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 - Périllon, Cécile A1 - Hilt, Sabine T1 - Groundwater influence differentially affects periphyton and macrophyte production in lakes JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Groundwater influx can significantly contribute to nutrient and carbon budgets of lakes, and its influence is the strongest in littoral areas dominated by macrophytes and periphyton. We have reviewed the effects of groundwater-borne nitrogen and phosphorus and dissolved inorganic and organic carbon (DIC, DOC) on these benthic primary producers in lakes. We develop a hypothesis for groundwater effects including the less studied impacts of periphyton shading on macrophytes. Groundwater-borne nutrients and DIC promote both macrophytes and periphyton. Direct studies on groundwater-borne DOC effects are lacking, but coloured DOC contributes to light attenuation and thus can restrict the growth of benthic primary producers. We predict that above certain threshold levels of nutrient influx by groundwater, periphyton and macrophyte biomass should decline owing to shading by phytoplankton and periphyton, respectively. However, because of their higher light requirements, those thresholds should be lower for macrophytes. For macrophytes, a threshold level is also predicted for a shift from DIC limitation to light limitation. Differences in light requirements are expected to result in lower thresholds of DOC loading for declines of macrophytes than periphyton. KW - Dissolved inorganic carbon KW - Dissolved organic carbon KW - Light KW - Macrophytes KW - Nutrients KW - Periphyton Y1 - 2016 U6 - https://doi.org/10.1007/s10750-015-2485-9 SN - 0018-8158 SN - 1573-5117 VL - 778 SP - 91 EP - 103 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Menger, Marcus A1 - Yarman, Aysu A1 - Erdössy, Júlia A1 - Yildiz, Huseyin Bekir A1 - Gyurcsányi, Róbert E. A1 - Scheller, Frieder W. T1 - MIPs and Aptamers for Recognition of Proteins in Biomimetic Sensing JF - Biosensors : open access journal N2 - Biomimetic binders and catalysts have been generated in order to substitute the biological pendants in separation techniques and bioanalysis. The two major approaches use either "evolution in the test tube" of nucleotides for the preparation of aptamers or total chemical synthesis for molecularly imprinted polymers (MIPs). The reproducible production of aptamers is a clear advantage, whilst the preparation of MIPs typically leads to a population of polymers with different binding sites. The realization of binding sites in the total bulk of the MIPs results in a higher binding capacity, however, on the expense of the accessibility and exchange rate. Furthermore, the readout of the bound analyte is easier for aptamers since the integration of signal generating labels is well established. On the other hand, the overall negative charge of the nucleotides makes aptamers prone to non-specific adsorption of positively charged constituents of the sample and the "biological" degradation of non-modified aptamers and ionic strength-dependent changes of conformation may be challenging in some application. KW - biomimetic recognition elements KW - aptamers KW - molecularly imprinted polymers KW - chemical sensors KW - aptasensors KW - in vitro selection KW - SELEX Y1 - 2016 U6 - https://doi.org/10.3390/bios6030035 SN - 2079-6374 VL - 6 SP - 4399 EP - 4413 PB - MDPI CY - Basel ER - TY - JOUR A1 - Yarman, Aysu A1 - Scheller, Frieder W. T1 - MIP-esterase/Tyrosinase Combinations for Paracetamol and Phenacetin JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - A new electrochemical MIP sensor for the most frequently used drug paracetamol (PAR) was prepared by electropolymerization of mixtures containing the template molecule and the functional monomers ophenylenediamine, resorcinol and aniline. The imprinting factor of 12 reflects the effective target binding to the MIP as compared with the non-imprinted electropolymer. Combination of the MIP with a nonspecific esterase allows the measurement of phenacetin - another analgesic drug. In the second approach the PAR containing sample solution was pretreated with tyrosinase in order to prevent electrochemical interferences by ascorbic acid and uric acid. Interference-free indication at a very low electrode potential without fouling of the electrode surface was achieved with the o-phenylenediamine: resorcinol-based MIP. KW - Paracetamol KW - Molecularly imprinted polymers KW - Electropolymerization KW - Tyrosinase KW - Esterase KW - Phenacetin Y1 - 2016 U6 - https://doi.org/10.1002/elan.201600042 SN - 1040-0397 SN - 1521-4109 VL - 28 SP - 2222 EP - 2227 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Kupfer, Alexander A1 - Maxwell, Erin A1 - Reinhard, Sandy A1 - Kuehnel, Susanne T1 - The evolution of parental investment in caecilian amphibians: a comparative approach JF - Biological journal of the Linnean Society : a journal of evolution N2 - Parental care is widespread among vertebrates and the observed patterns of parental care and investment are extremely diverse. Among amphibians, caecilians (Gymnophiona) exhibit considerable variation in reproductive modes, including both oviparity and viviparity, combined with highly unusual investment strategies (e.g. skin-feeding and intrauterine feeding). In the present study, current knowledge on the reproductive modes is integrated into an analysis of the evolutionary scenario of parental investment of caecilians. Phylogenetically basal caecilians possessing a biphasic life cycle that includes an aquatic larval stage invest in macrolecithal eggs directly corresponding to size at hatching. Some phylogenetically derived caecilians (i.e. the Teresomata) have a smaller clutch size and show a reduction to either medium-yolked (mesolecithal) or small-yolked (microlecithal) eggs. Via alternative pathways of parental investment, such as intrauterine feeding in viviparous taxa and maternal dermatotrophy in oviparous taxa, teresomatan caecilians increase both offspring size and quality. However, more data regarding reproductive biology are needed to obtain a fully resolved understanding of the evolution of reproduction