauphase (32 Tage) zu identifizieren und den C-Fluss in eine nächst höhere trophische Ebene (Protozoen) zu untersuchen.

Published
2014

69. Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil

Author

Kramer, Susanne, primary, Dibbern, Dörte, additional, Moll, Julia, additional, Huenninghaus, Maike, additional, Koller, Robert, additional, Krueger, Dirk, additional, Marhan, Sven, additional, Urich, Tim, additional, Wubet, Tesfaye, additional, Bonkowski, Michael, additional, Buscot, François, additional, Lueders, Tillmann, additional, and Kandeler, Ellen, additional

Published
2016
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70. Visual Acuity Loss and Associated Risk Factors in the Retrospective Progression of Stargardt Disease Study (ProgStar Report No. 2)

Author

Kong, Xiangrong, primary, Strauss, Rupert W., additional, Michaelides, Michel, additional, Cideciyan, Artur V., additional, Sahel, José-Alain, additional, Muñoz, Beatriz, additional, West, Sheila, additional, Scholl, Hendrik P.N., additional, Wolfson, Yulia, additional, Bittencourt, Millena, additional, Shah, Syed Mahmood, additional, Ahmed, Mohammed, additional, Schonbach, Etienne, additional, Fujinami, Kaoru, additional, Traboulsi, Elias, additional, Ehlers, Justis, additional, Marino, Meghan, additional, Crowe, Susan, additional, Briggs, Rachael, additional, Borer, Angela, additional, Pinter, Anne, additional, Fecko, Tami, additional, Brugnoni, Nikki, additional, Sunness, Janet S., additional, Applegate, Carol, additional, Russell, Leslie, additional, Moore, Anthony, additional, Webster, Andrew, additional, Connor, Sophie, additional, McCudden, Victoria, additional, Pefkianaki, Maria, additional, Aboshiha, Jonathan, additional, Liew, Gerald, additional, Holder, Graham, additional, Robson, Anthony, additional, King, Alexa, additional, Cajas Narvaez, Daniela Ivanova, additional, Barnard, Katy, additional, Grigg, Catherine, additional, Dunbar, Hannah, additional, Obadeyi, Yetunde, additional, Girard-Claudon, Karine, additional, Swann, Hilary, additional, Rughani, Avani, additional, Amoah, Charles, additional, Carrington, Dominic, additional, Bibi, Kanom, additional, Co, Emerson Ting, additional, Carter, Andrew, additional, Georgiou, Anne, additional, Lewis, Selma, additional, Shaheen, Saddaf, additional, Shinmar, Harpreet, additional, Burton, Linda, additional, Bernstein, Paul, additional, Wegner, Kimberley, additional, Sawyer, Briana Lauren, additional, Carlstrom, Bonnie, additional, Farnsworth, Kellian, additional, Fry, Cyrie, additional, Chandler, Melissa, additional, Jenkins, Glen, additional, Creel, Donnel, additional, Birch, David, additional, Wang, Yi-Zhong, additional, Rodriguez, Luis, additional, Locke, Kirsten, additional, Klein, Martin, additional, Mejia, Paulina, additional, Jacobson, Samuel G., additional, Schwartz, Sharon B., additional, Matsui, Rodrigo, additional, Gruzensky, Michaela, additional, Roman, Alejandro J., additional, Zrenner, Eberhart, additional, Nasser, Fadi, additional, Hahn, Gesa Astrid, additional, Wilhelm, Barbara, additional, Peters, Tobias, additional, Beier, Benjamin, additional, Koenig, Tilman, additional, Kramer, Susanne, additional, Mohand-Said, Saddek, additional, Audo, Isabelle, additional, Laurent-Coriat, Caroline, additional, Sliesoraityte, Ieva, additional, Zeitz, Christina, additional, Boyard, Fiona, additional, Tran, Minh Ha, additional, Chapon, Mathias, additional, Chaumette, Céline, additional, Amaudruz, Juliette, additional, Ganem, Victoria, additional, Sancho, Serge, additional, Girmens, Aurore, additional, Wojciechowski, Robert, additional, Khan, Shazia, additional, Emmert, David G., additional, Cain, Dennis, additional, Herring, Mark, additional, Bassinger, Jennifer, additional, Liberto, Lisa, additional, Ervin, Ann-Margret, additional, Munoz, Beatriz, additional, Kong, Xiangrong, additional, Dreger, Kurt, additional, Jones, Jennifer, additional, Sadda, Srinivas, additional, Jha, Anamika, additional, Ho, Alex, additional, Kramer, Brendan, additional, Hariri, Amirhossein, additional, Blanquel, Gloria Rebecca, additional, Lam, Ngoc, additional, Pitetta, Sean, additional, Shi, Yue, additional, Tawdros, Rita, additional, Petrossian, Christine, additional, Jenkins, Dennis, additional, Gupta, Muneeswar, additional, Zhou, Yong Dong, additional, Aguilar, Katherine, additional, Chan, Cynthia, additional, Santos, Lisa, additional, Seo, Brian, additional, Sison, Christopher, additional, Perez, Silvia, additional, Chao, Stephanie, additional, Miyasato, Kelly, additional, Higgins, Julia, additional, Luna, Zoila, additional, Menchaca, Anita, additional, Gonzalez, Norma, additional, Robledo, Vicky, additional, Carig, Karen, additional, Baker, Kirstie, additional, Ellenbogen, David, additional, Russell, James, additional, Bluemel, Daniel, additional, Moreno, Alex, additional, Pham, Royal, additional, Sanford, Theo, additional, Linares, Daisy, additional, and Tran, Mei, additional

