TY - JOUR A1 - Zuo, Zhili A1 - Gandhi, Neha S. A1 - Arndt, Katja Maren A1 - Mancera, Ricardo L. T1 - Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein JF - Biopolymers N2 - The c-Fosc-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions. KW - free energy of binding KW - coiled-coil KW - molecular dynamics KW - MM KW - GBSA KW - leucine zipper Y1 - 2012 U6 - https://doi.org/10.1002/bip.22099 SN - 0006-3525 VL - 97 IS - 11 SP - 899 EP - 909 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Ziege, Madlen A1 - Hennige-Schulz, Carmen A1 - Muecksch, Frauke A1 - Bierbach, David A1 - Tiedemann, Ralph A1 - Streit, Bruno A1 - Plath, Martin T1 - A comparison of two methods to assess audience-induced changes in male mate choice JF - Current zoology N2 - Multidirectional communicative interactions in social networks can have a profound effect on mate choice behavior. Male Atlantic molly Poecilia mexicana exhibit weaker mating preferences when an audience male is presented. This could be a male strategy to reduce sperm competition risk: interacting more equally with different females may be advantageous because rivals might copy mate choice decisions. In line with this hypothesis, a previous study found males to show a strong audience effect when being observed while exercising mate choice, but not when the rival was presented only before the choice tests. Audience effects on mate choice decisions have been quantified in poeciliid fishes using association preference designs, but it remains unknown if patterns found from measuring association times translate into actual mating behavior. Thus, we created five audience treatments simulating different forms of perceived sperm competition risk and determined focal males' mating preferences by scoring pre-mating (nipping) and mating behavior (gonopodial thrusting). Nipping did not reflect the pattern that was found when association preferences were measured, while a very similar pattern was uncovered in thrusting behavior. The strongest response was observed when the audience could eavesdrop on the focal male's behavior. A reduction in the strength of focal males' preferences was also seen after the rival male had an opportunity to mate with the focal male's preferred mate. In comparison, the reduction of mating preferences in response to an audience was greater when measuring association times than actual mating behavior. While measuring direct sexual interactions between the focal male and both stimulus females not only the male's motivational state is reflected but also females' behavior such as avoidance of male sexual harassment. KW - Communication networks KW - Male mate choice KW - Non-independent mate choice KW - Sexual selection KW - Sperm competition risk KW - Audience effect Y1 - 2012 SN - 1674-5507 VL - 58 IS - 1 SP - 84 EP - 94 PB - Current Zoology CY - Beijing ER - TY - JOUR A1 - Zhang, Gong A1 - Fedyunin, Ivan A1 - Kirchner, Sebastian A1 - Xiao, Chuanle A1 - Valleriani, Angelo A1 - Ignatova, Zoya T1 - FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads JF - Nucleic acids research N2 - The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets. Y1 - 2012 U6 - https://doi.org/10.1093/nar/gks196 SN - 0305-1048 VL - 40 IS - 11 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Zaccheus, Mona V. A1 - Bröker, Nina Kristin A1 - Lundborg, Magnus A1 - Uetrecht, Charlotte A1 - Barbirz, Stefanie A1 - Widmalm, Goran T1 - Structural studies of the O-antigen polysaccharide from Escherichia coli TD2158 having O18 serogroup specificity and aspects of its interaction with the tailspike endoglycosidase of the infecting bacteriophage HK620 JF - Carbohydrate research N2 - We have analyzed the O-antigen polysaccharide of the previously uncharacterized Escherichia coli strain TD2158 which is a host of bacteriophage HK620. This bacteriophage recognizes and cleaves the polysaccharide with its tailspike protein (TSP). The polysaccharide preparation as well as oligosaccharides obtained from HK620TSP endoglycosidase digests were analyzed with NMR spectroscopy. Additionally, sugar analysis was performed on the O-antigen polysaccharide and MALDI-TOF MS was used in oligosaccharide analysis. The present study revealed a heterogeneous polysaccharide with a hexasaccharide repeating unit of the following structure: alpha-D-Glcp-(1 -> 6) vertical