TY - JOUR A1 - Schlägel, Ulrike E. A1 - Lewis, Mark A. T1 - A framework for analyzing the robustness of movement models to variable step discretization JF - Journal of mathematical biology N2 - When sampling animal movement paths, the frequency at which location measurements are attempted is a critical feature for data analysis. Important quantities derived from raw data, e.g. travel distance or sinuosity, can differ largely based on the temporal resolution of the data. Likewise, when movement models are fitted to data, parameter estimates have been demonstrated to vary with sampling rate. Thus, biological statements derived from such analyses can only be made with respect to the resolution of the underlying data, limiting extrapolation of results and comparison between studies. To address this problem, we investigate whether there are models that are robust against changes in temporal resolution. First, we propose a mathematically rigorous framework, in which we formally define robustness as a model property. We then use the framework for a thorough assessment of a range of basic random walk models, in which we also show how robustness relates to other probabilistic concepts. While we found robustness to be a strong condition met by few models only, we suggest a new method to extend models so as to make them robust. Our framework provides a new systematic, mathematically founded approach to the question if, and how, sampling rate of movement paths affects statistical inference. KW - Animal movement KW - Random walk KW - Sampling rate KW - Discretization KW - GPS data KW - Parameter estimation Y1 - 2016 U6 - https://doi.org/10.1007/s00285-016-0969-5 SN - 0303-6812 SN - 1432-1416 VL - 73 SP - 815 EP - 845 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Mao, Hailiang A1 - Nakamura, Moritaka A1 - Viotti, Corrado A1 - Grebe, Markus T1 - A Framework for Lateral Membrane Trafficking and Polar Tethering of the PEN3 ATP-Binding Cassette Transporter JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity. Y1 - 2016 U6 - https://doi.org/10.1104/pp.16.01252 SN - 0032-0889 SN - 1532-2548 VL - 172 SP - 2245 EP - 2260 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Liaimer, Anton A1 - Jensen, John B. A1 - Dittmann, Elke T1 - A Genetic and Chemical Perspective on Symbiotic Recruitment of Cyanobacteria of the Genus Nostoc into the Host Plant Blasia pusilla L. JF - Frontiers in microbiology N2 - Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin. KW - Cyanobacteria KW - secondary metabolites KW - symbiosis KW - Blasia KW - Nostoc KW - allelopathy Y1 - 2016 U6 - https://doi.org/10.3389/fmicb.2016.01693 SN - 1664-302X VL - 7 SP - 449 EP - 474 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Lämke, Jörn A1 - Brzezinka, Krzysztof A1 - Altmann, Simone A1 - Bäurle, Isabel T1 - A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory JF - The EMBO journal N2 - In nature, plants often encounter chronic or recurring stressful conditions. Recent results indicate that plants can remember a past exposure to stress to be better prepared for a future stress incident. However, the molecular basis of this is poorly understood. Here, we report the involvement of chromatin modifications in the maintenance of acquired thermotolerance (heat stress [HS] memory). HS memory is associated with the accumulation of histone H3 lysine 4 di- and trimethylation at memory-related loci. This accumulation outlasts their transcriptional activity and marks them as recently transcriptionally active. High accumulation of H3K4 methylation is associated with hyper-induction of gene expression upon a recurring HS. This transcriptional memory and the sustained accumulation of H3K4 methylation depend on HSFA2, a transcription factor that is required for HS memory, but not initial heat responses. Interestingly, HSFA2 associates with memory-related loci transiently during the early stages following HS. In summary, we show that transcriptional memory after HS is associated with sustained H3K4 hyper-methylation and depends on a hit-and-run transcription factor, thus providing a molecular framework for HS memory. KW - chromatin KW - H3K4 methylation KW - heat shock transcription factor KW - priming KW - transcriptional memory Y1 - 2016 U6 - https://doi.org/10.15252/embj.201592593 SN - 0261-4189 SN - 1460-2075 VL - 35 SP - 162 EP - 175 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Kabelitz, Tina A1 - Brzezinka, Krzysztof A1 - Friedrich, Thomas A1 - Gorka, Michal A1 - Graf, Alexander A1 - Kappel, Christian A1 - Bäurle, Isabel T1 - A JUMONJI Protein with E3 Ligase and Histone H3 Binding Activities Affects Transposon Silencing in Arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Transposable elements (TEs) make up a large proportion of eukaryotic genomes. As their mobilization creates genetic variation that threatens genome integrity, TEs are epigenetically silenced through several pathways, and this may spread to neighboring sequences. JUMONJI (JMJ) proteins can function as antisilencing factors and prevent silencing of genes next to TEs. Whether TE silencing is counterbalanced by the activity of antisilencing factors is still unclear. Here, we characterize JMJ24 as a regulator of TE silencing. We show that loss of JMJ24 results in increased silencing of the DNA transposon AtMu1c, while overexpression of JMJ24 reduces silencing. JMJ24 has a JumonjiC (JmjC) domain and two RING domains. JMJ24 autoubiquitinates in vitro, demonstrating E3 ligase activity of the RING domain(s). JMJ24-JmjC binds the N-terminal tail of histone H3, and full-length JMJ24 binds histone H3 in vivo. JMJ24 activity is anticorrelated with histone H3 Lys 9 dimethylation (H3K9me2) levels at AtMu1c. Double mutant analyses with epigenetic silencing mutants suggest that JMJ24 antagonizes histone H3K9me2 and requires H3K9 methyltransferases for its activity on AtMu1c. Genome-wide transcriptome analysis indicates that JMJ24 affects silencing at additional TEs. Our results suggest that the JmjC domain of JMJ24 has lost demethylase activity but has been retained as a binding domain for histone H3. This is in line with phylogenetic analyses indicating that JMJ24 (with the mutated JmjC domain) is widely conserved in angiosperms. Taken together, this study assigns a role in TE silencing to a conserved JmjC-domain protein with E3 ligase activity, but no demethylase activity. Y1 - 2016 U6 - https://doi.org/10.1104/pp.15.01688 SN - 0032-0889 SN - 1532-2548 VL - 171 SP - 344 EP - 358 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Gorochowski, Thomas E. A1 - Aycilar-Kucukgoze, Irem A1 - Bovenberg, Roel A. L. A1 - Roubos, Johannes A. A1 - Ignatova, Zoya T1 - A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes JF - ACS synthetic biology N2 - Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources. KW - protein biosynthesis KW - translation KW - synthetic biology KW - systems biology Y1 - 2016 U6 - https://doi.org/10.1021/acssynbio.6b00040 SN - 2161-5063 VL - 5 SP - 710 EP - 720 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Krupinski, Pawel A1 - Bozorg, Behruz A1 - Larsson, Andre A1 - Pietra, Stefano A1 - Grebe, Markus A1 - Jönsson, Henrik T1 - A Model Analysis of Mechanisms for Radial Microtubular Patterns at Root Hair Initiation Sites JF - Frontiers in plant science N2 - Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs. KW - plant cell wall KW - finite element modeling KW - computational morphodynamics KW - root hair initiation KW - microtubules KW - cellulose fibers KW - composite material Y1 - 2016 U6 - https://doi.org/10.3389/fpls.2016.01560 SN - 1664-462X VL - 7 PB - Frontiers Research Foundation CY - Lausanne ER - TY - THES A1 - Pellizzer, Tommaso T1 - A novel approach