TY  - JOUR
A1  - Beerenwinkel, Niko
A1  - Sing, Tobias
A1  - Lengauer, Thomas
A1  - Rahnenfuhrer, Joerg
A1  - Roomp, Kirsten
A1  - Savenkov, Igor
A1  - Fischer, Roman
A1  - Hoffmann, Daniel
A1  - Selbig, Joachim
A1  - Korn, Klaus
A1  - Walter, Hauke
A1  - Berg, Thomas
A1  - Braun, Patrick
A1  - Faetkenheuer, Gerd
A1  - Oette, Mark
A1  - Rockstroh, Juergen
A1  - Kupfer, Bernd
A1  - Kaiser, Rolf
A1  - Daeumer, Martin
T1  - Computational methods for the design of effective therapies against drug resistant HIV strains
N2  - 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
Y1  - 2005
ER  - 
TY  - JOUR
A1  - Cordes, Frank
A1  - Kaiser, Rolf
A1  - Selbig, Joachim
T1  - Bioinformatics approach to predicting HIV drug resistance
N2  - 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
Y1  - 2006
UR  - http://www.expert-reviews.com/loi/erm
U6  - https://doi.org/10.1586/14737159.6.2.207
SN  - 1473-7159
ER  - 
TY  - JOUR
A1  - Simons, Nadja K.
A1  - Lewinsohn, Thomas
A1  - Bluethgen, Nico
A1  - Buscot, Francois
A1  - Boch, Steffen
A1  - Daniel, Rolf
A1  - Gossner, Martin M.
A1  - Jung, Kirsten
A1  - Kaiser, Kristin
A1  - Müller, Jörg
A1  - Prati, Daniel
A1  - Renner, Swen C.
A1  - Socher, Stephanie A.
A1  - Sonnemann, Ilja
A1  - Weiner, Christiane N.
A1  - Werner, Michael
A1  - Wubet, Tesfaye
A1  - Wurst, Susanne
A1  - Weisser, Wolfgang W.
T1  - Contrasting effects of grassland management modes on species-abundance distributions of multiple groups
JF  - Agriculture, ecosystems & environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere
N2  - 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.
KW  - Biodiversity
KW  - Cutting frequency
KW  - Management intensity
KW  - Rank-abundance
KW  - Species loss
KW  - Rarity
Y1  - 2017
U6  - https://doi.org/10.1016/j.agee.2016.12.022
SN  - 0167-8809
SN  - 1873-2305
VL  - 237
SP  - 143
EP  - 153
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Schall, Peter
A1  - Gossner, Martin M.
A1  - Heinrichs, Steffi
A1  - Fischer, Markus
A1  - Boch, Steffen
A1  - Prati, Daniel
A1  - Jung, Kirsten
A1  - Baumgartner, Vanessa
A1  - Blaser, Stefan
A1  - Böhm, Stefan
A1  - Buscot, Francois
A1  - Daniel, Rolf
A1  - Goldmann, Kezia
A1  - Kaiser, Kristin
A1  - Kahl, Tiemo
A1  - Lange, Markus
A1  - Müller, Jörg Hans
A1  - Overmann, Jörg
A1  - Renner, Swen C.
A1  - Schulze, Ernst-Detlef
A1  - Sikorski, Johannes
A1  - Tschapka, Marco
A1  - Türke, Manfred
A1  - Weisser, Wolfgang W.
A1  - Wemheuer, Bernd
A1  - Wubet, Tesfaye
A1  - Ammer, Christian
T1  - The impact of even-aged and uneven-aged forest management on regional biodiversity of multiple taxa in European beech forests
JF  - Journal of applied ecology : an official journal of the British Ecological Society
N2  - 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.
KW  - beta diversity
KW  - forest specialists
KW  - gamma diversity
KW  - heterogeneity
KW  - Hill numbers
KW  - saproxylic beetles
KW  - spatial grain
KW  - species accumulation curve
KW  - species richness
KW  - species turnover
Y1  - 2017
U6  - https://doi.org/10.1111/1365-2664.12950
SN  - 0021-8901
SN  - 1365-2664
VL  - 55
IS  - 1
SP  - 267
EP  - 278
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Westbrook, N.
A1  - Henkel, Carsten
A1  - Westbrook, C. I.
A1  - Landragin, A.
A1  - Labeyrie, G.
A1  - Cognet, L.
A1  - Savalli, V.
A1  - Horvath, G.
A1  - Aspect, Alain
A1  - Moelmer, Klaus
A1  - Courtois, J.-Y.
A1  - Phillips, W. D.
A1  - Kaiser, Rolf
A1  - Bagnato, V.
T1  - New physics with evanescent wave atomic mirrors : the van der Waals force and atomic diffraction
N2  - 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.
Y1  - 1998
ER  - 
TY  - JOUR
A1  - Kubin, Markus
A1  - Kern, Jan
A1  - Gul, Sheraz
A1  - Kroll, Thomas
A1  - Chatterjee, Ruchira
A1  - Loechel, Heike
A1  - Fuller, Franklin D.
