@article{BeerenwinkelSingLengaueretal.2005, author = {Beerenwinkel, Niko and Sing, Tobias and Lengauer, Thomas and Rahnenfuhrer, Joerg and Roomp, Kirsten and Savenkov, Igor and Fischer, Roman and Hoffmann, Daniel and Selbig, Joachim and Korn, Klaus and Walter, Hauke and Berg, Thomas and Braun, Patrick and Faetkenheuer, Gerd and Oette, Mark and Rockstroh, Juergen and Kupfer, Bernd and Kaiser, Rolf and Daeumer, Martin}, title = {Computational methods for the design of effective therapies against drug resistant HIV strains}, year = {2005}, abstract = {The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective pressure exerted by the human immune system and by combination drug therapy. We have developed several computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genomic data}, language = {en} } @article{CordesKaiserSelbig2006, author = {Cordes, Frank and Kaiser, Rolf and Selbig, Joachim}, title = {Bioinformatics approach to predicting HIV drug resistance}, issn = {1473-7159}, doi = {10.1586/14737159.6.2.207}, year = {2006}, abstract = {The emergence of drug resistance remains one of the most challenging issues in the treatment of HIV-1 infection. The extreme replication dynamics of HIV facilitates its escape from the selective pressure exerted by the human immune system and by the applied combination drug therapy. This article reviews computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genotypic and phenotypic data. Genotypic assays are based on the analysis of mutations associated with reduced drug susceptibility, but are difficult to interpret due to the numerous mutations and mutational patterns that confer drug resistance. Phenotypic resistance or susceptibility can be experimentally evaluated by measuring the inhibition of the viral replication in cell culture assays. However, this procedure is expensive and time consuming}, language = {en} } @article{SimonsLewinsohnBluethgenetal.2017, author = {Simons, Nadja K. and Lewinsohn, Thomas and Bluethgen, Nico and Buscot, Francois and Boch, Steffen and Daniel, Rolf and Gossner, Martin M. and Jung, Kirsten and Kaiser, Kristin and M{\"u}ller, J{\"o}rg and Prati, Daniel and Renner, Swen C. and Socher, Stephanie A. and Sonnemann, Ilja and Weiner, Christiane N. and Werner, Michael and Wubet, Tesfaye and Wurst, Susanne and Weisser, Wolfgang W.}, title = {Contrasting effects of grassland management modes on species-abundance distributions of multiple groups}, series = {Agriculture, ecosystems \& environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere}, volume = {237}, journal = {Agriculture, ecosystems \& environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-8809}, doi = {10.1016/j.agee.2016.12.022}, pages = {143 -- 153}, year = {2017}, abstract = {Intensive land use is a major cause of biodiversity loss, but most studies comparing the response of multiple taxa rely on simple diversity measures while analyses of other community attributes are only recently gaining attention. Species-abundance distributions (SADs) are a community attribute that can be used to study changes in the overall abundance structure of species groups, and whether these changes are driven by abundant or rare species. We evaluated the effect of grassland management intensity for three land-use modes (fertilization, mowing, grazing) and their combination on species richness and SADs for three belowground (arbuscular mycorrhizal fungi, prokaryotes and insect larvae) and seven aboveground groups (vascular plants, bryophytes and lichens; arthropod herbivores; arthropod pollinators; bats and birds). Three descriptors of SADs were evaluated: general shape (abundance decay rate), proportion of rare species (rarity) and proportional abundance of the commonest species (dominance). Across groups, taxonomic richness was largely unaffected by land-use intensity and only decreased with increasing mowing intensity. Of the three SAD descriptors, abundance decay rate became steeper with increasing combined land-use intensity across groups. This reflected a decrease in rarity among plants, herbivores and vertebrates. Effects of fertilization on the three descriptors were similar to the combined land-use intensity effects. Mowing intensity only affected the SAD descriptors of insect larvae and vertebrates, while grazing intensity produced a range of effects on different descriptors in distinct groups. Overall, belowground groups had more even abundance distribtitions than aboveground groups. Strong differences among aboveground groups and between above- and belowground groups indicate that no single taxonomic group can serve as an indicator for effects in other groups. In the past, the use of SADs has been hampered by concerns over theoretical models underlying specific forms of SADs. Our study shows that SAD descriptors that are not connected to a particular model are suitable to assess the effect of land use on community structure.