@article{CuiLvChenetal.2015, author = {Cui, Xiao and Lv, Yang and Chen, Miaolin and Nikoloski, Zoran and Twell, David and Zhang, Dabing}, title = {Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome}, series = {Molecular plant}, volume = {8}, journal = {Molecular plant}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1016/j.molp.2014.12.008}, pages = {935 -- 945}, year = {2015}, abstract = {The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens.}, language = {en} } @article{JetzschmannJagerszkiDechtriratetal.2015, author = {Jetzschmann, Katharina J. and Jagerszki, Gyula and Dechtrirat, Decha and Yarman, Aysu and Gajovic-Eichelmann, Nenad and Gilsing, Hans-Detlev and Schulz, Burkhard and Gyurcsanyi, Robert E. and Scheller, Frieder W.}, title = {Vectorially Imprinted Hybrid Nanofilm for Acetylcholinesterase Recognition}, series = {Advanced functional materials}, volume = {25}, journal = {Advanced functional materials}, number = {32}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1616-301X}, doi = {10.1002/adfm.201501900}, pages = {5178 -- 5183}, year = {2015}, abstract = {Effective recognition of enzymatically active tetrameric acetylcholinesterase (AChE) is accomplished by a hybrid nanofilm composed of a propidium-terminated self-assembled monolayer (Prop-SAM) which binds AChE via its peripheral anionic site (PAS) and an ultrathin electrosynthesized molecularly imprinted polymer (MIP) cover layer of a novel carboxylate-modified derivative of 3,4-propylenedioxythiophene. The rebinding of the AChE to the MIP/Prop-SAM nanofilm covered electrode is detected by measuring in situ the enzymatic activity. The oxidative current of the released thiocholine is dependent on the AChE concentration from approximate to 0.04 x 10(-6) to 0.4 x 10(-6)m. An imprinting factor of 9.9 is obtained for the hybrid MIP, which is among the best values reported for protein imprinting. The dissociation constant characterizing the strength of the MIP-AChE binding is 4.2 x 10(-7)m indicating the dominant role of the PAS-Prop-SAM interaction, while the benefit of the MIP nanofilm covering the Prop-SAM layer is the effective suppression of the cross-reactivity toward competing proteins as compared with the Prop-SAM. The threefold selectivity gain provided by i) the shape-specific MIP filter, ii) the propidium-SAM, iii) signal generation only by the AChE bound to the nanofilm shows promise for assessing AChE activity levels in cerebrospinal fluid.}, language = {en} } @misc{JonesGonzalezFortesConnelletal.2015, author = {Jones, Eppie R. and Gonz{\´a}lez-Fortes, Gloria M. and Connell, Sarah and Siska, Veronika and Eriksson, Anders and Martiniano, Rui and McLaughlin, Russell L. and Llorente, Marcos Gallego and Cassidy, Lara M. and Gamba, Cristina and Meshveliani, Tengiz and Bar-Yosef, Ofer and M{\"u}ller, Werner and Belfer-Cohen, Anna and Matskevich, Zinovi and Jakeli, Nino and Higham, Thomas F. G. and Currat, Mathias and Lordkipanidze, David and Hofreiter, Michael and Manica, Andrea and Pinhasi, Ron and Bradley, Daniel G.}, title = {Upper Palaeolithic genomes reveal deep roots of modern Eurasians}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1334}, issn = {1866-8372}, doi = {10.25932/publishup-43931}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439317}, pages = {8}, year = {2015}, abstract = {We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.}, language = {en} } @article{JonesGonzalezFortesConnelletal.2015, author = {Jones, Eppie R. and Gonz{\´a}lez-Fortes, Gloria M. and Connell, Sarah and Siska, Veronika and Eriksson, Anders and Martiniano, Rui and McLaughlin, Russell L. and Llorente, Marcos Gallego and Cassidy, Lara M. and Gamba, Cristina and Meshveliani, Tengiz and Bar-Yosef, Ofer and Mueller, Werner and Belfer-Cohen, Anna and Matskevich, Zinovi and Jakeli, Nino and Higham, Thomas F. G. and Currat, Mathias and Lordkipanidze, David and Hofreiter, Michael and Manica, Andrea and Pinhasi, Ron and Bradley, Daniel G.}, title = {Upper Palaeolithic genomes reveal deep roots of modern Eurasians}, series = {Nature Communications}, volume = {6}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms9912}, pages = {8}, year = {2015}, abstract = {We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers similar to 45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers similar to 25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe similar to 3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.}, language = {en} } @article{LudwigReissmannBeneckeetal.2015, author = {Ludwig, Arne and Reissmann, Monika and Benecke, Norbert and Bellone, Rebecca and Sandoval-Castellanos, Edson and Cieslak, Michael and Gonz{\´a}lez-Fortes, Gloria M. and Morales-Muniz, Arturo and Hofreiter, Michael and Pruvost, Melanie}, title = {Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses}, series = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, volume = {370}, journal = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, number = {1660}, publisher = {Royal Society}, address = {London}, issn = {0962-8436}, doi = {10.1098/rstb.2013.0386}, pages = {7}, year = {2015}, abstract = {Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.}, language = {en} } @article{MakowerSchuurmansGrothetal.2015, author = {Makower, A. Katharina and Schuurmans, J. Merijn and Groth, Detlef and Zilliges, Yvonne and Matthijs, Hans C. P. and Dittmann-Th{\"u}nemann, Elke}, title = {Transcriptomics-Aided dissection of the intracellular and extracellular roles of microcystin in microcystis aeruginosa PCC 7806}, series = {Applied and environmental microbiology}, volume = {81}, journal = {Applied and environmental microbiology}, number = {2}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0099-2240}, doi = {10.1128/AEM.02601-14}, pages = {544 -- 554}, year = {2015}, abstract = {Recent studies have provided evidence for both intracellular and extracellular roles of the potent hepatotoxin microcystin (MC) in the bloom-forming cyanobacterium Microcystis. Here, we surveyed transcriptomes of the wild-type strain M. aeruginosa PCC 7806 and the microcystin-deficient Delta mcyB mutant under low light conditions with and without the addition of external MC of the LR variant (MC-LR). Transcriptomic data acquired by microarray and quantitative PCR revealed substantial differences in the relative expression of genes of the central intermediary metabolism, photosynthesis, and energy metabolism. In particular, the data provide evidence for a lower photosystem I (PSI)-to-photosystem II (PSII) ratio and a more pronounced carbon limitation in the microcystin-deficient mutant. Interestingly, only 6\% of the transcriptional differences could be complemented by external microcystin-LR addition. This MC signaling effect was seen exclusively for genes of the secondary metabolism category. The orphan polyketide synthase gene cluster IPF38-51 was specifically downregulated in response to external MC-LR under low light. Our data suggest a hierarchical and light-dependent cross talk of secondary metabolites and support both an intracellular and an extracellular role of MC in Microcystis.}, language = {en} } @article{KoeslinFindekleeRiziBeckeretal.2015, author = {K{\"o}slin-Findeklee, Fabian and Rizi, Vajiheh Safavi and Becker, Martin A. and Parra-Londono, Sebastian and Arif, Muhammad and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd and Kunze, Reinhard and Horst, Walter J.}, title = {Transcriptomic analysis of nitrogen starvation- and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus L.)