to identify plastidic factors for plastome genome incompatibility and evidence for the central involvement of the chloroplast in leaf shaping Y1 - 2016 ER - TY - JOUR A1 - Reinecke, J. A1 - Wulf, M. A1 - Baeten, Lander A1 - Brunet, J. A1 - Decocq, G. A1 - De Frenne, G. A1 - Diekmann, M. A1 - Graae, B. J. A1 - Heinken, Thilo A1 - Hermy, M. A1 - Jamoneau, A. A1 - Lenoir, J. A1 - Plue, J. A1 - Orczewska, A. A1 - Van Calster, H. A1 - Verheyen, Kris A1 - Naaf, T. T1 - Acido- and neutrophilic temperate forest plants display distinct shifts in ecological pH niche across north-western Europe JF - Ecography : pattern and diversity in ecology ; research papers forum N2 - Ecological niches of organisms vary across geographical space, but niche shift patterns between regions and the underlying mechanisms remain largely unexplored. We studied shifts in the pH niche of 42 temperate forest plant species across a latitudinal gradient from northern France to boreo-nemoral Sweden. We asked 1) whether species restrict their niches with increasing latitude as they reach their northern range margin (environmental constraints); 2) whether species expand their niches with increasing latitude as regional plant species richness decreases (competitive release); and 3) whether species shift their niche position toward more acidic sites with increasing latitude as the relative proportion of acidic soils increases (local adaptation). Based on 1458 vegetation plots and corresponding soil pH values, we modelled species response curves using Huisman-Olff-Fresco models. Four niche measures (width, position, left and right border) were compared among regions by randomization tests. We found that with increasing latitude, neutrophilic species tended to retreat from acidic sites, indicating that these species retreat to more favorable sites when approaching their range margin. Alternatively, these species might benefit from enhanced nitrogen deposition on formerly nutrient-poor, acidic sites in southern regions or lag behind in post-glacial recolonization of potential habitats in northern regions. Most acidophilic species extended their niche toward more base-rich sites with increasing latitude, indicating competitive release from neutrophilic species. Alternatively, acidophilic species might benefit from optimal climatic conditions in the north where some have their core distribution area. Shifts in the niche position suggested that local adaptation is of minor importance. We conclude that shifts in the pH niche of temperate forest plants are the rule, but the directions of the niche shifts and possible explanations vary. Our study demonstrates that differentiating between acidophilic and neutrophilic species is crucial to identify general patterns and underlying mechanisms. Y1 - 2016 U6 - https://doi.org/10.1111/ecog.02051 SN - 0906-7590 SN - 1600-0587 VL - 39 SP - 1164 EP - 1175 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Geyer, Juliane T1 - Adapting biodiversity conservation management to climate change Y1 - 2016 ER - TY - JOUR A1 - Woodhouse, Jason Nicholas A1 - Makower, A. Katharina A1 - Yeung, Anna C. Y. A1 - Ongley, Sarah E. A1 - Micallef, Melinda L. A1 - Moffitt, Michelle C. A1 - Neilan, Brett A. T1 - Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria JF - Environmental microbiology reports N2 - A common misconception persists that the genomes of toxic and non-toxic cyanobacterial strains are largely conserved with the exception of the presence or absence of the genes responsible for toxin production. Implementation of -omics era technologies has challenged this paradigm, with comparative analyses providing increased insight into the differences between strains of the same species. The implementation of genomic, transcriptomic and proteomic approaches has revealed distinct profiles between toxin-producing and non-toxic strains. Further, metagenomics and metaproteomics highlight the genomic potential and functional state of toxic bloom events over time. In this review, we highlight how these technologies have shaped our understanding of the complex relationship between these molecules, their producers and the environment at large within which they persist. Y1 - 2016 U6 - https://doi.org/10.1111/1758-2229.12366 SN - 1758-2229 VL - 8 SP - 3 EP - 13 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Mayer, Magnus C. A1 - Schauenburg, Linda A1 - Thompson-Steckel, Greta A1 - Dunsing, Valentin A1 - Kaden, Daniela A1 - Voigt, Philipp A1 - Schaefer, Michael A1 - Chiantia, Salvatore A1 - Kennedy, Timothy E. A1 - Multhaup, Gerhard T1 - Amyloid precursor-like protein 1 (APLP1) exhibits stronger zinc-dependent neuronal adhesion than amyloid precursor protein and APLP2 JF - Journal of neurochemistry N2 - The amyloid precursor protein (APP) and its paralogs, amyloid precursor-like protein 1 (APLP1) and APLP2, are metalloproteins with a putative role both in synaptogenesis and in maintaining synapse structure. Here, we studied the effect of zinc on membrane localization, adhesion, and secretase cleavage of APP, APLP1, and APLP2 in cell culture and rat neurons. For this, we employed live-cell microscopy techniques, a microcontact printing adhesion assay and ELISA for protein detection in cell culture supernatants. We report that zinc induces the multimerization of proteins of the amyloid precursor protein family and enriches them at cellular adhesion sites. Thus, zinc facilitates the formation of de novo APP and APLP1 containing adhesion complexes, whereas it does not have such influence on APLP2. Furthermore, zinc-binding prevented cleavage of APP and APLPs by extracellular secretases. In conclusion, the complexation of zinc modulates neuronal functions of APP and APLPs by (i) regulating formation of adhesion complexes, most prominently for APLP1, and (ii) by reducing the concentrations of neurotrophic soluble APP/APLP ectodomains. KW - amyloid precursor protein KW - amyloid precursor-like protein KW - neuronal adhesion KW - number and brightness KW - zinc Y1 - 2016 U6 - https://doi.org/10.1111/jnc.13540 SN - 0022-3042 SN - 1471-4159 VL - 137 SP - 266 EP - 276 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Saffert, Paul A1 - Adamla, Frauke A1 - Schieweck, Rico A1 - Atkins, John F. A1 - Ignatova, Zoya T1 - An Expanded CAG Repeat in Huntingtin Causes+1 Frameshifting JF - The journal of biological chemistry N2 - Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5 end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1. KW - aggregation KW - Huntington disease KW - translation KW - translation regulation KW - trinucleotide repeat disease KW - frameshifting KW - seeding Y1 - 2016 U6 - https://doi.org/10.1074/jbc.M116.744326 SN - 0021-9258 SN - 1083-351X VL - 291 SP - 18505 EP - 18513 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Rajasundaram, Dhivyaa A1 - Selbig, Joachim T1 - analysis JF - Current opinion in plant biology N2 - The development of ‘omics’ technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of ‘omics’ data integration together with an overview of available statistical methods and tools. Y1 - 2016 U6 - https://doi.org/10.1016/j.pbi.2015.12.010 SN - 1369-5266 SN - 1879-0356 VL - 30 SP - 57 EP - 61 PB - Elsevier CY - London ER - TY - THES A1 - Bartholomäus, Alexander T1 - Analyzing Transcriptional and Translational Control in E. coli using Deep-Seq Data Y1 - 2016 ER - TY - JOUR A1 - Almathen, Faisal A1 - Charruau, Pauline A1 - Mohandesan, Elmira A1 - Mwacharo, Joram M. A1 - Orozco-terWengel, Pablo A1 - Pitt, Daniel A1 - Abdussamad, Abdussamad M. A1 - Uerpmann, Margarethe A1 - Uerpmann, Hans-Peter A1 - De Cupere, Bea A1 - Magee, Peter A1 - Alnaqeeb, Majed A. A1 - Salim, Bashir A1 - Raziq, Abdul A1 - Dessie, Tadelle