in caecilian amphibians. (C) 2016 The Linnean Society of London KW - Amphibia KW - Gymnophiona KW - life history KW - parental care KW - phylogeny KW - reproductive investment Y1 - 2016 U6 - https://doi.org/10.1111/bij.12805 SN - 0024-4066 SN - 1095-8312 VL - 119 SP - 4 EP - 14 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Lehmann, Andreas A1 - Scheffler, Christiane T1 - What does the mean menarcheal age mean?An analysis of temporal pattern in variability in a historical swiss population from the 19th and 20th centuries JF - American journal of human biology : the official journal of the Human Biology Council N2 - ObjectivesAge at menarche is one of the most important factors when observing growth and development. The aim of this study was to assess the temporal pattern in variability of menarcheal age for a historic Swiss population from the 19th and 20th centuries. ResultsMean menarcheal age declined from 17.34 years (n=358) around 1830 to 13.80 years (n=141) around 1950. Within-cohort variance decreased from 7.5 to 2.1 year(2). Skewness was negatively correlated with birth year (r=-0.58). ConclusionThis study provided evidence for a secular trend in various statistical parameters for age at menarche since the 19th century. Furthermore, the results of the analysis of temporal pattern in variability revealed that the secular trend in menarcheal age happened in two phases. Am. J. Hum. Biol. 28:705-713, 2016. (c) 2016 Wiley Periodicals, Inc. Y1 - 2016 U6 - https://doi.org/10.1002/ajhb.22854 SN - 1042-0533 SN - 1520-6300 VL - 28 SP - 705 EP - 713 PB - Wiley-Blackwell CY - Hoboken 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 - Adel, Mustafa A1 - Elbehery, Ali H. A. A1 - Aziz, Sherry K. A1 - Aziz, Ramy K. A1 - Grossart, Hans-Peter A1 - Siam, Rania T1 - Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments JF - Scientific reports N2 - The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 x 10(9) bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer. Y1 - 2016 U6 - https://doi.org/10.1038/srep32704 SN - 2045-2322 VL - 6 SP - 8882 EP - 8888 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Cuong Nguyen Huu, A1 - Kappel, Christian A1 - Keller, Barbara A1 - Sicard, Adrien A1 - Takebayashi, Yumiko A1 - Breuninger, Holger A1 - Nowak, Michael D. A1 - Bäurle, Isabel A1 - Himmelbach, Axel A1 - Burkart, Michael A1 - Ebbing-Lohaus, Thomas A1 - Sakakibara, Hitoshi A1 - Altschmied, Lothar A1 - Conti, Elena A1 - Lenhard, Michael T1 - Presence versus absence of CYP734A50 underlies the style-length dimorphism in primroses JF - eLife N2 - Heterostyly is a wide-spread floral adaptation to promote outbreeding, yet its genetic basis and evolutionary origin remain poorly understood. In Primula (primroses), heterostyly is controlled by the S-locus supergene that determines the reciprocal arrangement of reproductive organs and incompatibility between the two morphs. However, the identities of the component genes remain unknown. Here, we identify the Primula CYP734A50 gene, encoding a putative brassinosteroid-degrading enzyme, as the G locus that determines the style-length dimorphism. CYP734A50 is only present on the short-styled S-morph haplotype, it is specifically expressed in S-morph styles, and its loss or inactivation leads to long styles. The gene arose by a duplication specific to the Primulaceae lineage and shows an accelerated rate of molecular evolution. Thus, our results provide a mechanistic explanation for the Primula style-length dimorphism and begin to shed light on the evolution of the S-locus as a prime model for a complex plant supergene. Y1 - 2016 U6 - https://doi.org/10.7554/eLife.17956 SN - 2050-084X VL - 5 PB - eLife Sciences Publications CY - Cambridge 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 - Borgia, Alessandro A1 - Zheng, Wenwei A1 - Buholzer, Karin A1 - Borgia, Madeleine B. A1 - Schüler, Anja A1 - Hofmann, Hagen A1 - Soranno, Andrea A1 - Nettels, Daniel A1 - Gast, Klaus A1 - Grishaev, Alexander A1 - Best, Robert B. A1 - Schuler, Benjamin T1 - Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods JF - Journal of the American Chemical Society N2 - There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) have reported no: such increase of the radius of gyration (R-g). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination Of single-molecule Forster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius, with denaturant concentration obtained by 2f-FCS,and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant;induced unfolded state expansion, and to identify the Most likely sources of earlier discrepancies. Y1 - 2016 U6 - https://doi.org/10.1021/jacs.6b05917 SN - 0002-7863 VL - 138 SP - 11714 EP - 11726 PB - American Chemical Society CY - Washington 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 - JOUR A1 - Eldridge, Tilly A1 - Langowski, Lukasz A1 - Stacey, Nicola A1 - Jantzen, Friederike A1 - Moubayidin, Laila A1 - Sicard, Adrien A1 - Southam, Paul A1 - Kennaway, Richard A1 - Lenhard, Michael A1 - Coen, Enrico S. A1 - Ostergaard, Lars T1 - Fruit shape diversity in the Brassicaceae is generated by varying patterns of anisotropy JF - Development : Company of Biologists N2 - Fruits exhibit a vast array of different 3D shapes, from simple spheres and cylinders to more complex curved forms; however, the mechanism by which growth is oriented and coordinated to generate this diversity of forms is unclear. Here, we compare the growth patterns and orientations for two very different fruit shapes in the Brassicaceae: the heart-shaped Capsella rubella silicle and the near-cylindrical Arabidopsis thaliana silique. We show, through a combination of clonal and morphological analyses, that the different shapes involve different patterns of anisotropic growth during three phases. These experimental data can be accounted for by a tissue level model in which specified growth rates vary in space and time and are oriented by a proximodistal polarity field. The resulting tissue conflicts lead to deformation of the tissue as it grows. The model allows us to identify tissue-specific and temporally specific activities required to obtain the individual