bar vertical bar 2)-alpha-L-Rhap-(1 -> 6)-alpha-D-Glcp-(1 -> 4)-alpha-D-Galp-(1 -> 3)-alpha-D-GlcpNAc- (1 ->vertical bar beta-D-Glcp/beta-D-GlcpNAc-(1 -> 3) A repeating unit with a D-GlcNAc substitution of D-Gal has been described earlier as characteristic for serogroup O18A1. Accordingly, we termed repeating units with D-Glc substitution at D-Gal as O18A2. NMR analyses of the polysaccharide confirmed that O18A1- and O18A2-type repeats were present in a 1:1 ratio. However, HK620TSP preferentially bound the D-GlcNAc- substituted O18A1-type repeating units in its high affinity binding pocket with a dissociation constant of 140 mu M and disfavored the O18A2-type having a beta-D-Glcp-(1 -> 3)-linked group. As a result, in hexasaccharide preparations, O18A1 and O18A2 repeats were present in a 9: 1 ratio stressing the clear preference of O18A1- type repeats to be cleaved by HK620TSP. KW - Escherichia coli KW - Tailspike KW - Endoglycosidase KW - Lipopolysaccharide KW - NMR KW - Mass spectrometry Y1 - 2012 U6 - https://doi.org/10.1016/j.carres.2012.05.022 SN - 0008-6215 VL - 357 IS - 8 SP - 118 EP - 125 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Yarman, Aysu A1 - Gröbe, Glenn A1 - Neumann, Bettina A1 - Kinne, Mathias A1 - Gajovic-Eichelmann, Nenad A1 - Wollenberger, Ursula A1 - Hofrichter, Martin A1 - Ullrich, Rene A1 - Scheibner, Katrin A1 - Scheller, Frieder W. T1 - The aromatic peroxygenase from Marasmius rutola-a new enzyme for biosensor applications JF - Analytical & bioanalytical chemistry N2 - The aromatic peroxygenase (APO; EC 1.11.2.1) from the agraric basidomycete Marasmius rotula (MroAPO) immobilized at the chitosan-capped gold-nanoparticle-modified glassy carbon electrode displayed a pair of redox peaks with a midpoint potential of -278.5 mV vs. AgCl/AgCl (1 M KCl) for the Fe(2+)/Fe(3+) redox couple of the heme-thiolate-containing protein. MroAPO oxidizes aromatic substrates such as aniline, p-aminophenol, hydroquinone, resorcinol, catechol, and paracetamol by means of hydrogen peroxide. The substrate spectrum overlaps with those of cytochrome P450s and plant peroxidases which are relevant in environmental analysis and drug monitoring. In M. rotula peroxygenase-based enzyme electrodes, the signal is generated by the reduction of electrode-active reaction products (e.g., p-benzoquinone and p-quinoneimine) with electro-enzymatic recycling of the analyte. In these enzyme electrodes, the signal reflects the conversion of all substrates thus representing an overall parameter in complex media. The performance of these sensors and their further development are discussed. KW - Unspecific peroxygenase KW - Cytochrome P450 KW - Biosensors KW - Phenolic substances Y1 - 2012 U6 - https://doi.org/10.1007/s00216-011-5497-y SN - 1618-2642 VL - 402 IS - 1 SP - 405 EP - 412 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Wurzbacher, Christian A1 - Salka, Ivette A1 - Grossart, Hans-Peter T1 - Environmental actinorhodopsin expression revealed by a new in situ filtration and fixation sampler JF - Environmental microbiology reports N2 - Freshwater Actinobacteria are an important and dominant group of bacterioplankton in most temperate freshwater systems. Recently, metagenomic studies discovered rhodopsin-like protein-coding sequences present in Actinobacteria which could be a decisive hint for their success in freshwater ecosystems. We analysed the diversity of actinorhodopsin (ActR) in Lake Stechlin (northern Germany) and assessed the actR expression profile during a diurnal cycle. We obtained 85 positive actR clones which could be subsequently grouped to 17 operational taxonomic units assuming a 90% sequence similarity. The phylogenetic analysis points to a close relationship of all obtained sequences to the acI lineage of Actinobacteria, forming six independent clusters. For the first time, we followed in situ transcription of actR in Lake Stechlin revealing a rather constitutive circadian gene expression. For analysing in situ expression patterns of functional genes in aquatic ecosystems, such as actR, we invented a new in situ filtration and fixation sampler (IFFS). The IFFS enables the representative investigation of microbial transcriptomes in any aquatic ecosystem at all water depths. The IFFS sampler is simple and inexpensive, and we provide all engineering plans for an