TY  - JOUR
A1  - Staab, Paul R.
A1  - Walossek, Jörg
A1  - Nellessen, David
A1  - Grünberg, Raik
A1  - Arndt, Katja Maren
A1  - Müller, Kristian M.
T1  - SynBioWave : a real-time communication platform for molecular and synthetic biology
N2  - Synthetic Biology is advanced by many users and relies on the assembly of genetic elements to devices, systems and finally genomes. SynBioWave is a software suite that enables multiple distributed users to analyze and construct genetic parts in real-time collaboration. It builds on Google Wave and provides an extensible robot-robot-user communication framework, a menu driven user interface, biological data handling including DAS and an internal database communication. We demonstrate its use by implementing robots for gene-data retrieval, manipulation and display. The initial development of SynBioWave demonstrates the power of the underlying Google Wave protocol for Synthetic Biology and lays the foundation for continuous and user-friendly extensions. Specialized wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico.
Y1  - 2010
UR  - http://bioinformatics.oxfordjournals.org/
U6  - https://doi.org/10.1093/bioinformatics/btq518
SN  - 1367-4803
ER  - 
TY  - JOUR
A1  - Chipman, Ariel D.
A1  - Ferrier, David E. K.
A1  - Brena, Carlo
A1  - Qu, Jiaxin
A1  - Hughes, Daniel S. T.
A1  - Schroeder, Reinhard
A1  - Torres-Oliva, Montserrat
A1  - Znassi, Nadia
A1  - Jiang, Huaiyang
A1  - Almeida, Francisca C.
A1  - Alonso, Claudio R.
A1  - Apostolou, Zivkos
A1  - Aqrawi, Peshtewani
A1  - Arthur, Wallace
A1  - Barna, Jennifer C. J.
A1  - Blankenburg, Kerstin P.
A1  - Brites, Daniela
A1  - Capella-Gutierrez, Salvador
A1  - Coyle, Marcus
A1  - Dearden, Peter K.
A1  - Du Pasquier, Louis
A1  - Duncan, Elizabeth J.
A1  - Ebert, Dieter
A1  - Eibner, Cornelius
A1  - Erikson, Galina
A1  - Evans, Peter D.
A1  - Extavour, Cassandra G.
A1  - Francisco, Liezl
A1  - Gabaldon, Toni
A1  - Gillis, William J.
A1  - Goodwin-Horn, Elizabeth A.
A1  - Green, Jack E.
A1  - Griffiths-Jones, Sam
A1  - Grimmelikhuijzen, Cornelis J. P.
A1  - Gubbala, Sai
A1  - Guigo, Roderic
A1  - Han, Yi
A1  - Hauser, Frank
A1  - Havlak, Paul
A1  - Hayden, Luke
A1  - Helbing, Sophie
A1  - Holder, Michael
A1  - Hui, Jerome H. L.
A1  - Hunn, Julia P.
A1  - Hunnekuhl, Vera S.
A1  - Jackson, LaRonda
A1  - Javaid, Mehwish
A1  - Jhangiani, Shalini N.
A1  - Jiggins, Francis M.
A1  - Jones, Tamsin E.
A1  - Kaiser, Tobias S.
A1  - Kalra, Divya
A1  - Kenny, Nathan J.
A1  - Korchina, Viktoriya
A1  - Kovar, Christie L.
A1  - Kraus, F. Bernhard
A1  - Lapraz, Francois
A1  - Lee, Sandra L.
A1  - Lv, Jie
A1  - Mandapat, Christigale
A1  - Manning, Gerard
A1  - Mariotti, Marco
A1  - Mata, Robert
A1  - Mathew, Tittu
A1  - Neumann, Tobias
A1  - Newsham, Irene
A1  - Ngo, Dinh N.
A1  - Ninova, Maria
A1  - Okwuonu, Geoffrey
A1  - Ongeri, Fiona
A1  - Palmer, William J.
A1  - Patil, Shobha
A1  - Patraquim, Pedro
A1  - Pham, Christopher
A1  - Pu, Ling-Ling
A1  - Putman, Nicholas H.
A1  - Rabouille, Catherine
A1  - Ramos, Olivia Mendivil
A1  - Rhodes, Adelaide C.
A1  - Robertson, Helen E.
A1  - Robertson, Hugh M.
A1  - Ronshaugen, Matthew
A1  - Rozas, Julio
A1  - Saada, Nehad
A1  - Sanchez-Gracia, Alejandro
A1  - Scherer, Steven E.
A1  - Schurko, Andrew M.
A1  - Siggens, Kenneth W.