shapes. One such activity may be provided by the valve-identity gene FRUITFULL, which we show through comparative mutant analysis to modulate fruit shape during post-fertilisation growth of both species. Simple modulations of the model presented here can also broadly account for the variety of shapes in other Brassicaceae species, thus providing a simplified framework for fruit development and shape diversity. KW - Brassicaceae KW - Capsella KW - Arabidopsis KW - Fruit shape KW - Modelling KW - Anisotropic growth Y1 - 2016 U6 - https://doi.org/10.1242/dev.135327 SN - 0950-1991 SN - 1477-9129 VL - 143 SP - 3394 EP - 3406 PB - Company of Biologists Limited CY - Cambridge 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 - 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 - Avcilar-Kucukgoze, Irem A1 - Bartholomäus, Alexander A1 - Varela, Juan A. Cordero A1 - Kaml, Robert Franz-Xaver A1 - Neubauer, Peter A1 - Budisa, Nediljko A1 - Ignatova, Zoya T1 - Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli JF - Nucleic acids research N2 - Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser). These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth. Y1 - 2016 U6 - https://doi.org/10.1093/nar/gkw697 SN - 0305-1048 SN - 1362-4962 VL - 44 SP - 8324 EP - 8334 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Krasuska, Urszula A1 - Ciacka, Katarzyna A1 - Orzechowski, Slawomir A1 - Fettke, Jörg A1 - Bogatek, Renata A1 - Gniazdowska, Agnieszka T1 - Modification of the endogenous NO level influences apple embryos dormancy by alterations of nitrated and biotinylated protein patterns JF - Planta N2 - NO donors and Arg remove dormancy of apple embryos and stimulate germination. Compounds lowering NO level (cPTIO, L -NAME, CAN) strengthen dormancy. Embryo transition from dormancy state to germination is linked to increased nitric oxide synthase (NOS)-like activity. Germination of embryos is associated with declined level of biotin containing proteins and nitrated proteins in soluble protein fraction of root axis. Pattern of nitrated proteins suggest that storage proteins are putative targets of nitration. Nitric oxide (NO) acts as a key regulatory factor in removal of seed dormancy and is a signal necessary for seed transition from dormant state into germination. Modulation of NO concentration in apple (Malus domestica Borkh.) embryos by NO fumigation, treatment with NO donor (S-nitroso-N-acetyl-d,l-penicillamine, SNAP), application of 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO), N (omega)-nitro-l-arginine methyl ester (l-NAME), canavanine (CAN) or arginine (Arg) allowed us to investigate the NO impact on seed dormancy status. Arg analogs and NO scavenger strengthened embryo dormancy by lowering reactive nitrogen species level in embryonic axes. This effect was accompanied by strong inhibition of NOS-like activity, without significant influence on tissue NO2 (-) concentration. Germination sensu stricto of apple embryos initiated by dormancy breakage via short term NO treatment or Arg supplementation were linked to a reduced level of biotinylated proteins in root axis. Decrease of total soluble nitrated proteins was observed at the termination of germination sensu stricto. Also modulation of NO tissue status leads to modification in nitrated protein pattern. Among protein bands that correspond to molecular mass of approximately 95 kDa, storage proteins (legumin A-like and seed biotin-containing protein) were identified, and can be considered as good markers for seed dormancy status. Moreover, pattern of nitrated proteins suggest that biotin containing proteins are also targets of nitration. KW - Apple KW - Nitro-tyrosine KW - Nitric oxide synthase-like activity KW - Reactive nitrogen species KW - Seed germination Y1 - 2016 U6 - https://doi.org/10.1007/s00425-016-2553-z SN - 0032-0935 SN - 1432-2048 VL - 244 SP - 877 EP - 891 PB - Springer CY - New York ER - 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 - 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 - Bull, James K. A1 - Heurich, Marco A1 - Saveljev, Alexander P. A1 - Schmidt, Krzysztof A1 - Fickel, Jörns A1 - Förster, Daniel W. T1 - The effect of reintroductions on the genetic variability in Eurasian lynx populations: the cases of Bohemian-Bavarian and Vosges-Palatinian populations JF - Conservation genetics KW - Lynx KW - Microsatellites KW - Population history KW - Reintroduction Y1 - 2016 U6 - https://doi.org/10.1007/s10592-016-0839-0 SN - 1566-0621 SN - 1572-9737 VL - 17 SP - 1229 EP - 1234 PB - Springer CY - Dordrecht 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 - Mumm, Rebekka A1 - Hermanussen, Michael A1 - Scheffler, Christiane T1 - voice break as the marker of biological age JF - Acta paediatrica : nurturing the child N2 - Aim: We aimed to develop the first references for body height, body weight and body mass index (BMI) for boys based on the individual developmental tempo with respect to their voice break status. Methods: We re-analysed data from the German Health Interview and Examination Survey for Children and Adolescents (KiGGS study) on body height, body weight and body mass index based on the voice break, or mutation, in 3956 boys aged 10-17 years. We used the LMS method to construct smoothed references centiles for the studied variables in premutational, mutational and postmutational boys. Results: Body height, body weight and BMI differed significantly (p < 0.001) between the different stages of voice break. On average, boys were 5.9 cm taller, 5.8 kg heavier and had a 0.7 kg/m(2) higher BMI with every higher stage of voice break. Currently used growth references for chronological age in comparison with maturity-related references led to an average of 5.4% of boys being falsely classified as overweight. KW - Body mass index KW - Developmental tempo KW - Growth reference values KW - Overweight KW - Voice break Y1 - 2016 U6 - https://doi.org/10.1111/apa.13488 SN - 0803-5253 SN - 1651-2227 VL - 105 SP - e459 EP - e463 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Richter, Katharina Natalia A1 - Rolke, Daniel A1 - Blenau, Wolfgang A1 - Baumann, Otto T1 - Secretory cells in honeybee hypopharyngeal