A1 - Abdelhadi, Omer M. A1 - Banabazi, Mohammad H. A1 - Al-Eknah, Marzook A1 - Walzer, Chris A1 - Fayer, Bernard A1 - Hofreiter, Michael A1 - Peters, Joris A1 - Hanotte, Olivier A1 - Burger, Pamela A. T1 - Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments. KW - anthropogenic admixture KW - Camelus dromedarius KW - demographic history KW - paleogenetics KW - wild dromedary Y1 - 2016 U6 - https://doi.org/10.1073/pnas.1519508113 SN - 0027-8424 VL - 113 SP - 6707 EP - 6712 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - González-Fortes, Gloria M. A1 - Kolbe, Ben A1 - Fernandes, Daniel A1 - Meleg, Ioana N. A1 - Garcia-Vazquez, Ana A1 - Pinto-Llona, Ana C. A1 - Constantin, Silviu A1 - de Torres, Trino J. A1 - Ortiz, Jose E. A1 - Frischauf, Christine A1 - Rabeder, Gernot A1 - Hofreiter, Michael A1 - Barlow, Axel T1 - Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears JF - Molecular ecology N2 - Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago. KW - ancient DNA KW - extinction KW - homing KW - sociality KW - Ursus arctos KW - Ursus spelaeus Y1 - 2016 U6 - https://doi.org/10.1111/mec.13800 SN - 0962-1083 SN - 1365-294X VL - 25 SP - 4907 EP - 4918 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Schneider, Florian D. A1 - Brose, Ulrich A1 - Rall, Björn C. A1 - Guill, Christian T1 - Animal diversity and ecosystem functioning in dynamic food webs JF - Nature Communications N2 - Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity. Y1 - 2016 U6 - https://doi.org/10.1038/ncomms12718 SN - 2041-1723 VL - 7 SP - 3129 EP - 3138 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Czesnick, Hjördis A1 - Lenhard, Michael T1 - Antagonistic control of flowering time by functionally specialized poly(A) polymerases in Arabidopsis thaliana JF - The plant journal N2 - Polyadenylation is a critical 3-end processing step during maturation of pre-mRNAs, and the length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerase (PAPS) isoforms fulfilling specialized functions, as reflected by their different mutant phenotypes. While PAPS1 affects several processes, such as the immune response, organ growth and male gametophyte development, the roles of PAPS2 and PAPS4 are largely unknown. Here we demonstrate that PAPS2 and PAPS4 promote flowering in a partially redundant manner. The enzymes act antagonistically to PAPS1, which delays the transition to flowering. The opposite flowering-time phenotypes in paps1 and paps2 paps4 mutants are at least partly due to decreased or increased FLC activity, respectively. In contrast to paps2 paps4 mutants, plants with increased PAPS4 activity flower earlier than the wild-type, concomitant with reduced FLC expression. Double mutant analyses suggest that PAPS2 and PAPS4 act independently of the autonomous pathway components FCA, FY and CstF64. The direct polyadenylation targets of the three PAPS isoforms that mediate their effects on flowering time do not include FLC sense mRNA and remain to be identified. Thus, our results uncover a role for canonical PAPS isoforms in flowering-time control, raising the possibility that modulating the balance of the isoform activities could be used to fine tune the transition to flowering. Significance Statement The length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. Arabidopsis has three isoforms of nuclear poly(A) polymerase (PAPS): PAPS1 plays a major role in organ growth and plant defence. Here we show that PAPS2 and PAPS4 redundantly promote flowering and act antagonistically to PAPS1, which delays flowering. We suggest that modulating the activity of these isoforms fine-tunes the transition to flowering. KW - polyadenylation KW - 3-end processing KW - poly(A) polymerase KW - flowering time KW - autonomous pathway KW - Arabidopsis thaliana Y1 - 2016 U6 - https://doi.org/10.1111/tpj.13280 SN - 0960-7412 SN - 1365-313X VL - 88 SP - 570 EP - 583 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Memczak, Henry A1 - Lauster, Daniel A1 - Kar, Parimal A1 - Di Lella, Santiago A1 - Volkmer, Rudolf A1 - Knecht, Volker A1 - Herrmann, Andreas A1 - Ehrentreich-Foerster, Eva A1 - Bier, Frank Fabian A1 - Stoecklein, Walter F. M. T1 - Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding JF - PLoS one N2 - Antibodies against spike proteins of influenza are used as a tool for characterization of viruses and therapeutic approaches. However, development, production and quality control of antibodies is expensive and time consuming. To circumvent these difficulties, three peptides were derived from complementarity determining regions of an antibody heavy chain against influenza A spike glycoprotein. Their binding properties were studied experimentally, and by molecular dynamics simulations. Two peptide candidates showed binding to influenza A/Aichi/2/68 H3N2. One of them, termed PeB, with the highest affinity prevented binding to and infection of target cells in the micromolar region without any cytotoxic effect. PeB matches best the conserved receptor binding site of hemagglutinin. PeB bound also to other medical relevant influenza strains, such as human-pathogenic A/California/7/2009 H1N1, and avian-pathogenic A/MuteSwan/Rostock/R901/2006 H7N1. Strategies to improve the affinity and to adapt specificity are discussed and exemplified by a double amino acid substituted peptide, obtained by substitutional analysis. The peptides and their derivatives are of great potential for drug development as well as biosensing. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0159074 SN - 1932-6203 VL - 11 SP - 82 EP - 90 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Roggenbuck, Dirk A1 - Borghi, Maria Orietta A1 - Somma, Valentina A1 - Buettner, Thomas A1 - Schierack, Peter A1 - Hanack, Katja A1 - Grossi, Claudia A1 - Bodio, Caterina A1 - Macor, Paolo A1 - von Landenberg, Philipp A1 - Boccellato, Francesco A1 - Mahler, Michael A1 - Meroni, Pier Luigi T1 - Antiphospholipid antibodies detected by line immunoassay differentiate among patients with antiphospholipid syndrome, with infections and asymptomatic carriers JF - IEEE transactions on geoscience and remote sensing N2 - Background: Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)). Methods: Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (beta 2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-beta 2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human beta 2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human beta 2GPI or after CL-micelle absorption. Results: Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM a beta 2GPI and aCL. Anti-CL and anti-beta 2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and beta 2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized beta 2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-beta 2GPI humoAbs. Conclusions: The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1. KW - Antiphospholipid syndrome KW - Antiphospholipid antibody KW - Phospholipid binding proteins KW - Beta2-glycoprotein I KW - Line immunoassay Y1 - 2016 U6 - https://doi.org/10.1186/s13075-016-1018-x SN - 1478-6354 SN - 1478-6362 VL - 18 PB - BioMed Central CY - London ER - TY - JOUR A1 - Großart, Hans-Peter A1 - Rojas-Jimenez, Keilor T1 - Aquatic fungi: targeting the forgotten in microbial ecology JF - Current opinion in microbiology N2 - Fungi constitute important and conspicuous components of aquatic microbial communities, but their diversity and functional roles remain poorly characterized. New methods and conceptual frameworks are required to accurately describe their ecological roles, involvement in global cycling processes, and utility for human activities, considering both cultivation independent techniques as well as experiments in laboratory