A1  - Simmons, DeNard
A1  - Stief, Anna
A1  - Stolle, Eckart
A1  - Telford, Maximilian J.
A1  - Tessmar-Raible, Kristin
A1  - Thornton, Rebecca
A1  - van der Zee, Maurijn
A1  - von Haeseler, Arndt
A1  - Williams, James M.
A1  - Willis, Judith H.
A1  - Wu, Yuanqing
A1  - Zou, Xiaoyan
A1  - Lawson, Daniel
A1  - Muzny, Donna M.
A1  - Worley, Kim C.
A1  - Gibbs, Richard A.
A1  - Akam, Michael
A1  - Richards, Stephen
T1  - The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima
JF  - PLoS biology
N2  - Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Y1  - 2014
U6  - https://doi.org/10.1371/journal.pbio.1002005
SN  - 1545-7885
VL  - 12
IS  - 11
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Soliveres, Santiago
A1  - van der Plas, Fons
A1  - Manning, Peter
A1  - Prati, Daniel
A1  - Gossner, Martin M.
A1  - Renner, Swen C.
A1  - Alt, Fabian
A1  - Arndt, Hartmut
A1  - Baumgartner, Vanessa
A1  - Binkenstein, Julia
A1  - Birkhofer, Klaus
A1  - Blaser, Stefan
A1  - Blüthgen, Nico
A1  - Boch, Steffen
A1  - Böhm, Stefan
A1  - Börschig, Carmen
A1  - Buscot, Francois
A1  - Diekötter, Tim
A1  - Heinze, Johannes
A1  - Hölzel, Norbert
A1  - Jung, Kirsten
A1  - Klaus, Valentin H.
A1  - Kleinebecker, Till
A1  - Klemmer, Sandra
A1  - Krauss, Jochen
A1  - Lange, Markus
A1  - Morris, E. Kathryn
A1  - Müller, Jörg
A1  - Oelmann, Yvonne
A1  - Overmann, Jörg
A1  - Pasalic, Esther
A1  - Rillig, Matthias C.
A1  - Schaefer, H. Martin
A1  - Schloter, Michael
A1  - Schmitt, Barbara
A1  - Schöning, Ingo
A1  - Schrumpf, Marion
A1  - Sikorski, Johannes
A1  - Socher, Stephanie A.
A1  - Solly, Emily F.
A1  - Sonnemann, Ilja
A1  - Sorkau, Elisabeth
A1  - Steckel, Juliane
A1  - Steffan-Dewenter, Ingolf
A1  - Stempfhuber, Barbara
A1  - Tschapka, Marco
A1  - Türke, Manfred
A1  - Venter, Paul C.
A1  - Weiner, Christiane N.
A1  - Weisser, Wolfgang W.
A1  - Werner, Michael
A1  - Westphal, Catrin
A1  - Wilcke, Wolfgang
A1  - Wolters, Volkmar
A1  - Wubet, Tesfaye
A1  - Wurst, Susanne
A1  - Fischer, Markus
A1  - Allan, Eric
T1  - Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality
JF  - Nature : the international weekly journal of science
Y1  - 2016
U6  - https://doi.org/10.1038/nature19092
SN  - 0028-0836
SN  - 1476-4687
VL  - 536
SP  - 456
EP  - +
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Christ, Nicolas
A1  - Immenhauser, Adrian
A1  - Amour, Frederic
A1  - Mutti, Maria
A1  - Preston, Rosalind
A1  - Whitaker, Fiona F.
A1  - Peterhänsel, Arndt
A1  - Egenhoff, Sven O.
A1  - Dunn, Paul A.
A1  - Agar, Susan M.