Published
2016
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75. Die Auswirkung von Siloran- und Methacrylathaftvermittlern auf die Adhäsion siloranbasierter Dentalkomposite - eine in-vitro Scherhaftfestigkeitsuntersuchung

Author

Kramer, Susanne

Subjects
ddc:610, 610 Medizin, dental composites, Filtek Silorane, Hermes Flow, shearbondstrength, Adhesivesystem
Abstract

Mit der Einführung der Filtek Silorane steht dem Markt der konservativen Zahnheilkunde ein neuartiges Füllungsmaterial zur Verfügung, welches besonders mit seiner verringerten Volumenschrumpfung beworben wird. Aufgrund ihrer deutlich anderen Matrixchemie gegenüber den konventionellen, vielfach untersuchten Methacrylaten unterscheidet sich auch der Adhäsionsmechanismus der stark hydrophoben Silorane. Herkömmliche Methacrylatadhäsive reichen laut Hersteller nicht aus, um einen suffizienten Verbund zu erzielen. Benötigt wird vielmehr ein speziell entwickeltes Silorane Systeme Adhesive. Ziel der in-vitro Studie war es, mögliche Alternativen beim Bonding siloranbasierter Komposite auf ihre Scherhaftfestigkeit hin zu untersuchen. Auf je 320 Schmelz- und Dentinprüfkörpern aus menschlichen Molaren wurden die Scherhaftkräfte gemessen, die bei der Adhäsion von Filtek Siloranen (3M Espe) oder Hermes Flow (3M Espe) einem siloranbasierten, niedrigviskösen Komposit als Füllungsmaterialien auftraten. Die aufgetretenen Bruchmodi wurden lichtmikroskopisch bestimmt. Als Haftvermittler dienten drei erprobte konventionelle Methacrylatadhäsive: Optibond FL (Kerr), Adper Scotchbond Multi Purpose (3M Espe) und Clearfil SE Bond (Kuraray). Anwendungskombinationen waren: deren Primer alleine oder in Verbindung mit dem dazugehörigen Bonding oder in Kombination mit dem Bonding des Silorane System Adhesive. Außerdem wurde Hermes Flow als Haftvermitller in Zusammenhang mit den Methacrylatadhäsiven getestet. Es konnte gezeigt werden, dass keines der konventionellen Adhäsivsysteme alleine in der Lage war, auf beiden Zahnhartsubstanzen durchgehend höhere oder gleichwertige Haftwerte für siloranbasierte Komposite zu liefern als das Silorane System Adhesive. Alle drei getesteten Produkte konnten allerdings eine Verbesserung gegenüber dem empfohlenen Adhäsiv erreichen, wenn sie zusammen mit dem Bonding dieses speziellen Systems angewendet wurden. Als besonders erfolgsversprechend im Hinblick auf die gemessenen Haftkräfte erwies sich der Versuch, Clearfil SE Bond mit dem Silorane System Adhesive Bond zu kombinieren. Hermes Flow als Haftvermittler hingegen erreichte keine suffiziente Verbindung zu den Zahnhartsubstanzen., Objective: The so called Filtek Siloranes are a new, low shrinking dental composite with a chemical matrix different to commonly used methacrylate composites. This in vitro study investigates the effect of different methacrylate and silorane based adhesives on the adhesion of Filtek Siloranes to dental hard tissues. Study design: Shearbondstrength was measured for 640 specimens based on enamel and dentin of human molars. Filtek Siloranes and Hermes Flow, a silorane composite of low viscosity, were adhesive bonded with three clinical well tried methacrylat adhesives: Optibond FL (Kerr), Adper Scotchbond Multi Purpose (3M Espe) und Clearfil SE Bond (Kuraray). There were tested alternating combinations of methacrylate bonding components with and without Silorane Systeme Adhesive Bond and Hermes Flow used as bonding. The fracture modus was analyzed under the light microscope. Results: For silorane based composites none of the tested conventional adhesive systems supplied higher or equal shearbondstrength on both dental hard tissues on its own than Silorane Systeme Adhesive did. On the other hand all three improved adhesion compared to Silorane Systeme Adhesive if combined with Silorane Systeme Adhesive Bond. Conclusion: Particular promising for the adhesive bonding of silorane based composites appeared the combination of Clearfil SE Bond with Silorane Systeme Adhesive Bond. Hermes Flow reached no noteworthy adhesion used as bonding.