and in natural ecosystems. Here we highlight recent developments and extant knowledge gaps in aquatic mycology, and provide a conceptual model to expose the importance of fungi in aquatic food webs and related biogeochemical processes. Y1 - 2016 U6 - https://doi.org/10.1016/j.mib.2016.03.016 SN - 1369-5274 SN - 1879-0364 VL - 31 SP - 140 EP - 145 PB - Elsevier CY - London ER - TY - JOUR A1 - Brzezinka, Krzysztof A1 - Altmann, Simone A1 - Czesnick, Hjördis A1 - Nicolas, Philippe A1 - Gorka, Michal A1 - Benke, Eileen A1 - Kabelitz, Tina A1 - Jähne, Felix A1 - Graf, Alexander A1 - Kappel, Christian A1 - Bäurle, Isabel T1 - Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling JF - eLife N2 - Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/ SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory. Y1 - 2016 U6 - https://doi.org/10.7554/eLife.17061 SN - 2050-084X VL - 5 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Hanke-Gogokhia, Christin A1 - Wu, Zhijian A1 - Gerstner, Cecilia D. A1 - Frederick, Jeanne M. A1 - Zhang, Houbin A1 - Baehr, Wolfgang T1 - Arf-like Protein 3 (ARL3) Regulates Protein Trafficking and Ciliogenesis in Mouse Photoreceptors JF - The journal of biological chemistry N2 - Arf-like protein 3 (ARL3) is a ubiquitous small GTPase expressed in ciliated cells of plants and animals. Germline deletion of Arl3 in mice causes multiorgan ciliopathy reminiscent of Bardet-Biedl or Joubert syndromes. As photoreceptors are elegantly compartmentalized and have cilia, we probed the function of ARL3 (ADP-ribosylation factor (Arf)-like 3 protein) by generating rod photoreceptor-specific (prefix (rod)) and retina-specific (prefix (ret)) Arl3 deletions. In predegenerate (rod)Arl3(-/-) mice, lipidated phototransduction proteins showed trafficking deficiencies, consistent with the role of ARL3 as a cargo displacement factor for lipid-binding proteins. By contrast, (ret)Arl3(-/-) rods and cones expressing Cre recombinase during embryonic development formed neither connecting cilia nor outer segments and degenerated rapidly. Absence of cilia infers participation of ARL3 in ciliogenesis and axoneme formation. Ciliogenesis was rescued, and degeneration was reversed in part by subretinal injection of adeno-associated virus particles expressing ARL3-EGFP. The conditional knock-out phenotypes permitted identification of two ARL3 functions, both in the GTP-bound form as follows: one as a regulator of intraflagellar transport participating in photoreceptor ciliogenesis and the other as a cargo displacement factor transporting lipidated protein to the outer segment. Surprisingly, a farnesylated inositol polyphosphate phosphatase only trafficked from the endoplasmic reticulum to the Golgi, thereby excluding it from a role in photoreceptor cilia physiology. KW - animal model KW - gene knock-out KW - lipid-binding protein KW - photoreceptor KW - protein trafficking (Golgi) KW - retinal degeneration Y1 - 2016 U6 - https://doi.org/10.1074/jbc.M115.710954 SN - 0021-9258 SN - 1083-351X VL - 291 SP - 7142 EP - 7155 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Marce, Rafael A1 - George, Glen A1 - Buscarinu, Paola A1 - Deidda, Melania A1 - Dunalska, Julita A1 - de Eyto, Elvira A1 - Flaim, Giovanna A1 - Grossart, Hans-Peter A1 - Istvanovics, Vera A1 - Lenhardt, Mirjana A1 - Moreno-Ostos, Enrique A1 - Obrador, Biel A1 - Ostrovsky, Ilia A1 - Pierson, Donald C. A1 - Potuzak, Jan A1 - Poikane, Sandra A1 - Rinke, Karsten A1 - Rodriguez-Mozaz, Sara A1 - Staehr, Peter A. A1 - Sumberova, Katerina A1 - Waajen, Guido A1 - Weyhenmeyer, Gesa A. A1 - Weathers, Kathleen C. A1 - Zion, Mark A1 - Ibelings, Bas W. A1 - Jennings, Eleanor T1 - Automatic High Frequency Monitoring for Improved Lake and Reservoir Management JF - Frontiers in plant science N2 - Recent technological developments have increased the number of variables being monitored in lakes and reservoirs using automatic high frequency monitoring (AHFM). However, design of AHFM systems and posterior data handling and interpretation are currently being developed on a site-by-site and issue-by-issue basis with minimal standardization of protocols or knowledge sharing. As a result, many deployments become short-lived or underutilized, and many new scientific developments that are potentially useful for water management and environmental legislation remain underexplored. This Critical Review bridges scientific uses of AHFM with their applications by providing an overview of the current AHFM capabilities, together with examples of successful applications. We review the use of AHFM for maximizing the provision of ecosystem services supplied, by lakes and reservoirs (consumptive and non consumptive uses, food production, and recreation), and for reporting lake status in the EU Water Framework Directive. We also highlight critical issues to enhance the application of AHFM, and suggest the establishment of appropriate networks to facilitate knowledge sharing and technological transfer between potential users. Finally, we give advice on how modern sensor technology can successfully be applied on a larger scale to the management of lakes and reservoirs and maximize the ecosystem services they provide. Y1 - 2016 U6 - https://doi.org/10.1021/acs.est.6b01604 SN - 0013-936X SN - 1520-5851 VL - 50 SP - 10780 EP - 10794 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Feist, Peter A1 - Sin, Celine A1 - Zhang, Gong A1 - Valleriani, Angelo A1 - Ignatova, Zoya T1 - Bacteria differently regulate mRNA abundance to specifically respond to various stresses JF - Geology N2 - Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up-and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs. KW - transcription KW - translation KW - deep sequencing KW - Escherichia coli KW - copy numbers Y1 - 2016 U6 - https://doi.org/10.1098/rsta.2015.0069 SN - 1364-503X SN - 1471-2962 VL - 374 PB - Royal Society CY - London ER - TY - JOUR A1 - Leimkühler, Silke A1 - Iobbi-Nivol, Chantal T1 - Bacterial molybdoenzymes: old enzymes for new purposes JF - FEMS microbiology reviews N2 - Molybdoenzymes are widespread in eukaryotic and prokaryotic organisms where they play crucial functions in detoxification reactions in the metabolism of humans and bacteria, in nitrate assimilation in plants and in anaerobic respiration in bacteria. To be fully active, these enzymes require complex molybdenum-containing cofactors, which are inserted into the apoenzymes after folding. For almost all the bacterial molybdoenzymes, molybdenum cofactor insertion requires the involvement of specific chaperones. In this review, an overview on the molybdenum cofactor biosynthetic pathway is given together with the role of specific chaperones dedicated for molybdenum cofactor insertion and maturation. Many bacteria are involved in geochemical cycles on earth and therefore have an environmental impact. The roles of molybdoenzymes in bioremediation and for environmental applications are presented.This review gives an overview of the diverse mechanisms leading to the insertion of the different forms of the molybdenum cofactor into the respective target enzymes and summarizes the roles of different molybdoenzymes in the environment.This review gives an overview of the diverse mechanisms leading to the insertion of the different forms of the molybdenum cofactor into the respective target enzymes and summarizes the roles of different molybdoenzymes in the environment. KW - molybdenum cofactor KW - specific chaperons KW - TorD family KW - XdhC KW - molybdoenzyme maturation KW - bioremediation Y1 - 2016 U6 - https://doi.org/10.1093/femsre/fuv043 SN - 0168-6445 SN - 1574-6976 VL - 40 SP - 1 EP - 18 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Schmidt, Andreas