T1  - Triassic Latemar cycle tops - Subaerial exposure of platform carbonates under tropical arid climate
JF  - Sedimentary geology : international journal of applied and regional sedimentology
N2  - The Triassic Latemar platform in the Dolomites, Italy, is the site of several ongoing controversies. Perhaps the most interesting debate focuses on apparent cyclic deposition within the Latemar platform, whose nature and duration are still open to debate. Further disagreement concerns the lack of meteoric diagenesis-related isotope shifts at cycle tops that bear circumstantial petrographic evidence for subaerial emergence. Here, an evaluation of the nature of Latemar cycle tops is presented combining evidence from previous work and new field, petrographic and geochemical data. Cycle tops are ranked according to increasing exposure duration and spatial extent: type I surfaces lacking unequivocal evidence of prolonged supratidal conditions; type II dolomite caps formed in warm, evaporitic, intertidal lagoonal waters followed by exposure of perhaps intermediate duration; type III clastic-rich, red calcareous horizons with some showing platform-wide extent, representing prolonged supratidal conditions, and type IV discontinuities in tepee belts, genetically related to type II and III surfaces, but likely representing shorter-lived exposure stages. Petrographic and geochemical criteria indicate that most diagenesis occurred in the shallow marine and burial domain whilst an extensive meteoric overprint of cycle tops is lacking. This is underlined by the scarcity of meteoric diagenetic fabrics such as gravitational cements that, where present, are here interpreted as marine-vadose in origin. The scarcity of carbon and oxygen isotope signatures commonly assigned to subaerial exposure stages is best explained in the context of mid-Triassic climate. The low latitude, tropical but arid setting of the Latemar, situated in the western extension of the Tethys ocean, its isolation from nearby continental areas and overall short-term emergence episodes are in agreement with a limited degree of meteoric alteration of most cycle tops. High amounts of aeolian clastic material beneath some cycle tops, along with high Fe and Mn elemental abundances argue for intermittent subaerial conditions. This study proposes an enhancement of the classical Allan and Matthews (1982) isotope model for subaerial exposure under strongly arid climates. As the subaerial exposure nature of Latemar cycle tops, and therefore eustasy as the cause for cyclicity, have been previously challenged due to the lack of meteoric-induced isotopic signatures, the outcome of this study is of significance for the ongoing Latemar stratigraphic controversy.
KW  - Triassic
KW  - Latemar
KW  - Subaerial exposure
KW  - Carbonate platforms
KW  - Carbon and oxygen stable isotopes
KW  - Diagenesis
Y1  - 2012
U6  - https://doi.org/10.1016/j.sedgeo.2012.02.008
SN  - 0037-0738
VL  - 265
IS  - 28
SP  - 1
EP  - 29
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Gossner, Martin M.
A1  - Lewinsohn, Thomas M.
A1  - Kahl, Tiemo
A1  - Grassein, Fabrice
A1  - Boch, Steffen
A1  - Prati, Daniel
A1  - Birkhofer, Klaus
A1  - Renner, Swen C.
A1  - Sikorski, Johannes
A1  - Wubet, Tesfaye
A1  - Arndt, Hartmut
A1  - Baumgartner, Vanessa
A1  - Blaser, Stefan
A1  - Blüthgen, Nico
A1  - Börschig, Carmen
A1  - Buscot, Francois
A1  - Diekötter, Tim
A1  - Jorge, Leonardo Re
A1  - Jung, Kirsten
A1  - Keyel, Alexander C.
A1  - Klein, Alexandra-Maria
A1  - Klemmer, Sandra
A1  - Krauss, Jochen
A1  - Lange, Markus
A1  - Müller, Jörg
A1  - Overmann, Jörg
A1  - Pasalic, Esther
A1  - Penone, Caterina
A1  - Perovic, David J.
A1  - Purschke, Oliver
A1  - Schall, Peter
A1  - Socher, Stephanie A.
A1  - Sonnemann, Ilja
A1  - Tschapka, Marco
A1  - Tscharntke, Teja
A1  - Türke, Manfred
A1  - Venter, Paul Christiaan
A1  - Weiner, Christiane N.
A1  - Werner, Michael
A1  - Wolters, Volkmar
A1  - Wurst, Susanne
A1  - Westphal, Catrin
A1  - Fischer, Markus
A1  - Weisser, Wolfgang W.
A1  - Allan, Eric
T1  - Land-use intensification causes multitrophic homogenization of grassland communities
JF  - Nature : the international weekly journal of science
N2  - Land-use intensification is a major driver of biodiversity loss(1,2). Alongside reductions in local species diversity, biotic homogenization at larger spatial scales is of great concern for conservation. Biotic homogenization means a decrease in beta-diversity (the compositional dissimilarity between sites). Most studies have investigated losses in local (alpha)-diversity(1,3) and neglected biodiversity loss at larger spatial scales. Studies addressing beta-diversity have focused on single or a few organism groups (for example, ref. 4), and it is thus unknown whether land-use intensification homogenizes communities at different trophic levels, above-and belowground. Here we show that even moderate increases in local land-use intensity (LUI) cause biotic homogenization across microbial, plant and animal groups, both above- and belowground, and that this is largely independent of changes in alpha-diversity. We analysed a unique grassland biodiversity dataset, with abundances of more than 4,000 species belonging to 12 trophic groups. LUI, and, in particular, high mowing intensity, had consistent effects on beta-diversity across groups, causing a homogenization of soil microbial, fungal pathogen, plant and arthropod communities. These effects were nonlinear and the strongest declines in beta-diversity occurred in the transition from extensively managed to intermediate intensity grassland. LUI tended to reduce local alpha-diversity in aboveground groups, whereas the alpha-diversity increased in belowground groups. Correlations between the alpha-diversity of different groups, particularly between plants and their consumers, became weaker at high LUI. This suggests a loss of specialist species and is further evidence for biotic homogenization. The consistently negative effects of LUI on landscape-scale biodiversity underscore the high value of extensively managed grasslands for conserving multitrophic biodiversity and ecosystem service provision. Indeed, biotic homogenization rather than local diversity loss could prove to be the most substantial consequence of land-use intensification.