}, series = {Plant science : an international journal of experimental plant biology}, volume = {233}, journal = {Plant science : an international journal of experimental plant biology}, publisher = {Elsevier}, address = {Clare}, issn = {0168-9452}, doi = {10.1016/j.plantsci.2014.11.018}, pages = {174 -- 185}, year = {2015}, abstract = {High nitrogen (N) efficiency, characterized by high grain yield under N limitation, is an important agricultural trait in Brassica napus L. cultivars related to delayed senescence of older leaves during reproductive growth (a syndrome called stay-green). The aim of this study was thus to identify genes whose expression is specifically altered during N starvation-induced leaf senescence and that can be used as markers to distinguish cultivars at early stages of senescence prior to chlorophyll loss. To this end, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analyzed 4 days after the induction of senescence by either N starvation, leaf shading or detaching. In addition to N metabolism genes, N starvation mostly (and specifically) repressed genes related to photosynthesis, photorespiration and cell-wall structure, while genes related to mitochondrial electron transport and flavonoid biosynthesis were predominately up-regulated. A kinetic study over a period of 12 days with four B. napus cultivars differing in their stay-green characteristics confirmed the cultivar-specific regulation of six genes in agreement with their senescence behavior: the senescence regulator ANAC029, the anthocyanin synthesis-related genes ANS and DFR-like1, the ammonium transporter AMT1:4, the ureide transporter UPSS, and SPS1 involved in sucrose biosynthesis. The identified genes represent markers for the detection of cultivar-specific differences in N starvation-induced leaf senescence and can thus be employed as valuable tools in B. napus breeding. (C) 2015 Elsevier Ireland Ltd. All rights reserved.}, language = {en} } @article{GarapatiXueMunneBoschetal.2015, author = {Garapati, Prashanth and Xue, Gang-Ping and Munne-Bosch, Sergi and Balazadeh, Salma}, title = {Transcription Factor ATAF1 in Arabidopsis Promotes Senescence by Direct Regulation of Key Chloroplast Maintenance and Senescence Transcriptional Cascades}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {168}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00567}, pages = {1122 -- +}, year = {2015}, abstract = {Senescence represents a fundamental process of late leaf development. Transcription factors (TFs) play an important role for expression reprogramming during senescence; however, the gene regulatory networks through which they exert their functions, and their physiological integration, are still largely unknown. Here, we identify the Arabidopsis (Arabidopsis thaliana) abscisic acid (ABA)- and hydrogen peroxide-activated TF Arabidopsis thaliana ACTIVATING FACTOR1 (ATAF1) as a novel upstream regulator of senescence. ATAF1 executes its physiological role by affecting both key chloroplast maintenance and senescence-promoting TFs, namely GOLDEN2-LIKE1 (GLK1) and ORESARA1 (ARABIDOPSIS NAC092), respectively. Notably, while ATAF1 activates ORESARA1, it represses GLK1 expression by directly binding to their promoters, thereby generating a transcriptional output that shifts the physiological balance toward the progression of senescence. We furthermore demonstrate a key role of ATAF1 for ABA- and hydrogen peroxide-induced senescence, in accordance with a direct regulatory effect on ABA homeostasis genes, including NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3 involved in ABA biosynthesis and ABC TRANSPORTER G FAMILY MEMBER40, encoding an ABA transport protein. Thus, ATAF1 serves as a core transcriptional activator of senescence by coupling stress-related signaling with photosynthesis- and senescence-related transcriptional cascades.}, language = {en} } @article{GarapatiFeilLunnetal.2015, author = {Garapati, Prashanth and Feil, Regina and Lunn, John Edward and Van Dijck, Patrick and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd}, title = {Transcription Factor Arabidopsis Activating Factor1 Integrates Carbon Starvation Responses with Trehalose Metabolism}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {1}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00917}, pages = {379 -- 390}, year = {2015}, abstract = {Plants respond to low carbon supply by massive reprogramming of the transcriptome and metabolome. We show here that the carbon starvation-induced NAC (for NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON) transcription factor Arabidopsis (Arabidopsis thaliana) Transcription Activation Factor1 (ATAF1) plays an important role in this physiological process. We identified TREHALASE1, the only trehalase-encoding gene in Arabidopsis, as a direct downstream target of ATAF1. Overexpression of ATAF1 activates TREHALASE1 expression and leads to reduced trehalose-6-phosphate levels and a sugar starvation metabolome. In accordance with changes in expression of starch biosynthesis-and breakdown-related genes, starch levels are generally reduced in ATAF1 overexpressors but elevated in ataf1 knockout plants. At the global transcriptome level, genes affected by ATAF1 are broadly associated with energy and carbon starvation responses. Furthermore, transcriptional responses triggered by ATAF1 largely overlap with expression patterns observed in plants starved for carbon or energy supply. Collectively, our data highlight the existence of a positively acting feedforward loop between ATAF1 expression, which is induced by carbon starvation, and the depletion of cellular carbon/energy pools that is triggered by the transcriptional regulation of downstream gene regulatory networks by ATAF1.}, language = {en} } @article{GorochowskiIgnatovaBovenbergetal.2015, author = {Gorochowski, Thomas E. and Ignatova, Zoya and Bovenberg, Roel A. L. and Roubos, Johannes A.}, title = {Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate}, series = {Nucleic acids research}, volume = {43}, journal = {Nucleic acids research}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gkv199}, pages = {3022 -- 3032}, year = {2015}, abstract = {Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.}, language = {en} } @article{EggersArensFirlaetal.2015, author = {Eggers, Ute and Arens, Michael and Firla, Mario and Wallschl{\"a}ger, Hans-Dieter}, title = {To fledge or not to fledge: factors influencing the number of eggs and the eggs-to-fledglings rate in White Storks Ciconia ciconia in an agricultural environment}, series = {Journal of ornithology}, volume = {156}, journal = {Journal of ornithology}, number = {3}, publisher = {Springer}, address = {New York}, issn = {0021-8375}, doi = {10.1007/s10336-015-1182-9}, pages = {711 -- 723}, year = {2015}, abstract = {Numerous studies have explored the relationship between environmental factors and White Stork Ciconia ciconia reproduction, mainly expressing breeding success as the number of fledglings. Nonetheless, one of the most critical life-history stages in birds falls between egg-laying and fledging, and identifying the factors causing offspring mortality during this period provides valuable knowledge. We quantified the number of laid White Stork eggs and the proportion of eggs that turned into fledglings in an agriculture-dominated region in Eastern Germany. Moreover, we identified the factors among land cover, weather and arrival dates, which influenced these two reproductive measures the most, and analysed the monitored mortality causes. On average, four eggs were laid per nest, and 57.8 \% of the eggs turned into fledglings. The number of eggs laid was best explained by the negative effect of the arrival date of the second stork, while the percentage of eggs that turned into fledglings was more dependent on weather: most important parameters were mean temperature in the fifth and seventh weeks after the assumed breeding start (i.e. around the assumed hatching date), and the number of consecutive days with precipitation when nestlings are assumed to be approximately 3 weeks old. In an agricultural environment, weather effects that potentially disturb food availability might be more important than effects directly affecting the survival of White Stork offspring. The most frequent observed mortality cause, nest fights, furthermore revealed the relevance of intraspecific competition in the study population.