easy rebuild. Consequently, our IFFS is suitable to reliably study expression of any known functional gene of any aquatic microorganism. Y1 - 2012 U6 - https://doi.org/10.1111/j.1758-2229.2012.00350.x SN - 1758-2229 VL - 4 IS - 5 SP - 491 EP - 497 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Wu, Anhui A1 - Allu, Annapurna Devi A1 - Garapati, Prashanth A1 - Siddiqui, Hamad A1 - Dortay, Hakan A1 - Zanor, Maria-Ines A1 - Asensi-Fabado, Maria Amparo A1 - Munne-Bosch, Sergi A1 - Antonio, Carla A1 - Tohge, Takayuki A1 - Fernie, Alisdair R. A1 - Kaufmann, Kerstin A1 - Xue, Gang-Ping A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Jungbrunnen1, a reactive oxygen species-responsive NAC transcription factor, regulates longevity in arabidopsis JF - The plant cell N2 - The transition from juvenility through maturation to senescence is a complex process that involves the regulation of longevity. Here, we identify JUNGBRUNNEN1 (JUB1), a hydrogen peroxide (H2O2)-induced NAC transcription factor, as a central longevity regulator in Arabidopsis thaliana. JUB1 overexpression strongly delays senescence, dampens intracellular H2O2 levels, and enhances tolerance to various abiotic stresses, whereas in jub1-1 knockdown plants, precocious senescence and lowered abiotic stress tolerance are observed. A JUB1 binding site containing a RRYGCCGT core sequence is present in the promoter of DREB2A, which plays an important role in abiotic stress responses. JUB1 transactivates DREB2A expression in mesophyll cell protoplasts and transgenic plants and binds directly to the DREB2A promoter. Transcriptome profiling of JUB1 overexpressors revealed elevated expression of several reactive oxygen species-responsive genes, including heat shock protein and glutathione S-transferase genes, whose expression is further induced by H2O2 treatment. Metabolite profiling identified elevated Pro and trehalose levels in JUB1 overexpressors, in accordance with their enhanced abiotic stress tolerance. We suggest that JUB1 constitutes a central regulator of a finely tuned control system that modulates cellular H2O2 level and primes the plants for upcoming stress through a gene regulatory network that involves DREB2A. Y1 - 2012 U6 - https://doi.org/10.1105/tpc.111.090894 SN - 1040-4651 VL - 24 IS - 2 SP - 482 EP - 506 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Winck, Flavia V. A1 - Riano-Pachon, Diego M. A1 - Sommer, Frederik A1 - Rupprecht, Jens A1 - Müller-Röber, Bernd T1 - The nuclear proteome of the green alga Chlamydomonas reinhardtii JF - Proteomics N2 - Nuclear proteins play a central role in regulating gene expression. Their identification is important for understanding how the nuclear repertoire changes over time under different conditions. Nuclear proteins are often underrepresented in proteomic studies due to the frequently low abundance of proteins involved in regulatory processes. So far, only few studies describing the nuclear proteome of plant species have been published. Recently, the genome sequence of the unicellular green alga Chlamydomonas reinhardtii has been obtained and annotated, allowing the development of further detailed studies for this organism. However, a detailed description of its nuclear proteome has not been reported so far. Here, we present an analysis of the nuclear proteome of the sequenced Chlamydomonas strain cc503. Using LC-MS/MS, we identified 672 proteins from nuclei isolates with a maximum 1% peptide spectrum false discovery rate. Besides well-known proteins (e.g. histones), transcription factors and other transcriptional regulators (e.g. tubby and HMG) were identified. The presence of protein motifs in nuclear proteins was investigated by computational tools, and specific over-represented protein motifs were identified. This study provides new insights into the complexity of the nuclear environment and reveals novel putative protein targets for further studies of nuclear mechanisms. KW - Nuclear proteomics KW - Plant proteomics KW - Systems biology KW - Transcription factor Y1 - 2012 U6 - https://doi.org/10.1002/pmic.201000782 SN - 1615-9853 VL - 12 IS - 1 SP - 95 EP - 100 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Wildish, J. A1 - Pavesi, Laura A1 - Ketmaier, Valerio T1 - Talitrid amphipods (Crustacea: Amphipoda: Talitridae) and the driftwood ecological niche