A1 - Rabsch, Wolfgang A1 - Broeker, Nina K. A1 - Barbirz, Stefanie T1 - Bacteriophage tailspike protein based assay to monitor phase variable glucosylations in Salmonella O-antigens JF - BMC microbiology N2 - Background Non-typhoid Salmonella Typhimurium (S. Typhimurium) accounts for a high number of registered salmonellosis cases, and O-serotyping is one important tool for monitoring epidemiology and spread of the disease. Moreover, variations in glucosylated O-antigens are related to immunogenicity and spread in the host. However, classical autoagglutination tests combined with the analysis of specific genetic markers cannot always reliably register phase variable glucose modifications expressed on Salmonella O-antigens and additional tools to monitor O-antigen glucosylation phenotypes of S. Typhimurium would be desirable. Results We developed a test for the phase variable O-antigen glucosylation state of S. Typhimurium using the tailspike proteins (TSP) of Salmonella phages 9NA and P22. We used this ELISA like tailspike adsorption (ELITA) assay to analyze a library of 44 Salmonella strains. ELITA was successful in discriminating strains that carried glucose 1-6 linked to the galactose of O-polysaccharide backbone (serotype O1) from non-glucosylated strains. This was shown by O-antigen compositional analyses of the respective strains with mass spectrometry and capillary electrophoresis. The ELITA test worked rapidly in a microtiter plate format and was highly O-antigen specific. Moreover, TSP as probes could also detect glucosylated strains in flow cytometry and distinguish multiphasic cultures differing in their glucosylation state. Conclusions Tailspike proteins contain large binding sites with precisely defined specificities and are therefore promising tools to be included in serotyping procedures as rapid serotyping agents in addition to antibodies. In this study, 9NA and P22TSP as probes could specifically distinguish glucosylation phenotypes of Salmonella on microtiter plate assays and in flow cytometry. This opens the possibility for flow sorting of cell populations for subsequent genetic analyses or for monitoring phase variations during large scale O-antigen preparations necessary for vaccine production. KW - Salmonella Typhimurium KW - O-antigen KW - Tailspike protein KW - Bacteriophage KW - Phase variation KW - O-serotyping KW - Flow cytometry Y1 - 2016 U6 - https://doi.org/10.1186/s12866-016-0826-0 SN - 1471-2180 VL - 16 PB - BioMed Central CY - London ER - TY - JOUR A1 - Schmidt, Andreas A1 - Rabsch, Wolfgang A1 - Bröker, Nina Kristin A1 - Barbirz, Stefanie T1 - Bacteriophage tailspike protein based assay to monitor phase variable glucosylations in Salmonella O-antigens JF - BMC microbiology N2 - Background: Non-typhoid Salmonella Typhimurium (S. Typhimurium) accounts for a high number of registered salmonellosis cases, and O-serotyping is one important tool for monitoring epidemiology and spread of the disease. Moreover, variations in glucosylated O-antigens are related to immunogenicity and spread in the host. However, classical autoagglutination tests combined with the analysis of specific genetic markers cannot always reliably register phase variable glucose modifications expressed on Salmonella O-antigens and additional tools to monitor O-antigen glucosylation phenotypes of S. Typhimurium would be desirable. Results: We developed a test for the phase variable O-antigen glucosylation state of S. Typhimurium using the tailspike proteins (TSP) of Salmonella phages 9NA and P22. We used this ELISA like tailspike adsorption (ELITA) assay to analyze a library of 44 Salmonella strains. ELITA was successful in discriminating strains that carried glucose 1-6 linked to the galactose of O-polysaccharide backbone (serotype O1) from non-glucosylated strains. This was shown by O-antigen compositional analyses of the respective strains with mass spectrometry and capillary electrophoresis. The ELITA test worked rapidly in a microtiter plate format and was highly O-antigen specific. Moreover, TSP as probes could also detect glucosylated strains in flow cytometry and distinguish multiphasic cultures differing in their glucosylation state. Conclusions: Tailspike proteins contain large binding sites with precisely defined specificities and are therefore promising tools to be included in serotyping procedures as rapid serotyping agents in addition to antibodies. In this study, 9NA and P22TSP as probes could specifically distinguish glucosylation phenotypes of Salmonella on microtiter plate assays and in flow cytometry. This opens the possibility for flow sorting of cell populations for subsequent genetic analyses or for monitoring phase variations during large scale O-antigen preparations necessary for vaccine production. KW - Salmonella Typhimurium KW - O-antigen KW - Tailspike protein KW - Bacteriophage KW - Phase variation KW - O-serotyping KW - Flow cytometry Y1 - 2016 U6 - https://doi.org/10.1186/s12866-016-0826-0 SN - 1471-2180 VL - 16 SP - 2214 EP - 2226 PB - BioMed Central CY - London ER - TY - JOUR A1 - Kang, Yu A1 - Gohlke, Ulrich A1 - Engström, Olof A1 - Hamark, Christoffer A1 - Scheidt, Tom A1 - Kunstmann, Ruth Sonja A1 - Heinemann, Udo A1 - Widmalm, Göran A1 - Santer, Mark A1 - Barbirz, Stefanie T1 - Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions JF - Journal of the American Chemical Society N2 - Understanding interactions of bacterial surface polysaccharides with receptor protein scaffolds is important for the development of antibiotic therapies. The corresponding protein recognition domains frequently form low-affinity complexes with polysaccharides that are difficult to address with experimental techniques due to the conformational flexibility of the polysaccharide. In this work, we studied the tailspike protein (TSP) of the bacteriophage Sf6. Sf6TSP binds and hydrolyzes the high-rhamnose, serotype Y O-antigen polysaccharide of the Gram-negative bacterium Shigella flexneri (S. flexneri) as a first step of bacteriophage infection. Spectroscopic analyses and enzymatic cleavage assays confirmed that Sf6TSP binds long stretches of this polysaccharide. Crystal structure analysis and saturation transfer difference (STD) NMR spectroscopy using an enhanced method to interpret the data permitted the detailed description of affinity contributions and flexibility in an Sf6TSP-octasaccharide complex. Dodecasaccharide fragments corresponding to three repeating units of the O-antigen in complex with Sf6TSP were studied computationally by molecular dynamics simulations. They showed that distortion away from the low-energy solution conformation found in the octasaccharide complex is necessary for ligand binding. This is in agreement with a weak-affinity functional polysaccharide protein contact that facilitates correct placement and thus hydrolysis of the polysaccharide close to the catalytic residues. Our simulations stress that the flexibility of glycan epitopes together with a small number of specific protein contacts provide the driving force for Sf6TSP-polysaccharide complex formation in an overall weak-affinity interaction system. Y1 - 2016 U6 - https://doi.org/10.1021/jacs.6b00240 SN - 0002-7863 VL - 138 SP - 9109 EP - 9118 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Speller, Camilla A1 - van den Hurk, Youri A1 - Charpentier, Anne A1 - Rodrigues, Ana A1 - Gardeisen, Armelle A1 - Wilkens, Barbara A1 - McGrath, Krista A1 - Rowsell, Keri A1 - Spindler, Luke A1 - Collins, Matthew J. A1 - Hofreiter, Michael T1 - Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans JF - Philosophical transactions of the Royal Society of London : B, Biological sciences KW - ancient DNA KW - archaeozoology