}, language = {en} } @article{SchallGossnerHeinrichsetal.2017, author = {Schall, Peter and Gossner, Martin M. and Heinrichs, Steffi and Fischer, Markus and Boch, Steffen and Prati, Daniel and Jung, Kirsten and Baumgartner, Vanessa and Blaser, Stefan and B{\"o}hm, Stefan and Buscot, Francois and Daniel, Rolf and Goldmann, Kezia and Kaiser, Kristin and Kahl, Tiemo and Lange, Markus and M{\"u}ller, J{\"o}rg Hans and Overmann, J{\"o}rg and Renner, Swen C. and Schulze, Ernst-Detlef and Sikorski, Johannes and Tschapka, Marco and T{\"u}rke, Manfred and Weisser, Wolfgang W. and Wemheuer, Bernd and Wubet, Tesfaye and Ammer, Christian}, title = {The impact of even-aged and uneven-aged forest management on regional biodiversity of multiple taxa in European beech forests}, series = {Journal of applied ecology : an official journal of the British Ecological Society}, volume = {55}, journal = {Journal of applied ecology : an official journal of the British Ecological Society}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0021-8901}, doi = {10.1111/1365-2664.12950}, pages = {267 -- 278}, year = {2017}, abstract = {1. For managed temperate forests, conservationists and policymakers favour fine-grained uneven-aged (UEA) management over more traditional coarse-grained even-aged (EA) management, based on the assumption that within-stand habitat heterogeneity enhances biodiversity. There is, however, little empirical evidence to support this assumption. We investigated for the first time how differently grained forest management systems affect the biodiversity of multiple above- and below-ground taxa across spatial scales. 2. We sampled 15 taxa of animals, plants, fungi and bacteria within the largest contiguous beech forest landscape of Germany and classified them into functional groups. Selected forest stands have been managed for more than a century at different spatial grains. The EA (coarse-grained management) and UEA (fine-grained) forests are comparable in spatial arrangement, climate and soil conditions. These were compared to forests of a nearby national park that have been unmanaged for at least 20years. We used diversity accumulation curves to compare -diversity for Hill numbers D-0 (species richness), D-1 (Shannon diversity) and D-2 (Simpson diversity) between the management systems. Beta diversity was quantified as multiple-site dissimilarity. 3. Gamma diversity was higher in EA than in UEA forests for at least one of the three Hill numbers for six taxa (up to 77\%), while eight showed no difference. Only bacteria showed the opposite pattern. Higher -diversity in EA forests was also found for forest specialists and saproxylic beetles. 4. Between-stand -diversity was higher in EA than in UEA forests for one-third (all species) and half (forest specialists) of all taxa, driven by environmental heterogeneity between age-classes, while -diversity showed no directional response across taxa or for forest specialists. 5. Synthesis and applications. Comparing EA and uneven-aged forest management in Central European beech forests, our results show that a mosaic of different age-classes is more important for regional biodiversity than high within-stand heterogeneity. We suggest reconsidering the current trend of replacing even-aged management in temperate forests. Instead, the variability of stages and stand structures should be increased to promote landscape-scale biodiversity.}, language = {en} } @article{WestbrookHenkelWestbrooketal.1998, author = {Westbrook, N. and Henkel, Carsten and Westbrook, C. I. and Landragin, A. and Labeyrie, G. and Cognet, L. and Savalli, V. and Horvath, G. and Aspect, Alain and Moelmer, Klaus and Courtois, J.-Y. and Phillips, W. D. and Kaiser, Rolf and Bagnato, V.}, title = {New physics with evanescent wave atomic mirrors : the van der Waals force and atomic diffraction}, year = {1998}, abstract = {After a brief introduction to the field of atom optics and to atomic mirrors, we present experimental results obtained in our group during the last two years while studying the reflection of rubidium atoms by an evanescent wave. These involve the first measurement of the van der Waals force between an atom in its ground state and a dielectric wall, as well as the demonstration of a reflection grating for atoms at normal incidence. We also consider the influence of quantum reflection and tunnelling phenomena. Further studies using the atomic mirror as a probe of the van der Waals interaction, and of very small surface roughness are briefly discussed.