gland: polarized organization and age-dependent dynamics of plasma membrane JF - Cell & tissue research N2 - The honeybee hypopharyngeal gland consists in numerous units, each comprising a secretory cell and a canal cell. The secretory cell discharges its products into a convoluted tubular membrane system, the canaliculus, which is surrounded at regular intervals by rings of actin filaments. Using probes for various membrane components, we analyze the organization of the secretory cells relative to the apicobasal configuration of epithelial cells. The canaliculus was defined by labeling with an antibody against phosphorylated ezrin/radixin/moesin (pERM), a marker protein for the apical membrane domain of epithelial cells. Anti-phosphotyrosine visualizes the canalicular system, possibly by staining the microvillar tips. The open end of the canaliculus leads to a region in which the secretory cell is attached to the canal cell by adherens and septate junctions. The remaining plasma membrane stains for Na,K-ATPase and spectrin and represents the basolateral domain. We also used fluorophore-tagged phalloidin, anti-phosphotyrosine and anti-pERM as probes for the canaliculus in order to describe fine-structural changes in the organization of the canalicular system during the adult life cycle. These probes in conjunction with fluorescence microscopy allow the fast and detailed three-dimensional analysis of the canalicular membrane system and its structural changes in a developmental mode or in response to environmental factors. KW - Hypopharyngeal gland KW - Cell polarity KW - Moesin KW - Actin cytoskeleton KW - Honeybee Y1 - 2016 U6 - https://doi.org/10.1007/s00441-016-2423-9 SN - 0302-766X SN - 1432-0878 VL - 366 SP - 163 EP - 174 PB - Springer CY - New York ER - TY - JOUR A1 - Sarauli, David A1 - Borowski, Anja A1 - Peters, Kristina A1 - Schulz, Burkhard A1 - Fattakhova-Rohlfing, Dina A1 - Leimkühler, Silke A1 - Lisdat, Fred T1 - Investigation of the pH-Dependent Impact of Sulfonated Polyaniline on Bioelectrocatalytic Activity of Xanthine Dehydrogenase JF - ACS catalysis N2 - We report on the pH-dependent bioelectrocatalytic activity of the redox enzyme xanthine dehydrogenase (XDH) in the presence of sulfonated polyaniline PMSA1 (poly(2-methoxyaniline-5-sulfonic acid)-co-aniline). Ultraviolet-visible (UV-vis) spectroscopic measurements with both components in solution reveal electron transfer from the hypoxanthine (HX)-reduced enzyme to the polymer. The enzyme shows bioelectrocatalytic activity on indium tin oxide (ITO) electrodes, when the polymer is present. Depending on solution pH, different processes can be identified. It can be demonstrated that not only product-based communication with the electrode but also efficient polymer-supported bioelectrocatalysis occur. Interestingly, substrate dependent catalytic currents can be obtained in acidic and neutral solutions, although the highest activity of XDH with natural reaction partners is in the alkaline region. Furthermore, operation of the enzyme electrode without addition of the natural cofactor of XDH is feasible. Finally, macroporous ITO electrodes have been used as an immobilization platform for the fabrication of HX-sensitive electrodes. The study shows that the efficient polymer/enzyme interaction can be advantageously combined with the open structure of an electrode material of controlled pore size, resulting in good processability, stability, and defined signal transfer in the presence of a substrate. KW - enzyme bioelectrocatalysis KW - sulfonated polyanilines KW - xanthine dehydrogenase KW - pH-dependent electrochemistry KW - macroporous ITO electrodes Y1 - 2016 U6 - https://doi.org/10.1021/acscatal.6b02011 SN - 2155-5435 VL - 6 SP - 7152 EP - 7159 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Guardado-Calvo, Pablo A1 - Bignon, Eduardo A. A1 - Stettner, Eva A1 - Jeffers, Scott Allen A1 - Perez-Vargas, Jimena A1 - Pehau-Arnaudet, Gerard A1 - Tortoric, M. Alejandra A1 - Jestin, Jean-Luc A1 - England, Patrick A1 - Tischler, Nicole D. A1 - Rey, Felix A. T1 - Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc JF - PLoS Pathogens N2 - Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic beta-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha-and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single "fusion loop". We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal "tail" that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens. Y1 - 2016 U6 - https://doi.org/10.1371/journal.ppat.1005813 SN - 1553-7366 SN - 1553-7374 VL - 12 SP - 153 EP - 166 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Dongmo, Saustin A1 - Leyk, Janina A1 - Dosche, Carsten A1 - Richter-Landsberg, Christiane A1 - Wollenberger, Ursula A1 - Wittstock, Gunther T1 - Electrogeneration of O-2(center dot-) and H2O2 Using Polymer-modified Microelectrodes in the Environment of Living Cells JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - Microelectrodes modified with electropolymerized plumbagin (PLG) were used for the generation of superoxide radical (O-2(center dot-)) and hydrogen peroxide (H2O2) during oxygen reduction reaction (ORR) in an aqueous medium, specifically in serum-free cell culture media. This is enabled by the specific design of a polymer film on the microelectrode. The generation and diffusion of O-2(center dot-) during electrocatalytic ORR at a positionable PLG polymer-modified microelectrode was followed by fluorescence microscopy with the selective dye 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) and by amperometric detection using a cytochrome c-modified electrode at + 0.13 V. H2O2 production, either by direct oxygen reduction or as product of O-2(center dot-) disproportionation, was monitored by the reaction with Amplex UltraRed. The PLG polymer-modified microelectrodes were used to expose mammalian B6-RPE07 retinal cells to defined local fluxes of reactive oxygen species (ROS), and cellular responses and morphological alterations were observed. The use of a controllable source of ROS opens many possibilities to study how living cells respond to the presence of a certain flux of specific ROS. KW - reactive oxygen species KW - microelectrode KW - scanning electrochemical microscopy KW - biosensor KW - polymer-modified electrode KW - oxygen reduction reaction Y1 - 2016 U6 - https://doi.org/10.1002/elan.201600267 SN - 1040-0397 SN - 1521-4109 VL - 28 SP - 2400 EP - 2407 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Zeng, Ting A1 - Frasca, Stefano A1 - Rumschöttel, Jens A1 - Koetz, Joachim A1 - Leimkühler, Silke A1 - Wollenberger, Ursula T1 - Role of Conductive Nanoparticles in the Direct Unmediated Bioelectrocatalysis of Immobilized Sulfite Oxidase JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis KW - Direct electron transfer KW - Protein voltammetry KW - Human sulfite oxidase KW - Bioelectrocatalysis KW - Nanoparticles Y1 - 2016 U6 - https://doi.org/10.1002/elan.201600246 SN - 1040-0397 SN - 1521-4109 VL - 28 SP - 2303 EP - 2310 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Correia, Marcia A. S. A1 - Otrelo-Cardoso, Ana Rita A1 - Schwuchow, Viola A1 - Clauss, Kajsa G. V. Sigfridsson A1 - Haumann, Michael A1 - Romao, Maria Joao A1 - Leimkühler, Silke A1 - Santos-Silva, Teresa T1 - The Escherichia coli Periplasmic Aldehyde Oxidoreductase Is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes JF - ACS chemical biology N2 - The xanthine oxidase (XO) family comprises molybdenum-dependent enzymes that usually form homodimers (or dimers of heterodimers/trimers) organized in three domains that harbor two [2Fe-2S] clusters, one FAD, and a Mo cofactor. In this work, we crystallized an unusual member of the family, the periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli. This is the first example of an E. coli protein containing a molybdopterin-cytosine-dinucleotide cofactor and is the only heterotrimer of the XO family so far structurally characterized. The crystal structure revealed the presence of an unexpected [4Fe-4S] cluster, anchored to an additional 40 residues subdomain. According to phylogenetic analysis, proteins containing this cluster are widely spread in many bacteria phyla, putatively through repeated gene transfer events. The active site of PaoABC is highly exposed to the surface with no aromatic residues and an arginine (PaoC-R440) making a direct interaction with PaoC-E692, which acts as a base catalyst. In order to understand the importance of R440, kinetic assays were carried out, and the crystal structure of the PaoC-R440H variant was also determined. Y1 - 2016 U6 - https://doi.org/10.1021/acschembio.6b00572 SN - 1554-8929 SN - 1554-8937 VL - 11 SP - 2923 EP - 2935 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Patel, Riddhi P. A1 - Förster, Daniel W. A1 - Kitchener, Andrew C. A1 - Rayan, Mark D. A1 - Mohamed, Shariff W. A1 - Werner, Laura A1 - Lenz, Dorina A1 - Pfestorf, Hans A1 - Kramer-Schadt, Stephanie A1 - Radchuk, Viktoriia A1 - Fickel, Jörns A1 - Wilting, Andreas T1 - Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist JF - Royal Society Open Science N2 - Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based onmorphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to PeninsularMalaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis. KW - Felidae KW - Southeast Asia KW - last glacial maximum KW - Toba volcanic eruption KW - hybrid capture KW - next generation sequencing Y1 - 2016 U6 - https://doi.org/10.1098/rsos.160350 SN - 2054-5703 VL - 3 SP - 741 EP - 752 PB - Royal Society CY - London ER - TY - JOUR A1 - Heim, Olga A1 - Schröder, Assja A1 - Eccard, Jana A1 - Jung, Kirsten A1 - Voigt, Christian C. T1 - Seasonal activity patterns of European bats above intensively used farmland JF - The astrophysical journal : an international review of spectroscopy and astronomical physics ; Part 2, Letters N2 - Bats are top insect predators on farmland, yet they suffer from intensive farmland management. Here, we evaluated the seasonal activity patterns of European bats above large, arable fields and compared these patterns between ecologically distinct bat species. Using repeated passive acoustic monitoring on a total of 93 arable fields in 2 years in Brandenburg, Germany, we surveyed the activity of different bat species between early spring and autumn. We then used generalized additive mixed models to describe and compare the seasonal bat activity patterns between bat categories, which were build based on the affiliation to a functional group and migratory class, while controlling for local weather conditions. In general, the affiliation to a bat category in interaction with the season in addition to cloud cover and ambient air temperature explained a major part of bat activity. The season was also an important factor for the foraging activity of open-space specialists such as Nyctalus noctula but showed only a weak effect on species such as Pipistreilus nathusii which are adapted to edge-space habitats. Across the seasons, habitat use intensity was high during the period of swarming and migration and low during the energy demanding period of lactation. Seasonal patterns in foraging activity showed that open-space specialists foraged more intensively above agricultural fields during the migration period, while edge-space specialists foraged also during the energy demanding period of lactation. We conclude that the significant seasonal fluctuations in bat activity and significant differences between bat categories in open agricultural landscapes should be taken into consideration when designing monitoring schemes and management plans for bat species in regions dominated by agriculture. Also, management plans should be directed to improve the conditions on arable land especially for bat species which would be classified as narrow-space foragers such as Myotis species. (C) 2016 Elsevier B.V. All rights reserved. KW - Agricultural intensification KW - Seasonality KW - European bat species KW - Functional bat group KW - Migration KW - AgroScapeLabs Y1 - 2016 U6 - https://doi.org/10.1016/j.agee.2016.09.002 SN - 0167-8809 SN - 1873-2305 VL - 233 SP - 130 EP - 139 PB - Elsevier CY - Amsterdam 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 - Navarro-Retamal, Carlos A1 - Bremer, Anne A1 - Alzate-Morales, Jans H. A1 - Caballero, Julio