KW - cetaceans KW - collagen peptide mass fingerprinting KW - species identification KW - zooarchaeology by mass spectrometry Y1 - 2016 U6 - https://doi.org/10.1098/rstb.2015.0332 SN - 0962-8436 SN - 1471-2970 VL - 371 PB - Royal Society CY - London ER - TY - JOUR A1 - Sander, Martha Maria A1 - Scheffler, Christiane T1 - Bilateral asymmetry in left handers increased concerning morphological laterality in a recent sample of young adults JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie KW - anthropometry KW - handedness KW - laterality KW - bilateral asymmetry KW - left handers KW - upper extremity KW - reskilling KW - elbow breadth Y1 - 2016 U6 - https://doi.org/10.1127/anthranz/2016/0663 SN - 0003-5548 VL - 73 SP - 335 EP - 342 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Coutinho, Renato Mendes A1 - Klauschies, Toni A1 - Gaedke, Ursula T1 - Bimodal trait distributions with large variances question the reliability of trait-based aggregate models JF - Theoretical ecology N2 - Functionally diverse communities can adjust their species composition to altered environmental conditions, which may influence food web dynamics. Trait-based aggregate models cope with this complexity by ignoring details about species identities and focusing on their functional characteristics (traits). They describe the temporal changes of the aggregate properties of entire communities, including their total biomasses, mean trait values, and trait variances. The applicability of aggregate models depends on the validity of their underlying assumptions that trait distributions are normal and exhibit small variances. We investigated to what extent this can be expected to work by comparing an innovative model that accounts for the full trait distributions of predator and prey communities to a corresponding aggregate model. We used a food web structure with well-established trade-offs among traits promoting mutual adjustments between prey edibility and predator selectivity in response to selection. We altered the shape of the trade-offs to compare the outcome of the two models under different selection regimes, leading to trait distributions increasingly deviating from normality. Their biomass and trait dynamics agreed very well for stabilizing selection and reasonably well for directional selection, under which different trait values are favored at different times. However, for disruptive selection, the results of the aggregate model strongly deviated from the full trait distribution model that showed bimodal trait distributions with large variances. Hence, the outcome of aggregate models is reliable under ideal conditions but has to be questioned when confronted with more complex selection regimes and trait distributions, which are commonly observed in nature. KW - Fitness gradient KW - Communities as complex adaptive systems KW - Moment closure for trait-based aggregate model approaches KW - Multimodal trait distributions KW - Lumpiness in pattern formation and self-organization KW - Shape of trade-offs and stabilizing and disruptive selection Y1 - 2016 U6 - https://doi.org/10.1007/s12080-016-0297-9 SN - 1874-1738 SN - 1874-1746 VL - 9 SP - 389 EP - 408 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Prokopovic, Vladimir Z. A1 - Vikulina, Anna S. A1 - Sustr, David A1 - Duschl, Claus A1 - Volodkin, Dmitry T1 - Biodegradation-Resistant Multilayers Coated with Gold Nanoparticles. Toward a Tailor-made Artificial Extracellular Matrix JF - Journal of colloid and interface science N2 - Polymer multicomponent coatings such as multilayers mimic an extracellular, matrix (ECM) that attracts significant attention for the use of the multilayers as functional supports for advanced cell culture and tissue engineering. Herein, biodegradation and molecular transport in hyaluronan/polylysine multilayers coated with gold nanoparticles were described. Nanoparticle coating acts as a semipermeable barrier that governs molecular transport into/from the multilayers, and makes them biodegradation-resistant. Model protein lysozyme (mimics of ECM-soluble signals) diffuses into the multilayers as fast- and, slow-diffusing populations existing in an equilibrium,. Such a. composite system may have high potential to be exploited as degradation-resistant drug-delivery platforms suitable for cell-based applications. KW - hyaluronic acid KW - polylysine KW - diffusion KW - semipermeable KW - fluorescence recovery after photobleaching KW - layer-by-layer KW - enzymatic degradation KW - cell adhesion Y1 - 2016 U6 - https://doi.org/10.1021/acsami.6b10095 SN - 1944-8244 VL - 8 SP - 24345 EP - 24349 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Soliveres, Santiago A1 - van der Plas, Fons A1 - Manning, Peter A1 - Prati, Daniel A1 - Gossner, Martin M. A1 - Renner, Swen C. A1 - Alt, Fabian A1 - Arndt, Hartmut A1 - Baumgartner, Vanessa A1 - Binkenstein, Julia A1 - Birkhofer, Klaus A1 - Blaser, Stefan A1 - Blüthgen, Nico A1 - Boch, Steffen A1 - Böhm, Stefan A1 - Börschig, Carmen A1 - Buscot, Francois A1 - Diekötter, Tim A1 - Heinze, Johannes A1 - Hölzel, Norbert A1 - Jung, Kirsten A1 - Klaus, Valentin H. A1 - Kleinebecker, Till A1 - Klemmer, Sandra A1 - Krauss, Jochen A1 - Lange, Markus A1 - Morris, E. Kathryn A1 - Müller, Jörg A1 - Oelmann, Yvonne A1 - Overmann, Jörg A1 - Pasalic, Esther A1 - Rillig, Matthias C. A1 - Schaefer, H. Martin A1 - Schloter, Michael A1 - Schmitt, Barbara A1 - Schöning, Ingo A1 - Schrumpf, Marion A1 - Sikorski, Johannes A1 - Socher, Stephanie A. A1 - Solly, Emily F. A1 - Sonnemann, Ilja A1 - Sorkau, Elisabeth A1 - Steckel, Juliane A1 - Steffan-Dewenter, Ingolf A1 - Stempfhuber, Barbara A1 - Tschapka, Marco A1 - Türke, Manfred A1 - Venter, Paul C. A1 - Weiner, Christiane N. A1 - Weisser, Wolfgang W. A1 - Werner, Michael A1 - Westphal, Catrin A1 - Wilcke, Wolfgang A1 - Wolters, Volkmar A1 - Wubet, Tesfaye A1 - Wurst, Susanne A1 - Fischer, Markus A1 - Allan, Eric T1 - Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality JF - Nature : the international weekly journal of science Y1 - 2016 U6 - https://doi.org/10.1038/nature19092 SN - 0028-0836 SN - 1476-4687 VL - 536 SP - 456 EP - + PB - Nature Publ. Group CY - London ER - TY - THES A1 - Reichel, Victoria Eleonore T1 - Biomedical applications and multifunctional nanostructures based on magnetite nanoparticles synthesized in presence of biological additives Y1 - 2016 ER - TY - JOUR A1 - de Vinuesa, Amaya Garcia A1 - Abdelilah-Seyfried, Salim A1 - Knaus, Petra A1 - Zwijsen, An A1 - Bailly, Sabine T1 - BMP signaling in vascular biology and dysfunction JF - New journal of physics : the open-access journal for physics N2 - The vascular system is critical for developmental growth, tissue homeostasis and repair but also for tumor development. Bone morphogenetic protein (BMP) signaling has recently emerged as a fundamental pathway of the endothelium by regulating cardiovascular and lymphatic development and by being causative for several vascular dysfunctions. Two vascular disorders have been directly linked to impaired BMP signaling: pulmonary arterial hypertension and hereditary hemorrhagic telangiectasia. Endothelial BMP signaling critically depends on the cellular context, which includes among others vascular heterogeneity, exposure to flow, and the intertwining with other signaling cascades (Notch, WNT, Hippo and hypoxia). The purpose of this review is to highlight the most recent findings illustrating the clear need for reconsidering the role of BMPs in vascular biology. (C) 2015 Elsevier Ltd. All rights reserved. KW - Bone morphogenetic proteins (BMP) KW - Signaling KW - Vasculature KW - Development KW - Disease Y1 - 2016 U6 - https://doi.org/10.1016/j.cytogfr.2015.12.005 SN - 1359-6101 