}, language = {en} } @phdthesis{Jin2015, author = {Jin, Chenyu}, title = {Theoretical and experimental study of capillary effect on melting}, pages = {97}, year = {2015}, language = {en} } @misc{UestuenBartetzkoBoernke2015, author = {{\"U}st{\"u}n, Suayib and Bartetzko, Verena and B{\"o}rnke, Frederik}, title = {The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid}, series = {Frontiers in plant science}, journal = {Frontiers in plant science}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-406537}, pages = {11}, year = {2015}, abstract = {XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana.}, language = {en} } @article{UestuenBartetzkoBoernke2015, author = {{\"U}st{\"u}n, Suayib and Bartetzko, Verena and B{\"o}rnke, Frederik}, title = {The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid}, series = {Frontiers in plant science}, volume = {6}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2015.00599}, pages = {11}, year = {2015}, abstract = {XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana.}, language = {en} } @article{JohnsonRammKappeletal.2015, author = {Johnson, Kim L. and Ramm, Sascha and Kappel, Christian and Ward, Sally and Leyser, Ottoline and Sakamoto, Tomoaki and Kurata, Tetsuya and Bevan, Michael W. and Lenhard, Michael}, title = {The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131103}, pages = {17}, year = {2015}, abstract = {Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways.}, language = {en} } @phdthesis{Heyneke2015, author = {Heyneke, Elmien}, title = {The role of the calcineurin B-like interacting protein kinase, CIPK14 in regulating plant nutrient metabolism}, school = {Universit{\"a}t Potsdam}, pages = {135}, year = {2015}, language = {en} } @misc{YokoyamaLeimkuehler2015, author = {Yokoyama, Kenichi and Leimk{\"u}hler, Silke}, title = {The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria}, series = {Biochimica et biophysica acta : Molecular cell research}, volume = {1853}, journal = {Biochimica et biophysica acta : Molecular cell research}, number = {6}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-4889}, doi = {10.1016/j.bbamcr.2014.09.021}, pages = {1335 -- 1349}, year = {2015}, abstract = {The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{WeissJeltsch2015, author = {Weiß, Lina and Jeltsch, Florian}, title = {The response of simulated grassland communities to the cessation of grazing}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {303}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2015.02.002}, pages = {1 -- 11}, year = {2015}, abstract = {Changes in land-use are supposed to be among the severest prospective threats to plant diversity worldwide. In semi-natural temperate grasslands, the cessation of traditional land use like livestock grazing is considered to be one of the most important drivers of the diversity loss witnessed within the last decades. Despite of the enormous number of studies on successional pathways following grazing abandonment there is no general pattern of how grassland communities are affected in terms of diversity, trait composition and pace of succession. To gain a comprehensive picture is difficult given the heterogeneity of environments and the time and effort needed for long-term investigations. We here use a proven individual- and trait-based grassland community model to analyze short- and long-term consequences of grazing abandonment under different assumptions of resource availability, pre-abandonment grazing intensity and regional isolation of communities. Grazing abandonment led to a decrease of plant functional type (PFT) diversity in all but two scenarios in the long-term. In short-term we also found an increase or no change in Shannon diversity for several scenarios. With grazing abandonment we overall found an increase in maximum plant mass, clonal integration and longer lateral spread, a decrease in rosette plant types and in stress tolerant plants, as well as an increase in grazing tolerant and a decrease in grazing avoiding plant types. Observed changes were highly dependent on the regional configuration of communities, prevalent resource conditions and land use intensity before abandonment. While long-term changes took around 10-20 years in resource rich conditions, new equilibria established in resource poor conditions only after 30-40 years. Our results confirm the potential threats caused by recent land-use changes and the assumption that oligotrophic communities are more resistant than mesotrophic communities also for long-term abandonment. Moreover, results revealed that species-rich systems are not per se more resistant than species-poor grasslands. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @phdthesis{Zupok2015, author = {Zupok, Arkadiusz}, title = {The psbB-operon is a major locus for plastome-genome incompatibility in Oenothera}, school = {Universit{\"a}t Potsdam}, pages = {108}, year = {2015}, language = {en} } @article{BhaskarMaLendleinetal.2015, author = {Bhaskar, Thanga Bhuvanesh Vijaya and Ma, Nan and Lendlein, Andreas and Roch, Toralf}, title = {The interaction of human macrophage subsets with silicone as a biomaterial}, series = {Clinical hemorheology and microcirculation : blood flow and vessels}, volume = {61}, journal = {Clinical hemorheology and microcirculation : blood flow and vessels}, number = {2}, publisher = {IOS Press}, address = {Amsterdam}, issn = {1386-0291}, doi = {10.3233/CH-151991}, pages = {119 -- 133}, year = {2015}, abstract = {Silicones are widely used as biomaterials for medical devices such as extracorporeal equipments. However, there is often conflicting evidence about their supposed cell-and histocompatibility. Macrophages could mediate silicone-induced adverse responses such as foreign body reaction and fibrous encapsulation. The polarization behaviour of macrophages could determine the clinical outcome after implantation of biomaterials. Induction of classically activated macrophages (CAM) may induce and support uncontrolled inflammatory responses and undesired material degradation. In contrast, polarization into alternatively activated macrophages (AAM) is assumed to support healing processes and implant integration. This study compared the interaction of non-polarized macrophages (M0), CAM, and AAM with commercially available tissue culture polystyrene (TCP) and a medical grade silicone-based biomaterial, regarding the secretion of inflammatory mediators such as cytokines and chemokines. Firstly, by using the Limulus amoebocyte lysate (LAL) test the silicone films were shown to be free of soluble endotoxins, which is the prerequisite to investigate their interaction with primary immune cells. Primary human monocyte-derived macrophages (M0) were polarized into CAM and AAM by addition of suitable differentiation factors. These macrophage subsets were incubated on the materials for 24 hours and their viability and cytokine secretion was assessed. In comparison to TCP, cell adhesion was lower on silicone after 24 hours for all three macrophage subsets. However, compared to TCP, silicone induced higher levels of certain inflammatory and chemotactic cytokines in M0, CAM, and AAM macrophage subsets. Conclusively, it was shown that silicone has the ability to induce a pro-inflammatory state to different magnitudes dependent on the macrophage subsets. This priming of the macrophage phenotype by silicone could explain the incidence of severe foreign body complications observed in vivo.