A1 - Hincha, Dirk K. A1 - Gonzalez, Wendy A1 - Thalhammer, Anja T1 - Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain alpha-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40%) or prevented (100%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state. Y1 - 2016 U6 - https://doi.org/10.1039/c6cp02272c SN - 1463-9076 SN - 1463-9084 VL - 18 SP - 25806 EP - 25816 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Lukoszek, Radoslaw A1 - Feist, Peter A1 - Ignatova, Zoya T1 - Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq JF - BMC plant biology N2 - Background: Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different levels of gene expression. Results: Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are likely candidates to play a role in regulating translation of those genes. Conclusions: Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids is maintained upon heat exposure. KW - Translation KW - Ribosome profiling KW - Transcription KW - RNA-Seq KW - Secondary structure KW - G-quadruplexes KW - Heat stress response Y1 - 2016 U6 - https://doi.org/10.1186/s12870-016-0915-0 SN - 1471-2229 VL - 16 PB - BioMed Central CY - London 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 - Han, Xiao Xia A1 - Li, Junbo A1 - Öner, Ibrahim Halil A1 - Zhao, Bing A1 - Leimkühler, Silke A1 - Hildebrandt, Peter A1 - Weidinger, Inez M. T1 - Nickel electrodes as a cheap and versatile platform for studying structure and function of immobilized redox proteins JF - Analytica chimica acta : an international journal devoted to all branches of analytical chemistry N2 - Practical use of many bioelectronic and bioanalytical devices is limited by the need of expensive materials and time consuming fabrication. Here we demonstrate the use of nickel electrodes as a simple and cheap solid support material for bioelectronic applications. The naturally nanostructured electrodes showed a surprisingly high electromagnetic surface enhancement upon light illumination such that immobilization and electron transfer reactions of the model redox proteins cytochrome b(5) (Cyt b(5)) and cytochrome c (Cyt c) could be followed via surface enhanced resonance Raman spectroscopy. It could be shown that the nickel surface, when used as received, promotes a very efficient binding of the proteins upon preservation of their native structure. The immobilized redox proteins could efficiently exchange electrons with the electrode and could even act as an electron relay between the electrode and solubilized myoglobin. Our results open up new possibility for nickel electrodes as an exceptional good support for bioelectronic devices and biosensors on the one hand and for surface enhanced spectroscopic investigations on the other hand. (C) 2016 Elsevier B.V. All rights reserved. KW - Ni electrodes KW - Redox proteins KW - Surface enhanced Raman spectroscopy KW - Electron relay KW - Biocompatibility KW - Electron transfer Y1 - 2016 U6 - https://doi.org/10.1016/j.aca.2016.08.053 SN - 0003-2670 SN - 1873-4324 VL - 941 SP - 35 EP - 40 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Kruse, Stefan A1 - Wieczorek, Mareike A1 - Jeltsch, Florian A1 - Herzschuh, Ulrike T1 - Treeline dynamics in Siberia under changing climates as inferred from an individual-based model for Larix JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog KW - Forest change KW - IBM KW - ODD model description KW - Larix gmelinii KW - Permafrost ecosystem KW - Time-lag effects Y1 - 2016 U6 - https://doi.org/10.1016/j.ecolmodel.2016.08.003 SN - 0304-3800 SN - 1872-7026 VL - 338 SP - 101 EP - 121 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Lah, Ljerka A1 - Trense, Daronja A1 - Benke, Harald A1 - Berggren, Per A1 - Gunnlaugsson, Porvaldur A1 - Lockyer, Christina A1 - Öztürk, Ayaka A1 - Öztürk, Bayram A1 - Pawliczka, Iwona A1 - Roos, Anna A1 - Siebert, Ursula A1 - Skora, Krzysztof A1 - Vikingsson, Gisli A1 - Tiedemann, Ralph T1 - Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise JF - PLoS one N2 - The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymor-phisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0162792 SN - 1932-6203 VL - 11 PB - PLoS CY - San Fransisco 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 - JOUR A1 - Hilker, Monika A1 - Schwachtje, Jens A1 - Baier, Margarete A1 - Balazadeh, Salma A1 - Bäurle, Isabel A1 - Geiselhardt, Sven A1 - Hincha, Dirk K. A1 - Kunze, Reinhard A1 - Mueller-Roeber, Bernd A1 - Rillig, Matthias G. A1 - Rolff, Jens A1 - Schmülling, Thomas A1 - Steppuhn, Anke A1 - van Dongen, Joost A1 - Whitcomb, Sarah J. A1 - Wurst, Susanne A1 - Zuther, Ellen A1 - Kopka, Joachim T1 - Priming and memory of stress responses in organisms lacking a nervous system JF - Biological reviews KW - priming KW - stress signalling KW - epigenetics KW - memory KW - fitness KW - stress tolerance KW - defence KW - bet hedging Y1 - 2016 U6 - https://doi.org/10.1111/brv.12215 SN - 1464-7931 SN - 1469-185X VL - 91 SP - 1118 EP - 1133 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Gietler, Marta A1 - Nykiel, Malgorzata A1 - Orzechowski, Slawomir A1 - Zagdanska, Barbara A1 - Fettke, Jörg T1 - Proteomic analysis of S-nitrosylated and S-glutathionylated proteins in wheat seedlings with different dehydration tolerances JF - Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology N2 - A loss of dehydration tolerance in wheat seedlings on the fifth day following imbibition is associated with a disturbance in cellular redox homeostasis, as documented by a shift of the reduced/oxidized glutathione ratio to a more oxidized state and a significant increase in the ratio of protein thiols to the total thiol group content. Therefore, the identification and characterization of redox-sensitive proteins are important steps toward understanding the molecular mechanisms of the loss of dehydration tolerance. In the present study, proteins that were differentially expressed between fully turgid (control), dehydrated tolerant (four-day-old) and dehydrated sensitive (six-day-old) wheat seedlings were analysed. Protein spots having at least a significant (p < 0.05) two-fold change in protein abundance were selected by Delta2D as