SN - 1879-0305 VL - 27 SP - 65 EP - 79 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Sperfeld, Erik A1 - Raubenheimer, David A1 - Wacker, Alexander T1 - Bridging factorial and gradient concepts of resource co-limitation: towards a general framework applied to consumers JF - Ecology letters N2 - Organism growth can be limited either by a single resource or by multiple resources simultaneously (co-limitation). Efforts to characterise co-limitation have generated two influential approaches. One approach uses limitation scenarios of factorial growth assays to distinguish specific types of co-limitation; the other uses growth responses spanned over a continuous, multi-dimensional resource space to characterise different types of response surfaces. Both approaches have been useful in investigating particular aspects of co-limitation, but a synthesis is needed to stimulate development of this recent research area. We address this gap by integrating the two approaches, thereby presenting a more general framework of co-limitation. We found that various factorial (co-)limitation scenarios can emerge in different response surface types based on continuous availabilities of essential or substitutable resources. We tested our conceptual co-limitation framework on data sets of published and unpublished studies examining the limitation of two herbivorous consumers in a two-dimensional resource space. The experimental data corroborate the predictions, suggesting a general applicability of our co-limitation framework to generalist consumers and potentially also to other organisms. The presented framework might give insight into mechanisms that underlie co-limitation responses and thus can be a seminal starting point for evaluating co-limitation patterns in experiments and nature. KW - Consumer KW - essential nutrient KW - factorial design KW - food quality KW - growth rate KW - multi-nutrient limitation KW - nutritional ecology KW - performance landscape KW - substitutable resource KW - synergistic effect Y1 - 2016 U6 - https://doi.org/10.1111/ele.12554 SN - 1461-023X SN - 1461-0248 VL - 19 SP - 201 EP - 215 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Jöst, Jan Moritz Michael T1 - Broad leaves, narrow leaves or no leaves at all - a genetic and phenotypic dissection of barley leaf size mutants Y1 - 2016 ER - TY - THES A1 - Sviben, Sanja T1 - Calcite biomineralization in coccolithophores BT - new insights from ultrastructural and proteomic studies of Emiliania huxleyi Y1 - 2016 ER - TY - GEN A1 - Hanack, Katja A1 - Schloer, Anja A1 - Holzloehner, Pamela A1 - Listek, Martin A1 - Bauer, Cindy A1 - Butze, Monique A1 - Micheel, Burkhard A1 - Hentschel, Christian A1 - Sowa, Mandy A1 - Roggenbuck, Dirk A1 - Schierack, Peter A1 - Fuener, Jonas A1 - Schliebs, Erik A1 - Goihl, Alexander A1 - Reinhold, Dirk T1 - Camelid nanobodies specific to human pancreatic glycoprotein 2 T2 - The journal of immunology N2 - Pancreatic secretory zymogen-granule membrane glycoprotein 2 (GP2) has been identified to be a major autoantigenic target in Crohn’s disease patients. It was discussed recently that a long and a short isoform of GP2 exists whereas the short isoform is often detected by GP2-specific autoantibodies. In the outcome of inflammatory bowel diseases, these GP2-specific autoantibodies are discussed as new serological markers for diagnosis and therapeutic monitoring. To investigate this further, camelid nanobodies were generated by phage display and selected against the short isoform of GP2 in order to isolate specific tools for the discrimination of both isoforms. Nanobodies are single domain antibodies derived from camelid heavy chain only antibodies and characterized by a high stability and solubility. The selected candidates were expressed, purified and validated regarding their binding properties in different enzyme-linked immunosorbent assays formats, immunofluorescence, immunohistochemistry and surface plasmon resonance spectroscopy. Four different nanobodies could be selected whereof three recognize the short isoform of GP2 very specifically and one nanobody showed a high binding capacity for both isoforms. The KD values measured for all nanobodies were between 1.3 nM and 2.3 pM indicating highly specific binders suitable for the application as diagnostic tool in inflammatory bowel disease. Y1 - 2016 SN - 0022-1767 SN - 1550-6606 VL - 196 SP - 313 EP - 328 PB - American Assoc. of Immunologists CY - Bethesda ER - TY - JOUR A1 - Reverey, Florian A1 - Großart, Hans-Peter A1 - Premke, Katrin A1 - Lischeid, Gunnar T1 - Carbon and nutrient cycling in kettle hole sediments depending on hydrological dynamics: a review JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Kettle holes as a specific group of isolated, small lentic freshwater systems (LFS) often are (i) hot spots of biogeochemical cycling and (ii) exposed to frequent sediment desiccation and rewetting. Their ecological functioning is greatly determined by immanent carbon and nutrient transformations. The objective of this review is to elucidate effects of a changing hydrological regime (i.e., dry-wet cycles) on carbon and nutrient cycling in kettle hole sediments. Generally, dry-wet cycles have the potential to increase C and N losses as well as P availability. However, their duration and frequency are important controlling factors regarding direction and intensity of biogeochemical and microbiological responses. To evaluate drought impacts on sediment carbon and nutrient cycling in detail requires the context of the LFS hydrological history. For example, frequent drought events induce physiological adaptation of exposed microbial communities and thus flatten metabolic responses, whereas rare events provoke unbalanced, strong microbial responses. Different potential of microbial resilience to drought stress can irretrievably change microbial communities and functional guilds, gearing cascades of functional responses. Hence, dry-wet events can shift the biogeochemical cycling of organic matter and nutrients to a new equilibrium, thus affecting the dynamic balance between carbon burial and mineralization in kettle holes. KW - Drought KW - Rewetting KW - Temporary pond KW - Kettle hole KW - Organic matter KW - Nitrogen KW - Phosphorus Y1 - 2016 U6 - https://doi.org/10.1007/s10750-016-2715-9 SN - 0018-8158 SN - 1573-5117 VL - 775 SP - 1 EP - 20 PB - Springer CY - Dordrecht ER - TY - THES A1 - Ruiz-Martinez, Maria T1 - Characterisation and engineering of lignocellulolytic enzymes from the soil bacterium Sorangium cellulosum Y1 - 2016 ER - TY - THES A1 - Beine-Golovchuk, Olga T1 - Characterization and functional complementation of the arabidopsis ribosomal Reil1 - 1Reil2-1 double mutant Y1 - 2016 ER - TY - GEN A1 - Maier, Natalia A1 - Holzlöhner, Pamela A1 - Hoenow, Anja A1 - Scheunemann, Astrid A1 - Weschke, Daniel A1 - Hanack, Katja T1 - Characterization of monoclonal antibodies generated by in vitro immunization T2 - The journal of immunology N2 - Monoclonal antibodies are highly valuable tools in biomedicine but the generation by hybridoma technology is very time-consuming and elaborate. In order to circumvent the consisting drawbacks an in vitro immunization approach was established by which murine as well as human monoclonal antibodies against a viral coat protein could be developed. The in vitro immunization process was performed by isolation of murine hematopoietic stem cells or human monocytes and an in vitro differentiation into immature dendritic cells. After antigen loading the cells were co-cultivated with naive T and B lymphocytes for three days in order to obtain antigen-specific B lymphocytes in culture, followed by fusion with murine myeloma cells or