}, language = {en} } @article{CornettiValenteDunningetal.2015, author = {Cornetti, Luca and Valente, Luis M. and Dunning, Luke T. and Quan, Xueping and Black, Richard A. and Hebert, Olivier and Savolainen, Vincent}, title = {The Genome of the "Great Speciator" Provides Insights into Bird Diversification}, series = {Genome biology and evolution}, volume = {7}, journal = {Genome biology and evolution}, number = {9}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1759-6653}, doi = {10.1093/gbe/evv168}, pages = {2680 -- 2691}, year = {2015}, abstract = {Among birds, white-eyes (genusZosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the 'great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation.}, language = {en} } @article{HofreiterPaijmansGoodchildetal.2015, author = {Hofreiter, Michael and Paijmans, Johanna L. A. and Goodchild, Helen and Speller, Camilla F. and Barlow, Axel and Gonz{\´a}lez-Fortes, Gloria M. and Thomas, Jessica A. and Ludwig, Arne and Collins, Matthew J.}, title = {The future of ancient DNA: Technical advances and conceptual shifts}, series = {Bioessays : ideas that push the boundaries}, volume = {37}, journal = {Bioessays : ideas that push the boundaries}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0265-9247}, doi = {10.1002/bies.201400160}, pages = {284 -- 293}, year = {2015}, abstract = {Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.}, language = {en} } @article{SpricigoLeimkuehlerGortonetal.2015, author = {Spricigo, Roberto and Leimk{\"u}hler, Silke and Gorton, Lo and Scheller, Frieder W. and Wollenberger, Ursula}, title = {The Electrically Wired Molybdenum Domain of Human Sulfite Oxidase is Bioelectrocatalytically Active}, series = {European journal of inorganic chemistry : a journal of ChemPubSoc Europe}, journal = {European journal of inorganic chemistry : a journal of ChemPubSoc Europe}, number = {21}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1434-1948}, doi = {10.1002/ejic.201500034}, pages = {3526 -- 3531}, year = {2015}, abstract = {We report electron transfer between the catalytic molybdenum cofactor (Moco) domain of human sulfite oxidase (hSO) and electrodes through a poly(vinylpyridine)-bound [osmium(N,N'-methyl-2,2'-biimidazole)(3)](2+/3+) complex as the electron-transfer mediator. The biocatalyst was immobilized in this low-potential redox polymer on a carbon electrode. Upon the addition of sulfite to the immobilized separate Moco domain, the generation of a significant catalytic current demonstrated that the catalytic center is effectively wired and active. The bioelectrocatalytic current of the wired separate catalytic domain reached 25\% of the signal of the wired full molybdoheme enzyme hSO, in which the heme b(5) is involved in the electron-transfer pathway. This is the first report on a catalytically active wired molybdenum cofactor domain. The formal potential of this electrochemical mediator is between the potentials of the two cofactors of hSO, and as hSO can occupy several conformations in the polymer matrix, it is imaginable that electron transfer from the catalytic site to the electrode through the osmium center occurs for the hSO molecules in which the Moco domain is sufficiently accessible. The observation of catalytic oxidation currents at low potentials is favorable for applications in bioelectronic devices.}, language = {en} } @article{NowakRussoSchlapbachetal.2015, author = {Nowak, Michael D. and Russo, Giancarlo and Schlapbach, Ralph and Cuong Nguyen Huu, and Lenhard, Michael and Conti, Elena}, title = {The draft genome of Primula veris yields insights into the molecular basis of heterostyly}, series = {Genome biology : biology for the post-genomic era}, volume = {16}, journal = {Genome biology : biology for the post-genomic era}, publisher = {BioMed Central}, address = {London}, issn = {1465-6906}, doi = {10.1186/s13059-014-0567-z}, pages = {16}, year = {2015}, abstract = {Background: The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources. Results: We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63\% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers. Conclusions: The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.}, language = {en} } @misc{MendelLeimkuehler2015, author = {Mendel, Ralf R. and Leimk{\"u}hler, Silke}, title = {The biosynthesis of the molybdenum cofactors}, series = {Journal of biological inorganic chemistry}, volume = {20}, journal = {Journal of biological inorganic chemistry}, number = {2}, publisher = {Springer}, address = {New York}, issn = {0949-8257}, doi = {10.1007/s00775-014-1173-y}, pages = {337 -- 347}, year = {2015}, abstract = {The biosynthesis of the molybdenum cofactors (Moco) is an ancient, ubiquitous, and highly conserved pathway leading to the biochemical activation of molybdenum. Moco is the essential component of a group of redox enzymes, which are diverse in terms of their phylogenetic distribution and their architectures, both at the overall level and in their catalytic geometry. A wide variety of transformations are catalyzed by these enzymes at carbon, sulfur and nitrogen atoms, which include the transfer of an oxo group or two electrons to or from the substrate. More than 50 molybdoenzymes were identified to date. In all molybdoenzymes except nitrogenase, molybdenum is coordinated to a dithiolene group on the 6-alkyl side chain of a pterin called molybdopterin (MPT). The biosynthesis of Moco can be divided into three general steps, with a fourth one present only in bacteria and archaea: (1) formation of the cyclic pyranopterin monophosphate, (2) formation of MPT, (3) insertion of molybdenum into molybdopterin to form Moco, and (4) additional modification of Moco in bacteria with the attachment of a nucleotide to the phosphate group of MPT, forming the dinucleotide variant of Moco. This review will focus on the biosynthesis of Moco in bacteria, humans and plants.}, language = {en} } @article{LotkowskaTohgeFernieetal.2015, author = {Lotkowska, Magda E. and Tohge, Takayuki and Fernie, Alisdair R. and Xue, Gang-Ping and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd}, title = {The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00605}, pages = {1862 -- 1880}, year = {2015}, abstract = {MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions.}, language = {en} } @unpublished{MuellerRoeber2015, author = {M{\"u}ller-R{\"o}ber, Bernd}, title = {That "crispert" in Plant Cultivation}, series = {Journal f{\"u}r Verbraucherschutz und Lebensmittelsicherheit = Journal of consumer protection and food safety}, volume = {10}, journal = {Journal f{\"u}r Verbraucherschutz und Lebensmittelsicherheit = Journal of consumer protection and food safety}, number = {4}, publisher = {Springer}, address = {Basel}, issn = {1661-5751}, doi = {10.1007/s00003-015-0985-1}, pages = {305 -- 306}, year = {2015}, language = {de} } @phdthesis{Quast2015, author = {Quast, Robert B.}, title = {Synthesis and site-directed modification of membrane proteins using non-canonical amino acids in a cell-free system derived from cultured Spodoptera frugiperda cells}, school = {Universit{\"a}t Potsdam}, pages = {87}, year = {2015}, language = {en} } @article{DiekmannMuellerHeinkenetal.2015, author = {Diekmann, Martin and M{\"u}ller, Josef and Heinken, Thilo and Dupre, Cecilia}, title = {Survey and statistical analysis of plant reintroductions in Germany}, series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, journal = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, number = {35}, publisher = {Floristisch-Soziologische Arbeitsgemeinschaft}, address = {G{\"o}ttingen}, issn = {0722-494X}, pages = {249 -- 265}, year = {2015}, abstract = {Aim - Plant reintroductions and other forms of targeted species translocations will in the future gain growing importance for nature conservation. In fragmented habitats, species reintroductions offer one of the most efficient tools for preserving or restoring plant diversity. In our study, we have compiled available data about plant reintroduction projects in Germany to answer the following questions: (1) What are the characteristics, habitat preferences and ecological strategies of species considered in plant reintroduction trials, and are these representative