differentially expressed, identified by MALDI-TOF and LC-MS/MS, and classified according to their function. The observed changes in the proteomic patterns of the differentially S-nitrosylated and S-glutathionylated proteins were highly specific in dehydration-tolerant and-sensitive wheat seedlings. The metabolic function of these proteins indicates that dehydration tolerance is mainly related to nucleic acids, protein metabolism, and energy metabolism. It has been proven that leaf-specific thionins BTH6 and DB4, chloroplastic 50S ribosomal protein L16, phospholipase A1-II delta, and chloroplastic thioredoxin M2 are both S-nitrosylated and S-glutathionylated upon water deficiency. Our results revealed the existence of interplay between S-nitrosylation and S-glutathionylation, two redox-regulated protein posttranslational modifications that could enhance plant defence mechanisms and/or facilitate the acclimation of plants to unfavourable environmental conditions. (C) 2016 Elsevier Masson SAS. All rights reserved. KW - Dehydration tolerance KW - Proteomics KW - Redox sensitive proteins KW - S-glutathionylation KW - S-nitrosylation KW - Triticum aestivum L. Y1 - 2016 U6 - https://doi.org/10.1016/j.plaphy.2016.08.017 SN - 0981-9428 VL - 108 SP - 507 EP - 518 PB - Elsevier CY - Paris ER - TY - JOUR A1 - Allu, Annapurna Devi A1 - Brotman, Yariv A1 - Xue, Gang-Ping A1 - Balazadeh, Salma T1 - Transcription factor ANAC032 modulates JA/SA signalling in response to Pseudomonas syringae infection JF - EMBO reports N2 - Responses to pathogens, including host transcriptional reprogramming, require partially antagonistic signalling pathways dependent on the phytohormones salicylic (SA) and jasmonic (JA) acids. However, upstream factors modulating the interplay of these pathways are not well characterized. Here, we identify the transcription factor ANAC032 from Arabidopsis thaliana as one such regulator in response to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst). ANAC032 directly represses MYC2 activation upon Pst attack, resulting in blockage of coronatine-mediated stomatal reopening which restricts entry of bacteria into plant tissue. Furthermore, ANAC032 activates SA signalling by repressing NIMIN1, a key negative regulator of SA-dependent defence. Finally, ANAC032 reduces expression of JA-responsive genes, including PDF1.2A. Thus, ANAC032 enhances resistance to Pst by generating an orchestrated transcriptional output towards key SA- and JA-signalling genes coordinated through direct binding of ANAC032 to the MYC2, NIMIN1 and PDF1.2A promoters. KW - Arabidopsis KW - jasmonic acid KW - pathogens KW - salicylic acid KW - transcription factor Y1 - 2016 U6 - https://doi.org/10.15252/embr.201642197 SN - 1469-221X SN - 1469-3178 VL - 17 SP - 1578 EP - 1589 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Bergmann, Joana A1 - Verbruggen, Erik A1 - Heinze, Johannes A1 - Xiang, Dan A1 - Chen, Baodong A1 - Joshi, Jasmin Radha A1 - Rillig, Matthias C. T1 - The interplay between soil structure, roots, and microbiota as a determinant of plant-soil feedback JF - Ecology and evolution N2 - Plant-soil feedback (PSF) can influence plant community structure via changes in the soil microbiome. However, how these feedbacks depend on the soil environment remains poorly understood. We hypothesized that disintegrating a naturally aggregated soil may influence the outcome of PSF by affecting microbial communities. Furthermore, we expected plants to differentially interact with soil structure and the microbial communities due to varying root morphology. We carried out a feedback experiment with nine plant species (five forbs and four grasses) where the training phase consisted of aggregated versus disintegrated soil. In the feedback phase, a uniform soil was inoculated in a fully factorial design with soil washings from conspecific- versus heterospecific-trained soil that had been either disintegrated or aggregated. This way, the effects of prior soil structure on plant performance in terms of biomass production and allocation were examined. In the training phase, soil structure did not affect plant biomass. But on disintegrated soil, plants with lower specific root length (SRL) allocated more biomass aboveground. PSF in the feedback phase was negative overall. With training on disintegrated soil, conspecific feedback was positively correlated with SRL and significantly differed between grasses and forbs. Plants with higher SRL were likely able to easily explore the disintegrated soil with smaller pores, while plants with lower SRL invested in belowground biomass for soil exploration and seemed to be more susceptible to fungal pathogens. This suggests that plants with low SRL could be more limited by PSF on disintegrated soils of early successional stages. This study is the first to examine the influence of soil structure on PSF. Our results suggest that soil structure determines the outcome of PSF mediated by SRL. We recommend to further explore the effects of soil structure and propose to include root performance when working with PSF. KW - arbuscular mycorrhizal fungi KW - biomass allocation KW - plant functional traits KW - plant-soil (belowground) interactions KW - soil aggregation KW - specific root length KW - succession KW - water-stable aggregates Y1 - 2016 U6 - https://doi.org/10.1002/ece3.2456 SN - 2045-7758 VL - 6 SP - 7633 EP - 7644 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Bookers, Anke A1 - Jacob, Louis A1 - Bohlken, Jens A1 - Rapp, Michael A. A1 - Kostev, Karel T1 - Persistence with antipsychotics in dementia patients in Germany JF - International journal of clinical pharmacology and therapeutics N2 - Background/Aims: To analyze the duration of treatment with antipsychotics in German dementia patients. Methods: This study included patients aged 60 years and over with dementia who received a first-time antipsychotic prescription by psychiatrists between 2009 and 2013. The main outcome measure was the treatment rate for more than 6 months following the index date. Results: A total of 12,979 patients with dementia (mean age 82 years, 52.1% living in nursing homes) were included. After 2 years of follow-up, 54.8%, 57.2%, 61.1%, and 65.4% of patients aged 60 - 69, 70 - 79, 80 - 89, and 90 - 99 years, respectively, received antipsychotic prescriptions. 