Published
2013
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78. Modulation of human endogenous retrovirus (HERV) transcription during persistent and de novo HIV-1 infection

Author

Vincendeau, Michelle, primary, Göttesdorfer, Ingmar, additional, Schreml, Julia M H, additional, Wetie, Armand G Ngounou, additional, Mayer, Jens, additional, Greenwood, Alex D, additional, Helfer, Markus, additional, Kramer, Susanne, additional, Seifarth, Wolfgang, additional, Hadian, Kamyar, additional, Brack-Werner, Ruth, additional, and Leib-Mösch, Christine, additional

Published
2015
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82. Characterization of a PKA-like kinase from Trypanosoma brucei

Author

Kramer, Susanne

Subjects
FOS: Biological sciences, Trypanosoma brucei PKA cAMP cGMP
Abstract

The protozoan parasite Trypanosoma brucei causes human sleeping sickness and Nagana in domestic animals and depends on the tsetse fly for dissemination. The complex T. brucei life cycle requires differentiation from the dividing long slender forms via the cell cycle arrested short stumpy forms (both in the mammalian bloodstream) to the procyclic forms of the insect vector. The signaling pathways that regulate differentiation are unknown but there is evidence for an involvement of cAMP. In search of the putative cAMP receptor, three catalytic and one regulatory PKA-like subunits have been previously cloned from T. brucei. The catalytic subunits possess all features of a classical PKA in terms of inhibitor and substrate specificity. It was shown that each of the catalytic PKAlike subunits binds to the regulatory subunit to form a dimeric PKA-like holoenzyme. Most surprisingly, we found that T. brucei PKA-like kinase, despite of its apparent similarities to a PKA, was not activated but instead inhibited by cAMP. Out of several other cyclic nucleotides that were tested on their effects on PKA-like kinase, only cGMP was able to activate the kinase, but in millimolar and thus most likely unphysiological concentrations. Assuming that the activation of PKA-like kinase might depend on its native, subcellular environment, an in vivo kinase assay was established in this work. It is based on the immunological detection of the phosphorylated form of the PKA reporter substrate VASP that was transgenically expressed in T. brucei. Interestingly, results from the in vivo assay did confirm the in vitro data, suggesting that T. brucei PKA-like kinase is in fact inhibited rather than activated by cAMP. Even though these findings challenge the original assumption that T. brucei PKA-like kinase transmits the differentation signal mimicked by cAMP antagonists, data from this work nevertheless provide evidence for an involvement of T. brucei PKA-like kinase in relaying extracellular cues. This is suggested from an increase in in vivo PKA activity in the presence of treatments that have either been shown to induce LS to SS differentiation (etazolate) or to participate in SS to PCF differentiation (cold shock, mild acid stress). In addition, in vivo PKA activity was stimulated with the PDE inhibitor dipyridamole and at hypoosmotic stress. In the context of a putative role for T. brucei PKA-like kinase in the regulation of differentiation, two of the catalytic isoforms (PKAC1 and PKAC2) were of particular interest. We found significant life cycle stage dependent differences in protein expression between the two almost identical isoforms. PKAC1 was nearly exclusively present in bloodstream forms and PKAC2 in procyclic cells. In addition, PKAC1, but not PKAC2 carries a phosphorylation that is restricted to the SS stage. This phosphorylation was mapped to the C-terminal threonine 324 by mass spectrometry. The functions of these life cycle stage dependent differences between PKAC1 and PKAC2 remain unknown. Reverse genetics did not reveal any functional differences between the isoforms, in fact, PKAC1 was even able to complement PKAC2 in procyclic PKAC2 knock-out cells. Results from several reverse genetic experiments indicate that T. brucei PKA-like kinase plays an important role in cell division. Depletion of either PKA-like subunit leads to a cytokinesis block. Depletion of the regulatory PKA-like subunit additionally results in altered basal body segregation. Given that 1) both cytokinesis and basal body movement had been previously suggested to be regulated by the trypanosomal flagellum (Kohl et al., 2003) and 2) the flagellum hosts T. brucei PKA-like kinase (C. Krumbholz, this lab) we propose that trypanosomal flagella act as signaling compartments for coordination of cell division.