of the entire class of threatened species in Germany? (2) Is the judgment of the success or failure of plant reintroductions biased by the choice of species used in the experiments? (3) Do reintroduction efforts focus on those species for which Germany has a particularly high responsibility for conservation? Methods - Information about reintroduction projects in Germany were obtained from published and internet sources as well as unpublished reports. In our search we focused on single-species trials in the framework of scientific or conservation projects. For all threatened species included in our database, we compiled information on their systematics, life form, ecological strategies and habitat preferences. A list of all species being threatened nationally or regionally, comprising both reintroduced and not reintroduced species, served as a reference for statistical analysis. Results - The list of vascular plants used in conservation-oriented reintroductions consisted of 196 taxa. Species of families with large and conspicuous, mostly insect-pollinated flowers (for example, Orchidaceae) were over-represented among the reintroduced species compared to those threatened species not included in reintroduction trials. Species considered were also more often than expected found in semi-natural open habitats such as heathlands and grasslands. Notably, many projects focused on calcareous grasslands, characterized by dry, high-pH and infertile soils. In contrast, species of more near-natural vegetation (alpine and rocky formations, forests) were under-represented. About 25\% of the species that were reintroduced are not threatened on the national scale. Out of 150 species for which Germany has a particularly high responsibility for conservation, only 14 (9.3\%) were reintroduced. For only about 1/3 of all reintroduction attempts, success or failure were documented; whereas the success rate appears to be relatively low in nutrient-poor environments, trials with nutrient-demanding and competitive species were more successful. Conclusions - We conclude that conservation-oriented reintroduction attempts should focus more on species for which the country or a region has a particular high responsibility. Reintroductions, to a larger extent than at present, also need to consider the different chances of success in different habitat types and environments.}, language = {de} } @article{PengUteschYarmanetal.2015, author = {Peng, Lei and Utesch, Tillmann and Yarman, Aysu and Jeoung, Jae-Hun and Steinborn, Silke and Dobbek, Holger and Mroginski, Maria Andrea and Tanne, Johannes and Wollenberger, Ursula and Scheller, Frieder W.}, title = {Surface-Tuned Electron Transfer and Electrocatalysis of Hexameric Tyrosine-Coordinated Heme Protein}, series = {Chemistry - a European journal}, volume = {21}, journal = {Chemistry - a European journal}, number = {20}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0947-6539}, doi = {10.1002/chem.201405932}, pages = {7596 -- 7602}, year = {2015}, abstract = {Molecular modeling, electrochemical methods, and quartz crystal microbalance were used to characterize immobilized hexameric tyrosine-coordinated heme protein (HTHP) on bare carbon or on gold electrodes modified with positively and negatively charged self-assembled monolayers (SAMs), respectively. HTHP binds to the positively charged surface but no direct electron transfer (DET) is found due to the long distance of the active sites from the electrode surfaces. At carboxyl-terminated surfaces, the neutrally charged bottom of HTHP can bind to the SAM. For this "disc" orientation all six hemes are close to the electrode and their direct electron transfer should be efficient. HTHP on all negatively charged SAMs showed a quasi-reversible redox behavior with rate constant k(s) values between 0.93 and 2.86 s(-1) and apparent formal potentials E-app(0)' between -131.1 and -249.1 mV. On the MUA/MU-modified electrode, the maximum surface concentration corresponds to a complete monolayer of the hexameric HTHP in the disc orientation. HTHP electrostatically immobilized on negatively charged SAMs shows electrocatalysis of peroxide reduction and enzymatic oxidation of NADH.}, language = {en} } @article{CoelhoFotiHartmannetal.2015, author = {Coelho, Catarina and Foti, Alessandro and Hartmann, Tobias and Santos-Silva, Teresa and Leimk{\"u}hler, Silke and Romao, Maria Joao}, title = {Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase}, series = {Nature chemical biology}, volume = {11}, journal = {Nature chemical biology}, number = {10}, publisher = {Nature Publ. Group}, address = {New York}, issn = {1552-4450}, doi = {10.1038/NCHEMBIO.1895}, pages = {779 -- +}, year = {2015}, abstract = {Aldehyde oxidase (AOX) is a xanthine oxidase (XO)-related enzyme with emerging importance due to its role in the metabolism of drugs and xenobiotics. We report the first crystal structures of human AOX1, substrate free (2.6-angstrom resolution) and in complex with the substrate phthalazine and the inhibitor thioridazine (2.7-angstrom resolution). Analysis of the protein active site combined with steady-state kinetic studies highlight the unique features, including binding and substrate orientation at the active site, that characterize human AOX1 as an important drug-metabolizing enzyme. Structural analysis of the complex with the noncompetitive inhibitor thioridazine revealed a new, unexpected and fully occupied inhibitor-binding site that is structurally conserved among mammalian AOXs and XO. The new structural insights into the catalytic and inhibition mechanisms of human AOX that we now report will be of great value for the rational analysis of clinical drug interactions involving inhibition of AOX1 and for the prediction and design of AOX-stable putative drugs.}, language = {en} } @article{HahnEngelhardReschkeetal.2015, author = {Hahn, Aaron and Engelhard, Christopher and Reschke, Stefan and Teutloff, Christian and Bittl, Robert and Leimk{\"u}hler, Silke and Risse, Thomas}, title = {Structural Insights into the Incorporation of the Mo Cofactor into Sulfite Oxidase from Site-Directed Spin Labeling}, series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, volume = {54}, journal = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, number = {40}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1433-7851}, doi = {10.1002/anie.201504772}, pages = {11865 -- 11869}, year = {2015}, abstract = {Mononuclear molybdoenzymes catalyze a broad range of redox reactions and are highly conserved in all kingdoms of life. This study addresses the question of how the Mo cofactor (Moco) is incorporated into the apo form of human sulfite oxidase (hSO) by using site-directed spin labeling to determine intramolecular distances in the nanometer range. Comparative measurements of the holo and apo forms of hSO enabled the localization of the corresponding structural changes, which are localized to a short loop (residues 263-273) of the Moco-containing domain. A flap-like movement of the loop provides access to the Moco binding-pocket in the apo form of the protein and explains the earlier studies on the in vitro reconstitution of apo-hSO with Moco. Remarkably, the loop motif can be found in a variety of structurally similar molybdoenzymes among various organisms, thus suggesting a common mechanism of Moco incorporation.