A1  - Sierra, Raymond G.
A1  - Quevedo, Wilson
A1  - Weniger, Christian
A1  - Rehanek, Jens
A1  - Firsov, Anatoly
A1  - Laksmono, Hartawan
A1  - Weninger, Clemens
A1  - Alonso-Mori, Roberto
A1  - Nordlund, Dennis L.
A1  - Lassalle-Kaiser, Benedikt
A1  - Glownia, James M.
A1  - Krzywinski, Jacek
A1  - Moeller, Stefan
A1  - Turner, Joshua J.
A1  - Minitti, Michael P.
A1  - Dakovski, Georgi L.
A1  - Koroidov, Sergey
A1  - Kawde, Anurag
A1  - Kanady, Jacob S.
A1  - Tsui, Emily Y.
A1  - Suseno, Sandy
A1  - Han, Zhiji
A1  - Hill, Ethan
A1  - Taguchi, Taketo
A1  - Borovik, Andrew S.
A1  - Agapie, Theodor
A1  - Messinger, Johannes
A1  - Erko, Alexei
A1  - Föhlisch, Alexander
A1  - Bergmann, Uwe
A1  - Mitzner, Rolf
A1  - Yachandra, Vittal K.
A1  - Yano, Junko
A1  - Wernet, Philippe
T1  - Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers
JF  - Structural dynamics
N2  - 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).
Y1  - 2017
U6  - https://doi.org/10.1063/1.4986627
SN  - 2329-7778
VL  - 4
PB  - American Institute of Physics
CY  - Melville
ER  - 
TY  - JOUR
A1  - Kroll, Thomas
A1  - Kern, Jan
A1  - Kubin, Markus
A1  - Ratner, Daniel
A1  - Gul, Sheraz
A1  - Fuller, Franklin D.
A1  - Löchel, Heike
A1  - Krzywinski, Jacek
A1  - Lutman, Alberto
A1  - Ding, Yuantao
A1  - Dakovski, Georgi L.
A1  - Moeller, Stefan
A1  - Turner, Joshua J.
A1  - Alonso-Mori, Roberto
A1  - Nordlund, Dennis L.
A1  - Rehanek, Jens
A1  - Weniger, Christian
A1  - Firsov, Alexander
A1  - Brzhezinskaya, Maria
A1  - Chatterjee, Ruchira
A1  - Lassalle-Kaiser, Benedikt
A1  - Sierra, Raymond G.
A1  - Laksmono, Hartawan
A1  - Hill, Ethan
A1  - Borovik, Andrew S.
A1  - Erko, Alexei
A1  - Föhlisch, Alexander
A1  - Mitzner, Rolf
A1  - Yachandra, Vittal K.
A1  - Yano, Junko
A1  - Wernet, Philippe
A1  - Bergmann, Uwe
T1  - X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser
JF  - Optics express : the international electronic journal of optics
N2  - 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
Y1  - 2016
U6  - https://doi.org/10.1364/OE.24.022469
SN  - 1094-4087
VL  - 24
SP  - 22469
EP  - 22480
PB  - Optical Society of America
CY  - Washington
ER  - 
TY  - JOUR
A1  - Mitzner, Rolf
A1  - Rehanek, Jens
A1  - Kern, Jan
A1  - Gul, Sheraz
A1  - Hattne, Johan
A1  - Taguchi, Taketo
A1  - Alonso-Mori, Roberto
A1  - Tran, Rosalie
A1  - Weniger, Christian
A1  - Schröder, Henning
A1  - Quevedo, Wilson
A1  - Laksmono, Hartawan
A1  - Sierra, Raymond G.
A1  - Han, Guangye
A1  - Lassalle-Kaiser, Benedikt
A1  - Koroidov, Sergey
A1  - Kubicek, Katharina
A1  - Schreck, Simon
A1  - Kunnus, Kristjan
A1  - Brzhezinskaya, Maria
A1  - Firsov, Alexander
A1  - Minitti, Michael P.
A1  - Turner, Joshua J.
A1  - Möller, Stefan
A1  - Sauter, Nicholas K.
A1  - Bogan, Michael J.
A1  - Nordlund, Dennis
A1  - Schlotter, William F.
A1  - Messinger, Johannes
A1  - Borovik, Andrew S.
A1  - Techert, Simone
A1  - de Groot, Frank M. F.
A1  - Föhlisch, Alexander
A1  - Erko, Alexei
A1  - Bergmann, Uwe
A1  - Yachandra, Vittal K.
A1  - Wernet, Philippe
A1  - Yano, Junko
T1  - L-edge x-ray absorption spectroscopy of dilute systems relevant to metalloproteins using an X-ray free-electron laser
JF  - The journal of physical chemistry letters
N2  - 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.
Y1  - 2013
U6  - https://doi.org/10.1021/jz401837f
SN  - 1948-7185
VL  - 4
IS  - 21
SP  - 3641
EP  - 3647
PB  - American Chemical Society
CY  - Washington
ER  -