63.9% of subjects living in nursing homes and 55.0% of subjects living at home also continued their treatment (p-value < 0.001). Conclusion: The percentage of dementia patients treated with anti psychotics is very high. KW - persistence KW - antipsychotics KW - dementia Y1 - 2016 U6 - https://doi.org/10.5414/CP202631 SN - 0946-1965 VL - 54 SP - 835 EP - 840 PB - Dustri-Verlag Dr. Karl Feistle CY - Deisenhofen-München 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 - Zwickel, Theresa A1 - Kahl, Sandra M. A1 - Klaffke, Horst A1 - Rychlik, Michael A1 - Müller, Marina E. H. T1 - Spotlight on the Underdogs-An Analysis of Underrepresented Alternaria Mycotoxins Formed Depending on Varying Substrate, Time and Temperature Conditions JF - Toxins N2 - Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 degrees C, 25 degrees C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 degrees C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions. KW - Alternaria infectoria KW - A. tenuissima KW - mycotoxin profile KW - wheat KW - rice KW - Alternaria toxin sulfates KW - modified Alternaria toxins KW - altertoxins KW - altenuic acid KW - HPLC-MS/MS Y1 - 2016 U6 - https://doi.org/10.3390/toxins8110344 SN - 2072-6651 VL - 8 SP - 570 EP - 583 PB - MDPI CY - Basel 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 - Sakschewski, Boris A1 - von Bloh, Werner A1 - Boit, Alice A1 - Poorter, Lourens A1 - Pe~na-Claros, Marielos A1 - Heinke, Jens A1 - Joshi, Jasmin Radha A1 - Thonicke, Kirsten T1 - Resilience of Amazon forests emerges from plant trait diversity JF - Nature climate change Y1 - 2016 U6 - https://doi.org/10.1038/NCLIMATE3109 SN - 1758-678X SN - 1758-6798 VL - 6 SP - 1032 EP - + PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Üstün, Suayib A1 - Sheikh, Arsheed A1 - Gimenez-Ibanez, Selena A1 - Jones, Alexandra A1 - Ntoukakis, Vardis A1 - Börnke, Frederik T1 - The Proteasome Acts as a Hub for Plant Immunity and Is Targeted by Pseudomonas Type III Effectors JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Recent evidence suggests that the ubiquitin-proteasome system is involved in several aspects of plant immunity and that a range of plant pathogens subvert the ubiquitin-proteasome system to enhance their virulence. Here, we show that proteasome activity is strongly induced during basal defense in Arabidopsis (Arabidopsis thaliana). Mutant lines of the proteasome subunits RPT2a and RPN12a support increased bacterial growth of virulent Pseudomonas syringae pv tomato DC3000 (Pst) and Pseudomonas syringae pv maculicola ES4326. Both proteasome subunits are required for pathogen-associated molecular pattern-triggered immunity responses. Analysis of bacterial growth after a secondary infection of systemic leaves revealed that the establishment of systemic acquired resistance (SAR) is impaired in proteasome mutants, suggesting that the proteasome also plays an important role in defense priming and SAR. In addition, we show that Pst inhibits proteasome activity in a type III secretion-dependent manner. A screen for type III effector proteins from Pst for their ability to interfere with proteasome activity revealed HopM1, HopAO1, HopA1, and HopG1 as putative proteasome inhibitors. Biochemical characterization of HopM1 by mass spectrometry indicates that HopM1 interacts with several E3 ubiquitin ligases and proteasome subunits. This supports the hypothesis that HopM1 associates with the proteasome, leading to its inhibition. Thus, the proteasome is an essential component of pathogen-associated molecular pattern-triggered immunity and SAR, which is targeted by multiple bacterial effectors. Y1 - 2016 U6 - https://doi.org/10.1104/pp.16.00808 SN - 0032-0889 SN - 1532-2548 VL - 172 SP - 1941 EP - 1958 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Ali, Tahir A1 - Runge, Fabian A1 - Dutbayev, Ayan A1 - Schmuker, Angelika A1 - Solovyeva, Irina A1 - Nigrelli, Lisa A1 - Buch, Ann-Katrin A1 - Xia, Xiaojuan A1 - Ploch, Sebastian A1 - Orren, Ouria A1 - Kummer, Volker A1 - Paule, Juraj A1 - Celik, Ali A1 - Vakhrusheva, Ljudmila A1 - Gabrielyan, Ivan A1 - Thines, Marco T1 - Microthlaspi erraticum (Jord.) T. Ali et Thines has a wide distribution, ranging from the Alps to the Tien Shan JF - Flora : morphology, distribution, functional ecology of plants N2 - Microthlaspi is a predominantly Eurasian genus which also occurs in the northernmost parts of Africa (Maghreb). The most widespread species of the genus is M. perfoliatum, which can be found from Sweden to Algeria and from Portugal to China. The other species are thought to have much more confined distribution ranges, often covering only a few hundred kilometres. This is also believed for the diploid M. erraticum, which was recently re-appraised as a taxon independent from the tetra- to hexaploid M. perfoliatum. Previously, M. erraticum was believed to be present only in Central Europe, from the East of France to Slovenia. In order to gain a deeper understanding of the ecology, evolution and migration history of Microthlaspi it was the focus of the current study to investigate, if M. erraticum is present in habitats outside Central Europe, but with microclimates similar to Central Europe. It is demonstrated that M. erraticum is much more widespread than previously thought, while other lineages apart from M. perfoliatum s.str. and M. erraticum seem to have restricted distribution ranges. The latter species was observed from the Alps and their foreland, the Balkans, the mountainous areas around the Black Sea, Southern Siberia, as well as the Altai and Tien Shan mountains. This demonstrates a widespread occurrence of this easily-overlooked species. (C) 2016 Elsevier GmbH. All rights reserved. KW - Biogeography KW - Coluteocarpeae KW - Noccaea KW - Phylogeny KW - Species complex KW - Thlaspi perfoliatum Y1 - 2016 U6 - https://doi.org/10.1016/j.flora.2016.09.008 SN - 0367-2530 SN - 1618-0585 VL - 225 SP - 76 EP - 81 PB - American Chemical Society CY - Jena 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 -