}, language = {en} } @article{LiesenjohannLiesenjohannTrebatickaetal.2015, author = {Liesenjohann, Thilo and Liesenjohann, Monique and Trebaticka, Lenka and Sundell, Janne and Haapakoski, Marko and Ylonen, Hannu and Eccard, Jana}, title = {State-dependent foraging: lactating voles adjust their foraging behavior according to the presence of a potential nest predator and season}, series = {Behavioral ecology and sociobiology}, volume = {69}, journal = {Behavioral ecology and sociobiology}, number = {5}, publisher = {Springer}, address = {New York}, issn = {0340-5443}, doi = {10.1007/s00265-015-1889-x}, pages = {747 -- 754}, year = {2015}, abstract = {Parental care often produces a trade-off between meeting nutritional demands of offspring and the duties of offspring protection, especially in altricial species. Parents have to leave their young unattended for foraging trips, during which nestlings are exposed to predators. We investigated how rodent mothers of altricial young respond to risk of nest predation in their foraging decisions. We studied foraging behavior of lactating bank voles (Myodes glareolus) exposed to a nest predator, the common shrew (Sorex araneus). We conducted the experiment in summer (high resource provisioning for both species) and autumn (less food available) in 12 replicates with fully crossed factors "shrew presence" and "season." We monitored use of feeding stations near and far from the nest as measurement of foraging activity and strategic foraging behavior. Vole mothers adapted their strategies to shrew presence and optimized their foraging behavior according to seasonal constraints, resulting in an interaction of treatment and season. In summer, shrew presence reduced food intake from feeding stations, while it enhanced intake in autumn. Shrew presence decreased the number of visited feeding stations in autumn and concentrated mother's foraging efforts to fewer stations. Independent of shrew presence or season, mothers foraged more in patches further away from the nest than near the nest. Results indicate that females are not investing in nest guarding but try to avoid the accumulation of olfactory cues near the nest leading a predator to the young. Additionally, our study shows how foraging strategies and nest attendance are influenced by seasonal food provision.}, language = {en} } @article{KielbSezerKatzetal.2015, author = {Kielb, Patrycja and Sezer, Murat and Katz, Sagie and Lopez, Francesca and Schulz, Christopher and Gorton, Lo and Ludwig, Roland and Wollenberger, Ursula and Zebger, Ingo and Weidinger, Inez M.}, title = {Spectroscopic Observation of Calcium-Induced Reorientation of Cellobiose Dehydrogenase Immobilized on Electrodes and its Effect on Electrocatalytic Activity}, series = {ChemPhysChem : a European journal of chemical physics and physical chemistry}, volume = {16}, journal = {ChemPhysChem : a European journal of chemical physics and physical chemistry}, number = {9}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1439-4235}, doi = {10.1002/cphc.201500112}, pages = {1960 -- 1968}, year = {2015}, abstract = {Cellobiose dehydrogenase catalyzes the oxidation of various carbohydrates and is considered as a possible anode catalyst in biofuel cells. It has been shown that the catalytic performance of this enzyme immobilized on electrodes can be increased by presence of calcium ions. To get insight into the Ca2+-induced changes in the immobilized enzyme we employ surface-enhanced vibrational (SERR and SEIRA) spectroscopy together with electrochemistry. Upon addition of Ca2+ ions electrochemical measurements show a shift of the catalytic turnover signal to more negative potentials while SERR measurements reveal an offset between the potential of heme reduction and catalytic current. Comparing SERR and SEIRA data we propose that binding of Ca2+ to the heme induces protein reorientation in a way that the electron transfer pathway of the catalytic FAD center to the electrode can bypass the heme cofactor, resulting in catalytic activity at more negative potentials.}, language = {en} } @article{VenailGrossOakleyetal.2015, author = {Venail, Patrick and Gross, Kevin and Oakley, Todd H. and Narwani, Anita and Allan, Eric and Flombaum, Pedro and Isbell, Forest and Joshi, Jasmin Radha and Reich, Peter B. and Tilman, David and van Ruijven, Jasper and Cardinale, Bradley J.}, title = {Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies}, series = {Functional ecology : an official journal of the British Ecological Society}, volume = {29}, journal = {Functional ecology : an official journal of the British Ecological Society}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0269-8463}, doi = {10.1111/1365-2435.12432}, pages = {615 -- 626}, year = {2015}, abstract = {Hundreds of experiments have now manipulated species richness (SR) of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity (PD) among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than SR because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. Here, we reanalyse data from 16 experiments that have manipulated plant SR in grassland ecosystems and examined the impact on above-ground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the PD of plants impacts average community biomass production as well as the stability of community biomass production through time. Using four complementary analyses, we show that, after statistically controlling for variation in SR, PD (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for SR, PD was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability. In contrast to the non-significant relationships between PD, biomass and stability, our analyses show that SR per se tends to increase the mean biomass production of plant communities, after controlling for PD. The relationship between SR and temporal variation in community biomass was either positive, non-significant or negative depending on which analysis was used. However, the increases in community biomass with SR, independently of PD, always led to increased stability. These results suggest that PD is no better as a predictor of ecosystem functioning than SR.Synthesis. Our study on grasslands offers a cautionary tale when trying to relate PD to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of SR as a way to maintain productive and stable communities under changing environmental conditions.}, language = {en} } @article{AdamlaIgnatova2015, author = {Adamla, Frauke and Ignatova, Zoya}, title = {Somatic expression of unc-54 and vha-6 mRNAs declines but not pan-neuronal rgef-1 and unc-119 expression in aging Caenorhabditis elegans}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep10692}, pages = {10}, year = {2015}, abstract = {Aging is a highly controlled biological process characterized by a progressive deterioration of various cellular activities. One of several hallmarks of aging describes a link to transcriptional alteration, suggesting that it may impact the steady-state mRNA levels. We analyzed the mRNA steady-state levels of polyCAG-encoding transgenes and endogenous genes under the control of well-characterized promoters for intestinal (vha-6), muscular (unc-54, unc-15) and pan-neuronal (rgef-1, unc-119) expression in the nematode Caenorhabditis elegans. We find that there is not a uniform change in transcriptional profile in aging, but rather a tissue-specific difference in the mRNA levels of these genes. While levels of mRNA in the intestine (vha-6) and muscular (unc-54, unc-15) cells decline with age, pan-neuronal tissue shows more stable mRNA expression (rgef-1, unc-119) which even slightly increases with the age of the animals. Our data on the variations in the mRNA abundance from exemplary cases of endogenous and transgenic gene expression contribute to the emerging evidence for tissue-specific variations in the aging process.