human/murine heteromyeloma cells. Antigen-specific hybridomas were selected and the generated antibodies were purified and characterized in this study by ELISA, western blot, gene sequencing, affinity measurements. Further the characteristics were compared to a monoclonal antibody against the same target generated by conventional hybridoma technology. Isotype detection revealed a murine IgM and a human IgG4 antibody in comparison to an IgG1 for the conventionally generated antibody. The antibodies derived from in vitro immunization showed indeed a lower affinity for the antigen as compared to the conventionally generated one, which is probably based on the significantly shorter B cell maturation (3 days) during the immunization process. Nevertheless, they were suitable for building up a sandwich based detection system. Therefore, the in vitro immunization approach seems to be a good and particularly fast alternative to conventional hybridoma technology. Y1 - 2016 SN - 0022-1767 SN - 1550-6606 VL - 196 PB - American Assoc. of Immunologists CY - Bethesda ER - TY - THES A1 - Beltran, Juan Camilo Moreno T1 - Characterization of the Clp protease complex and identification of putative substrates in N. tabacum Y1 - 2016 ER - TY - JOUR A1 - Messerschmidt, Katrin A1 - Hochrein, Lena A1 - Dehm, Daniel A1 - Schulz, Karina A1 - Mueller-Roeber, Bernd T1 - Characterizing seamless ligation cloning extract for synthetic biological applications JF - Analytical biochemistry : methods in the biological sciences N2 - Synthetic biology aims at designing and engineering organisms. The engineering process typically requires the establishment of suitable DNA constructs generated through fusion of multiple protein coding and regulatory sequences. Conventional cloning techniques, including those involving restriction enzymes and ligases, are often of limited scope, in particular when many DNA fragments must be joined or scar-free fusions are mandatory. Overlap-based-cloning methods have the potential to overcome such limitations. One such method uses seamless ligation cloning extract (SLiCE) prepared from Escherichia coli cells for straightforward and efficient in vitro fusion of DNA fragments. Here, we systematically characterized extracts prepared from the unmodified E. coli strain DH10B for SLiCE-mediated cloning and determined DNA sequence-associated parameters that affect cloning efficiency. Our data revealed the virtual absence of length restrictions for vector backbone (up to 13.5 kbp) and insert (90 bp to 1.6 kbp). Furthermore, differences in GC content in homology regions are easily tolerated and the deletion of unwanted vector sequences concomitant with targeted fragment insertion is straightforward. Thus, SLiCE represents a highly versatile DNA fusion method suitable for cloning projects in virtually all molecular. and synthetic biology projects. (C) 2016 Elsevier Inc. All rights reserved. KW - SLiCE KW - Seamless ligation cloning KW - Homologous recombination KW - Synthetic biology Y1 - 2016 U6 - https://doi.org/10.1016/j.ab.2016.05.029 SN - 0003-2697 SN - 1096-0309 VL - 509 SP - 24 EP - 32 PB - Elsevier CY - San Diego ER - TY - THES A1 - Brzezinka, Krzysztof T1 - Chromatin dynamics during heat stress memory in plants Y1 - 2016 ER - TY - JOUR A1 - Ronquillo, Cecinio C. A1 - Hanke-Gogokhia, Christin A1 - Revelo, Monica P. A1 - Frederick, Jeanne M. A1 - Jiang, Li A1 - Baehr, Wolfgang T1 - Ciliopathy-associated IQCB1/NPHP5 protein is required for mouse photoreceptor outer segment formation JF - The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology N2 - Null mutations in the human IQCB1/NPHP5 (nephrocystin-5) gene that encodes NPHP5 are the most frequent cause of Senior-LOken syndrome, a ciliopathy that is characterized by Leber congenital amaurosis and nephronophthisis. We generated germline Nphp5-knockout mice by placing a -Geo gene trap in intron 4, thereby truncating NPHP5 at Leu87 and removing all known functional domains. At eye opening, Nphp5(-/-) mice exhibited absence of scotopic and photopic electroretinogram responses, a phenotype that resembles Leber congenital amaurosis. Outer segment transmembrane protein accumulation in Nphp5(-/-) endoplasmic reticulum was evident as early as postnatal day (P)6. EGFP-CETN2, a centrosome and transition zone marker, identified basal bodies in Nphp5(-/-) photoreceptors, but without fully developed transition zones. Ultrastructure of P6 and 10 Nphp5(-/-) photoreceptors revealed aberrant transition zones of reduced diameter. Nphp5(-/-) photoreceptor degeneration was complete at 1 mo of age but was delayed significantly in Nphp5(-/-);Nrl(-/-) (cone only) retina. Nphp5(-/-) mouse embryonic fibroblast developed normal cilia, and Nphp5(-/-) kidney histology at 1 yr of age showed no significant pathology. Results establish that nephrocystin-5 is essential for photoreceptor outer segment formation but is dispensable for kidney and mouse embryonic fibroblast ciliary formation. KW - Senior-LOken syndrome KW - nephronophthisis KW - Leber congenital amaurosis KW - nephrocystins Y1 - 2016 U6 - https://doi.org/10.1096/fj.201600511R SN - 0892-6638 SN - 1530-6860 VL - 30 SP - 3400 EP - 3412 PB - Federation of American Societies for Experimental Biology CY - Bethesda ER - TY - JOUR A1 - Bilton, Mark C. A1 - Metz, Johannes A1 - Tielboerger, Katja T1 - Climatic niche groups: A novel application of a common assumption predicting plant community response to climate change JF - Perspectives in plant ecology, evolution and systematics N2 - Defining species by their climatic niche is the simple and intuitive principle underlying Bioclimatic Envelope Model (BEM) predictions for climate change effects. However, these correlative models are often criticised for neglecting many ecological processes. Here, we apply the same niche principle to entire communities within a medium/long-term climate manipulation study, where ecological processes are inherently included. In a nine generation study in Israel, we manipulated rainfall (Drought -30%; Irrigation +30%; Control natural rainfall) at two sites which differ chiefly in rainfall quantity and variability. We analysed community responses to the manipulations by grouping species based on their climatic rainfall niche. These responses were compared to analyses based on single species, total densities, and commonly used taxonomic groupings. Climate Niche Groups yielded clear and consistent results: within communities, those species distributed in drier regions performed relatively better in the drought treatment, and those from wetter climates performed better when irrigated. In contrast, analyses based on other principles revealed little insight into community dynamics. Notably, most relationships were weaker at the drier, more variable site, suggesting that enhanced adaptation to variability may buffer climate change impacts. We provide robust experimental evidence that using climatic niches commonly applied in BEMs is a valid approach for eliciting community changes in response to climate change. However, we also argue that additional empirical information needs to be gathered using experiments in situ to correctly assess community vulnerability. Climatic Niche Groups used in this way, may therefore provide a powerful tool and directional testing framework to generalise and compare climate change impacts across habitats. (C) 2016 The Authors. Published by Elsevier GmbH. KW - Annual plant communities KW - Bioclimatic envelope modelling KW - Climate change manipulations KW - Experimental evidence KW - Plant functional groups KW - Rainfall niche Y1 - 2016 U6 - https://doi.org/10.1016/j.ppees.2016.02.006 SN - 1433-8319 VL - 19 SP - 61 EP - 69 PB - Elsevier CY - Jena ER -