a morphological and molecular study JF - Journal of natural history : an international journal of systematics, interactive biology and biodiversity. - London : Taylor & Francis   1.1967 - N2 - Coastal regions of the North East Atlantic and Mediterranean Seas have four known species of driftwood talitrids. Records are extremely scanty, often limited to the type locality and dating to 1950. We were able to study three of them, all belonging to the genus Macarorchestia, using fresh and archived samples including type material. Allometric and molecular analyses support: (1) a close relationship among all the three classically defined Macarorchestia species, (2) Macarorchestia was well separated from non-driftwood taxa, and (3) a putative new driftwood talitrid discovered during this study was not closely related to Macarorchestia. Genetic divergence between the new species and Macarorchestia remyi is as high as the average distance among a number of talitrid species included in the study for comparison. A key is provided to identify all three of the presently known species of Macarorchestia, using morphological characters employed in the allometric study. KW - Macarorchestia remyi KW - Macarorchestia roffensis KW - Macarorchestia martini KW - Driftwood habitat KW - COI-DNA barcoding KW - allometry Y1 - 2012 U6 - https://doi.org/10.1080/00222933.2012.717971 SN - 0022-2933 VL - 46 IS - 43-44 SP - 2677 EP - 2700 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Wernet, Philippe A1 - Kunnus, Kristjan A1 - Schreck, Simon A1 - Quevedo, Wilson A1 - Kurian, Reshmi A1 - Techert, Simone A1 - de Groot, Frank M. F. A1 - Odelius, Michael A1 - Föhlisch, Alexander T1 - Dissecting local atomic and intermolecular interactions of transition-metal ions in solution with selective X-ray spectroscopy JF - The journal of physical chemistry letters N2 - Determining covalent and charge-transfer contributions to bonding in solution has remained an experimental challenge. Here, the quenching of fluorescence decay channels as expressed in dips in the L-edge X-ray spectra of solvated 3d transition-metal ions and complexes was reported as a probe. With a full set of experimental and theoretical ab initio L-edge X-ray spectra of aqueous Cr3+, including resonant inelastic X-ray scattering, we address covalency and charge transfer for this prototypical transition-metal ion in solution. We dissect local atomic effects from intermolecular interactions and quantify X-ray optical effects. We find no evidence for the asserted ultrafast charge transfer to the solvent and show that the dips are readily explained by X-ray optical effects and local atomic state dependence of the fluorescence yield. Instead, we find, besides ionic interactions, a covalent contribution to the bonding in the aqueous complex of ligand-to-metal charge-transfer character. Y1 - 2012 U6 - https://doi.org/10.1021/jz301486u SN - 1948-7185 VL - 3 IS - 23 SP - 3448 EP - 3453 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Wells, Konstans A1 - O'Hara, R. B. A1 - Boehm, S. M. A1 - Gockel, Sonja A1 - Hemp, Andreas A1 - Renner, S. C. A1 - Pfeiffer, S. A1 - Boehning-Gaese, Katrin A1 - Kalko, Elisabeth K. V. T1 - Trait-dependent occupancy dynamics of birds in temperate forest landscapes fine-scale observations in a hierarchical multi-species framework JF - Animal conservation N2 - Silvicultural practices lead to changes in forest composition and structure and may impact species diversity from the overall regional species pool to stand-level species occurrence. We explored to what extent fine-scale occupancy patterns in differently managed forest stands are driven by environment and ecological traits in three regions in Germany using a multi-species hierarchical model. We tested for the possible impact of environmental variables and ecological traits on occupancy dynamics in a joint modelling exercise while taking possible variation in coefficient estimates over years and plots into account. Bird species richness differed across regions and years, and trends in species richness across years were different in the three regions. On the species level, forest management affected occupancy of species in all regions, but only 35% of the total assemblage-level variation in occurrence probability was explained by either forest type and successional stage and