}, language = {en} } @article{HeinzeWernerWeberetal.2015, author = {Heinze, Johannes and Werner, Tony and Weber, Ewald and Rillig, Matthias C. and Joshi, Jasmin Radha}, title = {Soil biota effects on local abundances of three grass species along a land-use gradient}, series = {Oecologia}, volume = {179}, journal = {Oecologia}, number = {1}, publisher = {Springer}, address = {New York}, issn = {0029-8549}, doi = {10.1007/s00442-015-3336-0}, pages = {249 -- 259}, year = {2015}, abstract = {Biotic plant-soil interactions and land-use intensity are known to affect plant individual fitness as well as competitiveness and therefore plant-species abundances in communities. Therefore, a link between soil biota and land-use intensity on local abundance of plant species in grasslands can be expected. In two greenhouse experiments, we investigated the effects of soil biota from grassland sites differing in land-use intensity on three grass species that vary in local abundances along this land-use gradient. We were interested in those soil-biota effects that are associated with land-use intensity, and whether these effects act directly or indirectly. Therefore, we grew the three plant species in two separate experiments as single individuals and in mixtures and compared their performance. As single plants, all three grasses showed a similar performance with and without soil biota. In contrast, in mixtures growth of the species in response to the presence or absence of soil biota differed. This resulted in different soil-biota effects that tend to correspond with patterns of species-specific abundances in the field for two of the three species tested. Our results highlight the importance of indirect interactions between plants and soil microorganisms and suggest that combined effects of soil biota and plant-plant interactions are involved in structuring plant communities. In conclusion, our experiments suggest that soil biota may have the potential to alter effects of plant-plant interactions and therefore influence plant-species abundances and diversity in grasslands.}, language = {en} } @article{CzesnickLenhard2015, author = {Czesnick, Hj{\"o}rdis and Lenhard, Michael}, title = {Size Control in Plants-Lessons from Leaves and Flowers}, series = {Cold Spring Harbor perspectives in biology}, volume = {7}, journal = {Cold Spring Harbor perspectives in biology}, number = {8}, publisher = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, NY}, issn = {1943-0264}, doi = {10.1101/cshperspect.a019190}, pages = {16}, year = {2015}, abstract = {To achieve optimal functionality, plant organs like leaves and petals have to grow to a certain size. Beginning with a limited number of undifferentiated cells, the final size of an organ is attained by a complex interplay of cell proliferation and subsequent cell expansion. Regulatory mechanisms that integrate intrinsic growth signals and environmental cues are required to enable optimal leaf and flower development. This review focuses on plant-specific principles of growth reaching from the cellular to the organ level. The currently known genetic pathways underlying these principles are summarized and network connections are highlighted. Putative non-cell autonomously acting mechanisms that might coordinate plant-cell growth are discussed.}, language = {en} } @article{ReinhardKupfer2015, author = {Reinhard, Sandy and Kupfer, Alexander}, title = {Sexual dimorphism in a French population of the marbled newt, Triturus marmoratus (Urodela: Salamandridae)}, series = {Salamandra : German journal of herpetology}, volume = {51}, journal = {Salamandra : German journal of herpetology}, number = {2}, publisher = {Deutsche Gesellschaft f{\"u}r Herpetologie und Terrarienkunde}, address = {Darmstadt}, issn = {0036-3375}, pages = {121 -- 128}, year = {2015}, abstract = {Amphibians have developed a large set of life-history strategies and demonstrate an impressive diversity of reproductive patterns compared to other vertebrates. Various selection pressures impact on males and females and see them produce different degrees of sexual dimorphism in order to maximise their reproductive success. In an extended morphometric analysis that included 27 body-and head-related characters, we studied the pattern of sexual dimorphism of a French population of the marbled newt, Triturus marmoratus. We analysed the characters by employing GLM methods (ANCOVA) and found 16 of them to be dimorphic between the sexes. In general, females differ in head-body size, such as snout-vent length, but males rather in shape or body proportions (e.g., limb proportions). The various expressions of sexual size dimorphism among large-bodied marbled newts and allies demonstrate that more than one evolutionary model works simultaneously on different traits.}, language = {en} } @article{ReinhardRennerKupfer2015, author = {Reinhard, Sandy and Renner, Sandra and Kupfer, Alexander}, title = {Sexual dimorphism and age of Mediterranean salamanders}, series = {Zoology}, volume = {118}, journal = {Zoology}, number = {1}, publisher = {Elsevier}, address = {Jena}, issn = {0944-2006}, doi = {10.1016/j.zool.2014.08.002}, pages = {19 -- 26}, year = {2015}, abstract = {We analysed sexual size dimorphism (SSD) for two Mediterranean species of the "true" salamander clade possessing distinct life histories (Salamandra algira and Mertensiella caucasica) and equilibrated the morphometric approach to individual age by using skeletochronology. For species that have a short breeding season and live at high altitudes, such as Mediterranean amphibians, the fecundity advantage hypothesis predicts female-biased SSD to maximise reproductive success. Our results showed no SSD in either species; however, morphometric data indicated a male-biased dimorphism in limb (arm and leg) dimensions in both species when compared to body size. Limb dimorphisms are likely related to the particular mating system, which involves an amplexus during spermatophore transfer. Arm length appeared sexually dimorphic during ontogeny both in viviparous Salamandra algira and oviparous Mertensiella caucasica. A review on SSD indicated monomorphy of body size as a common lineage-specific pattern among the "true" salamander clade, but also the common presence of other traits such as sexually dimorphic limb proportions. (C) 2014 Elsevier GmbH. All rights reserved.}, language = {en} } @misc{VogtSchippers2015, author = {Vogt, Julia H. M. and Schippers, Jos H. M.}, title = {Setting the PAS, the role of circadian PAS domain proteins during environmental adaptation in plants}, series = {Frontiers in plant science}, volume = {6}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2015.00513}, pages = {10}, year = {2015}, abstract = {The per-ARNT-sim (PAS) domain represents an ancient protein module that can be found across all kingdoms of life. The domain functions as a sensing unit for a diverse array of signals, including molecular oxygen, small metabolites, and light. In plants, several PAS domain-containing proteins form an integral part of the circadian clock and regulate responses to environmental change. Moreover, these proteins function in pathways that control development and plant stress adaptation responses. Here, we discuss the role of PAS domain-containing proteins in anticipation, and adaptation to environmental changes in plants.}, language = {en} } @article{SchwarteWegnerHavensteinetal.2015, author = {Schwarte, Sandra and Wegner, Fanny and Havenstein, Katja and Groth, Detlef and Steup, Martin and Tiedemann, Ralph}, title = {Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana}, series = {Plant molecular biology : an international journal of fundamental research and genetic engineering}, volume = {87}, journal = {Plant molecular biology : an international journal of fundamental research and genetic engineering}, number = {4-5}, publisher = {Springer}, address = {Dordrecht}, issn = {0167-4412}, doi = {10.1007/s11103-015-0293-2}, pages = {489 -- 519}, year = {2015}, abstract = {Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts.}, language = {en} } @phdthesis{Thieme2015, author = {Thieme, Christoph J.