}, language = {en} } @article{KubinKernGuletal.2017, author = {Kubin, Markus and Kern, Jan and Gul, Sheraz and Kroll, Thomas and Chatterjee, Ruchira and Loechel, Heike and Fuller, Franklin D. and Sierra, Raymond G. and Quevedo, Wilson and Weniger, Christian and Rehanek, Jens and Firsov, Anatoly and Laksmono, Hartawan and Weninger, Clemens and Alonso-Mori, Roberto and Nordlund, Dennis L. and Lassalle-Kaiser, Benedikt and Glownia, James M. and Krzywinski, Jacek and Moeller, Stefan and Turner, Joshua J. and Minitti, Michael P. and Dakovski, Georgi L. and Koroidov, Sergey and Kawde, Anurag and Kanady, Jacob S. and Tsui, Emily Y. and Suseno, Sandy and Han, Zhiji and Hill, Ethan and Taguchi, Taketo and Borovik, Andrew S. and Agapie, Theodor and Messinger, Johannes and Erko, Alexei and F{\"o}hlisch, Alexander and Bergmann, Uwe and Mitzner, Rolf and Yachandra, Vittal K. and Yano, Junko and Wernet, Philippe}, title = {Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers}, series = {Structural dynamics}, volume = {4}, journal = {Structural dynamics}, publisher = {American Institute of Physics}, address = {Melville}, issn = {2329-7778}, doi = {10.1063/1.4986627}, pages = {16}, year = {2017}, abstract = {X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn similar to 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions. (C) 2017 Author(s).}, language = {en} } @article{KrollKernKubinetal.2016, author = {Kroll, Thomas and Kern, Jan and Kubin, Markus and Ratner, Daniel and Gul, Sheraz and Fuller, Franklin D. and L{\"o}chel, Heike and Krzywinski, Jacek and Lutman, Alberto and Ding, Yuantao and Dakovski, Georgi L. and Moeller, Stefan and Turner, Joshua J. and Alonso-Mori, Roberto and Nordlund, Dennis L. and Rehanek, Jens and Weniger, Christian and Firsov, Alexander and Brzhezinskaya, Maria and Chatterjee, Ruchira and Lassalle-Kaiser, Benedikt and Sierra, Raymond G. and Laksmono, Hartawan and Hill, Ethan and Borovik, Andrew S. and Erko, Alexei and F{\"o}hlisch, Alexander and Mitzner, Rolf and Yachandra, Vittal K. and Yano, Junko and Wernet, Philippe and Bergmann, Uwe}, title = {X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser}, series = {Optics express : the international electronic journal of optics}, volume = {24}, journal = {Optics express : the international electronic journal of optics}, publisher = {Optical Society of America}, address = {Washington}, issn = {1094-4087}, doi = {10.1364/OE.24.022469}, pages = {22469 -- 22480}, year = {2016}, abstract = {X-ray free electron lasers (XFELs) enable unprecedented new ways to study the electronic structure and dynamics of transition metal systems. L-edge absorption spectroscopy is a powerful technique for such studies and the feasibility of this method at XFELs for solutions and solids has been demonstrated. However, the required x-ray bandwidth is an order of magnitude narrower than that of self-amplified spontaneous emission (SASE), and additional monochromatization is needed. Here we compare L-edge x-ray absorption spectroscopy (XAS) of a prototypical transition metal system based on monochromatizing the SASE radiation of the linac coherent light source (LCLS) with a new technique based on self-seeding of LCLS. We demonstrate how L-edge XAS can be performed using the self-seeding scheme without the need of an additional beam line monochromator. We show how the spectral shape and pulse energy depend on the undulator setup and how this affects the x-ray spectroscopy measurements. (C) 2016 Optical Society of America}, language = {en} } @article{MitznerRehanekKernetal.2013, author = {Mitzner, Rolf and Rehanek, Jens and Kern, Jan and Gul, Sheraz and Hattne, Johan and Taguchi, Taketo and Alonso-Mori, Roberto and Tran, Rosalie and Weniger, Christian and Schr{\"o}der, Henning and Quevedo, Wilson and Laksmono, Hartawan and Sierra, Raymond G. and Han, Guangye and Lassalle-Kaiser, Benedikt and Koroidov, Sergey and Kubicek, Katharina and Schreck, Simon and Kunnus, Kristjan and Brzhezinskaya, Maria and Firsov, Alexander and Minitti, Michael P. and Turner, Joshua J. and M{\"o}ller, Stefan and Sauter, Nicholas K. and Bogan, Michael J. and Nordlund, Dennis and Schlotter, William F. and Messinger, Johannes and Borovik, Andrew S. and Techert, Simone and de Groot, Frank M. F. and F{\"o}hlisch, Alexander and Erko, Alexei and Bergmann, Uwe and Yachandra, Vittal K. and Wernet, Philippe and Yano, Junko}, title = {L-edge x-ray absorption spectroscopy of dilute systems relevant to metalloproteins using an X-ray free-electron laser}, series = {The journal of physical chemistry letters}, volume = {4}, journal = {The journal of physical chemistry letters}, number = {21}, publisher = {American Chemical Society}, address = {Washington}, issn = {1948-7185}, doi = {10.1021/jz401837f}, pages = {3641 -- 3647}, year = {2013}, abstract = {L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming 0 K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.}, language = {en} }