Published
2005
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86. Alterations in DRBD3 Ribonucleoprotein Complexes in Response to Stress in Trypanosoma brucei

Author

Fernández-Moya, Sandra M., García-Pérez, A., Kramer, Susanne, Carrington, Mark, Estévez, Antonio M., Fernández-Moya, Sandra M., García-Pérez, A., Kramer, Susanne, Carrington, Mark, and Estévez, Antonio M.

Abstract

Regulation of RNA polymerase II transcription initiation is apparently absent in trypanosomes. Instead, these eukaryotes control gene expression mainly at the post-transcriptional level. Regulation is exerted through the action of numerous RNA-binding proteins that modulate mRNA processing, turnover, translation and localization. In this work we show that the RNA-binding protein DRBD3 resides in the cytoplasm, but localizes to the nucleus upon oxidative challenge and to stress granules under starvation conditions. DRBD3 associates with other proteins to form a complex, the composition of which is altered by cellular stress. Interestingly, target mRNAs remain bound to DRBD3 under stress conditions. Our results suggest that DRBD3 transports regulated mRNAs within the cell in the form of ribonucleoprotein complexes that are remodeled in response to environmental cues. © 2012 Fernández-Moya et al.

Published
2012

91. Effects of resource availability and quality on the structure of the micro-food web of an arable soil across depth

Author

Scharroba, Anika, primary, Dibbern, Dörte, additional, Hünninghaus, Maike, additional, Kramer, Susanne, additional, Moll, Julia, additional, Butenschoen, Olaf, additional, Bonkowski, Michael, additional, Buscot, Francois, additional, Kandeler, Ellen, additional, Koller, Robert, additional, Krüger, Dirk, additional, Lueders, Tillmann, additional, Scheu, Stefan, additional, and Ruess, Liliane, additional

Published
2012
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92. Restoring Methicillin-Resistant Staphylococcus aureus Susceptibility to β-Lactam Antibiotics

Author

Tan, Christopher M., primary, Therien, Alex G., additional, Lu, Jun, additional, Lee, Sang H., additional, Caron, Alexandre, additional, Gill, Charles J., additional, Lebeau-Jacob, Christian, additional, Benton-Perdomo, Liliana, additional, Monteiro, João M., additional, Pereira, Pedro M., additional, Elsen, Nathaniel L., additional, Wu, Jin, additional, Deschamps, Kathleen, additional, Petcu, Mihai, additional, Wong, Simon, additional, Daigneault, Etienne, additional, Kramer, Susanne, additional, Liang, Lianzhu, additional, Maxwell, Eugene, additional, Claveau, David, additional, Vaillancourt, John, additional, Skorey, Kathryn, additional, Tam, John, additional, Wang, Hao, additional, Meredith, Timothy C., additional, Sillaots, Susan, additional, Wang-Jarantow, Lisa, additional, Ramtohul, Yeeman, additional, Langlois, Eric, additional, Landry, France, additional, Reid, John C., additional, Parthasarathy, Gopal, additional, Sharma, Sujata, additional, Baryshnikova, Anastasia, additional, Lumb, Kevin J., additional, Pinho, Mariana G., additional, Soisson, Stephen M., additional, and Roemer, Terry, additional

Published
2012
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93. Carbon flow into microbial and fungal biomass as a basis for the belowground food web of agroecosystems

Author

Kramer, Susanne, primary, Marhan, Sven, additional, Ruess, Liliane, additional, Armbruster, Wolfgang, additional, Butenschoen, Olaf, additional, Haslwimmer, Heike, additional, Kuzyakov, Yakov, additional, Pausch, Johanna, additional, Scheunemann, Nicole, additional, Schoene, Jochen, additional, Schmalwasser, Andreas, additional, Totsche, Kai Uwe, additional, Walker, Frank, additional, Scheu, Stefan, additional, and Kandeler, Ellen, additional

Published
2012
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