}, title = {Sequence and structure determinants of microRNA maturation and the elucidation of RNA transport in plants}, school = {Universit{\"a}t Potsdam}, pages = {137}, year = {2015}, language = {en} } @article{AlbertAuffretCosynsetal.2015, author = {Albert, Aurelie and Auffret, Alistair G. and Cosyns, Eric and Cousins, Sara A. O. and Eichberg, Carsten and Eycott, Amy E. and Heinken, Thilo and Hoffmann, Maurice and Jaroszewicz, Bogdan and Malo, Juan E. and Marell, Anders and Mouissie, Maarten and Pakeman, Robin J. and Picard, Melanie and Plue, Jan and Poschlod, Peter and Provoost, Sam and Schulze, Kiowa Alraune and Baltzinger, Christophe}, title = {Seed dispersal by ungulates as an ecological filter: a trait-based meta-analysis}, series = {Oikos}, volume = {124}, journal = {Oikos}, number = {9}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.02512}, pages = {1109 -- 1120}, year = {2015}, abstract = {Plant communities are often dispersal-limited and zoochory can be an efficient mechanism for plants to colonize new patches of potentially suitable habitat. We predicted that seed dispersal by ungulates acts as an ecological filter - which differentially affects individuals according to their characteristics and shapes species assemblages - and that the filter varies according to the dispersal mechanism (endozoochory, fur-epizoochory and hoof-epizoochory). We conducted two-step individual participant data meta-analyses of 52 studies on plant dispersal by ungulates in fragmented landscapes, comparing eight plant traits and two habitat indicators between dispersed and non-dispersed plants. We found that ungulates dispersed at least 44\% of the available plant species. Moreover, some plant traits and habitat indicators increased the likelihood for plant of being dispersed. Persistent or nitrophilous plant species from open habitats or bearing dry or elongated diaspores were more likely to be dispersed by ungulates, whatever the dispersal mechanism. In addition, endozoochory was more likely for diaspores bearing elongated appendages whereas epizoochory was more likely for diaspores released relatively high in vegetation. Hoof-epizoochory was more likely for light diaspores without hooked appendages. Fur-epizoochory was more likely for diaspores with appendages, particularly elongated or hooked ones. We thus observed a gradient of filtering effect among the three dispersal mechanisms. Endozoochory had an effect of rather weak intensity (impacting six plant characteristics with variations between ungulate-dispersed and non-dispersed plant species mostly below 25\%), whereas hoof-epizoochory had a stronger effect (eight characteristics included five ones with above 75\% variation), and fur-epizoochory an even stronger one (nine characteristics included six ones with above 75\% variation). Our results demonstrate that seed dispersal by ungulates is an ecological filter whose intensity varies according to the dispersal mechanism considered. Ungulates can thus play a key role in plant community dynamics and have implications for plant spatial distribution patterns at multiple scales.}, language = {en} } @article{DelCampoBartholomaeusFedyuninetal.2015, author = {Del Campo, Cristian and Bartholom{\"a}us, Alexander and Fedyunin, Ivan and Ignatova, Zoya}, title = {Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function}, series = {PLoS Genetics : a peer-reviewed, open-access journal}, volume = {11}, journal = {PLoS Genetics : a peer-reviewed, open-access journal}, number = {10}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005613}, pages = {23}, year = {2015}, abstract = {Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.}, language = {en} } @article{CisekTokarzSteupetal.2015, author = {Cisek, Richard and Tokarz, Danielle and Steup, Martin and Tetlow, Ian J. and Emes, Michael J. and Hebelstrup, Kim H. and Blennow, Andreas and Barzda, Virginijus}, title = {Second harmonic generation microscopy investigation of the crystalline ultrastructure of three barley starch lines affected by hydration}, series = {Biomedical optics express}, volume = {6}, journal = {Biomedical optics express}, number = {10}, publisher = {Optical Society of America}, address = {Washington}, issn = {2156-7085}, doi = {10.1364/BOE.6.003694}, pages = {3694 -- 3700}, year = {2015}, abstract = {Second harmonic generation (SHG) microscopy is employed to study changes in crystalline organization due to altered gene expression and hydration in barley starch granules. SHG intensity and susceptibility ratio values (R'(SHG)) are obtained using reduced Stokes-Mueller polarimetric microscopy. The maximum R'(SHG) values occur at moderate moisture indicating the narrowest orientation distribution of nonlinear dipoles from the cylindrical axis of glucan helices. The maximum SHG intensity occurs at the highest moisture and amylopectin content. These results support the hypothesis that SHG is caused by ordered hydrogen and hydroxyl bond networks which increase with hydration of starch granules. (C) 2015 Optical Society of America}, language = {en} } @article{WangTohgeIvakovetal.2015, author = {Wang, Ting and Tohge, Takayuki and Ivakov, Alexander and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and Mutwil, Marek and Schippers, Jos H. M. and Persson, Staffan}, title = {Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00962}, pages = {1027 -- +}, year = {2015}, abstract = {Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance.}, language = {en} } @article{PietraLangGrebe2015, author = {Pietra, Stefano and Lang, Patricia and Grebe, Markus}, title = {SABRE is required for stabilization of root hair patterning in Arabidopsis thaliana}, series = {Physiologia Plantarum}, volume = {153}, journal = {Physiologia Plantarum}, number = {3}, doi = {DOI: 10.1111/ppl.12257}, pages = {440 -- 453}, year = {2015}, abstract = {Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning.}, language = {en} } @article{PietraLangGrebe2015, author = {Pietra, Stefano and Lang, Patricia and Grebe, Markus}, title = {SABRE is required for stabilization of root hair patterning in Arabidopsis thaliana}, series = {Physiologia plantarum}, volume = {153}, journal = {Physiologia plantarum}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0031-9317}, doi = {10.1111/ppl.12257}, pages = {440 -- 453}, year = {2015}, abstract = {Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning.}, language = {en} } @misc{PetrovHilleMuellerRoeberetal.2015, author = {Petrov, Veselin and Hille, Jacques and M{\"u}ller-R{\"o}ber, Bernd and Gechev, Tsanko S.}, title = {ROS-mediated abiotic stress-induced programmed cell death in plants}, series = {Frontiers in plant science}, volume = {6}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2015.00069}, pages = {16}, year = {2015}, abstract = {During the course of their ontogenesis plants are continuously exposed to a large variety of abiotic stress factors which can damage tissues and jeopardize the survival of the organism unless properly countered. While animals can simply escape and thus evade stressors, plants as sessile organisms have developed complex strategies to withstand them. When the intensity of a detrimental factor is high, one of the defense programs employed by plants is the induction of programmed cell death (PCD). This is an active, genetically controlled process which is initiated to isolate and remove damaged tissues thereby ensuring the survival of the organism. The mechanism of PCD induction usually includes an increase in the levels of reactive oxygen species (ROS) which are utilized as mediators of the stress signal. Abiotic stress-induced PCD is not only a process of fundamental biological importance, but also of considerable interest to agricultural practice as it has the potential to significantly influence crop yield. Therefore, numerous scientific enterprises have focused on elucidating the mechanisms leading to and controlling PCD in response to adverse conditions in plants. This knowledge may help develop novel strategies to obtain more resilient crop varieties with improved tolerance and enhanced productivity. The aim of the present review is to summarize the recent advances in research on ROS-induced PCD related to abiotic stress and the role of the organelles in the process.}, language = {en} }