@misc{ZurellElithSchroederEsselbach2012, author = {Zurell, Damaris and Elith, Jane and Schr{\"o}der-Esselbach, Boris}, title = {Predicting to new environments tools for visualizing model behaviour and impacts on mapped distributions}, series = {Diversity \& distributions : a journal of biological invasions and biodiversity}, volume = {18}, journal = {Diversity \& distributions : a journal of biological invasions and biodiversity}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1366-9516}, doi = {10.1111/j.1472-4642.2012.00887.x}, pages = {628 -- 634}, year = {2012}, abstract = {Data limitations can lead to unrealistic fits of predictive species distribution models (SDMs) and spurious extrapolation to novel environments. Here, we want to draw attention to novel combinations of environmental predictors that are within the sampled range of individual predictors but are nevertheless outside the sample space. These tend to be overlooked when visualizing model behaviour. They may be a cause of differing model transferability and environmental change predictions between methods, a problem described in some studies but generally not well understood. We here use a simple simulated data example to illustrate the problem and provide new and complementary visualization techniques to explore model behaviour and predictions to novel environments. We then apply these in a more complex real-world example. Our results underscore the necessity of scrutinizing model fits, ecological theory and environmental novelty.}, language = {en} } @article{ZuoGandhiArndtetal.2012, author = {Zuo, Zhili and Gandhi, Neha S. and Arndt, Katja Maren and Mancera, Ricardo L.}, title = {Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein}, series = {Biopolymers}, volume = {97}, journal = {Biopolymers}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0006-3525}, doi = {10.1002/bip.22099}, pages = {899 -- 909}, year = {2012}, abstract = {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.}, language = {en} } @article{ZiegeHennigeSchulzMueckschetal.2012, author = {Ziege, Madlen and Hennige-Schulz, Carmen and Muecksch, Frauke and Bierbach, David and Tiedemann, Ralph and Streit, Bruno and Plath, Martin}, title = {A comparison of two methods to assess audience-induced changes in male mate choice}, series = {Current zoology}, volume = {58}, journal = {Current zoology}, number = {1}, publisher = {Current Zoology}, address = {Beijing}, issn = {1674-5507}, pages = {84 -- 94}, year = {2012}, abstract = {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.}, language = {en} } @article{ZhangFedyuninKirchneretal.2012, author = {Zhang, Gong and Fedyunin, Ivan and Kirchner, Sebastian and Xiao, Chuanle and Valleriani, Angelo and Ignatova, Zoya}, title = {FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads}, series = {Nucleic acids research}, volume = {40}, journal = {Nucleic acids research}, number = {11}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gks196}, pages = {11}, year = {2012}, abstract = {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.}, language = {en} } @article{ZaccheusBroekerLundborgetal.2012, author = {Zaccheus, Mona V. and Br{\"o}ker, Nina Kristin and Lundborg, Magnus and Uetrecht, Charlotte and Barbirz, Stefanie and Widmalm, Goran}, title = {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}, series = {Carbohydrate research}, volume = {357}, journal = {Carbohydrate research}, number = {8}, publisher = {Elsevier}, address = {Oxford}, issn = {0008-6215}, doi = {10.1016/j.carres.2012.05.022}, pages = {118 -- 125}, year = {2012}, abstract = {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.}, language = {en} } @article{YarmanGroebeNeumannetal.2012, author = {Yarman, Aysu and Gr{\"o}be, Glenn and Neumann, Bettina and Kinne, Mathias and Gajovic-Eichelmann, Nenad and Wollenberger, Ursula and Hofrichter, Martin and Ullrich, Rene and Scheibner, Katrin and Scheller, Frieder W.}, title = {The aromatic peroxygenase from Marasmius rutola-a new enzyme for biosensor applications}, series = {Analytical \& bioanalytical chemistry}, volume = {402}, journal = {Analytical \& bioanalytical chemistry}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-011-5497-y}, pages = {405 -- 412}, year = {2012}, abstract = {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.}, language = {en} } @phdthesis{Yarman2012, author = {Yarman, Aysu}, title = {Biomimetic sensors for substrates of peroxidases and cytochrome P450s}, address = {Potsdam}, pages = {121 S.}, year = {2012}, language = {en} } @article{WurzbacherSalkaGrossart2012, author = {Wurzbacher, Christian and Salka, Ivette and Grossart, Hans-Peter}, title = {Environmental actinorhodopsin expression revealed by a new in situ filtration and fixation sampler}, series = {Environmental microbiology reports}, volume = {4}, journal = {Environmental microbiology reports}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/j.1758-2229.2012.00350.x}, pages = {491 -- 497}, year = {2012}, abstract = {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.}, language = {en} } @phdthesis{Wurzbacher2012, author = {Wurzbacher, Christian}, title = {Ecological function and biodiversity of aquatic fungi in lentic freshwater systems}, address = {Potsdam}, pages = {131 S.}, year = {2012}, language = {en} } @phdthesis{Wu2012, author = {Wu, Xu-Na}, title = {Functional characterization of AtSP1, a nutrient-induced receptor-like kinase}, address = {Potsdam}, pages = {112 S.}, year = {2012}, language = {en} }