Y1  - 2016
U6  - https://doi.org/10.1038/nature20575
SN  - 0028-0836
SN  - 1476-4687
VL  - 540
SP  - 266
EP  - +
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Soliveres, Santiago
A1  - Manning, Peter
A1  - Prati, Daniel
A1  - Gossner, Martin M.
A1  - Alt, Fabian
A1  - Arndt, Hartmut
A1  - Baumgartner, Vanessa
A1  - Binkenstein, Julia
A1  - Birkhofer, Klaus
A1  - Blaser, Stefan
A1  - Bluethgen, Nico
A1  - Boch, Steffen
A1  - Boehm, Stefan
A1  - Boerschig, Carmen
A1  - Buscot, Francois
A1  - Diekoetter, Tim
A1  - Heinze, Johannes
A1  - Hoelzel, Norbert
A1  - Jung, Kirsten
A1  - Klaus, Valentin H.
A1  - Klein, Alexandra-Maria
A1  - Kleinebecker, Till
A1  - Klemmer, Sandra
A1  - Krauss, Jochen
A1  - Lange, Markus
A1  - Morris, E. Kathryn
A1  - Mueller, Joerg
A1  - Oelmann, Yvonne
A1  - Overmann, Jörg
A1  - Pasalic, Esther
A1  - Renner, Swen C.
A1  - Rillig, Matthias C.
A1  - Schaefer, H. Martin
A1  - Schloter, Michael
A1  - Schmitt, Barbara
A1  - Schoening, Ingo
A1  - Schrumpf, Marion
A1  - Sikorski, Johannes
A1  - Socher, Stephanie A.
A1  - Solly, Emily F.
A1  - Sonnemann, Ilja
A1  - Sorkau, Elisabeth
A1  - Steckel, Juliane
A1  - Steffan-Dewenter, Ingolf
A1  - Stempfhuber, Barbara
A1  - Tschapka, Marco
A1  - Tuerke, Manfred
A1  - Venter, Paul
A1  - Weiner, Christiane N.
A1  - Weisser, Wolfgang W.
A1  - Werner, Michael
A1  - Westphal, Catrin
A1  - Wilcke, Wolfgang
A1  - Wolters, Volkmar
A1  - Wubet, Tesfaye
A1  - Wurst, Susanne
A1  - Fischer, Markus
A1  - Allan, Eric
T1  - Locally rare species influence grassland ecosystem multifunctionality
JF  - Philosophical transactions of the Royal Society of London : B, Biological sciences
N2  - Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities.
KW  - biodiversity
KW  - common species
KW  - ecosystem function
KW  - identity hypothesis
KW  - land use
KW  - multitrophic
Y1  - 2016
U6  - https://doi.org/10.1098/rstb.2015.0269
SN  - 0962-8436
SN  - 1471-2970
VL  - 371
SP  - 3175
EP  - 3185
PB  - Royal Society
CY  - London
ER  - 
TY  - GEN
A1  - Perscheid, Cindy
A1  - Faber, Lukas
A1  - Kraus, Milena
A1  - Arndt, Paul
A1  - Janke, Michael
A1  - Rehfeldt, Sebastian
A1  - Schubotz, Antje
A1  - Slosarek, Tamara
A1  - Uflacker, Matthias
T1  - A tissue-aware gene selection approach for analyzing multi-tissue gene expression data
T2  - 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
N2  - High-throughput RNA sequencing (RNAseq) produces large data sets containing expression levels of thousands of genes. The analysis of RNAseq data leads to a better understanding of gene functions and interactions, which eventually helps to study diseases like cancer and develop effective treatments. Large-scale RNAseq expression studies on cancer comprise samples from multiple cancer types and aim to identify their distinct molecular characteristics. Analyzing samples from different cancer types implies analyzing samples from different tissue origin. Such multi-tissue RNAseq data sets require a meaningful analysis that accounts for the inherent tissue-related bias: The identified characteristics must not originate from the differences in tissue types, but from the actual differences in cancer types. However, current analysis procedures do not incorporate that aspect. As a result, we propose to integrate a tissue-awareness into the analysis of multi-tissue RNAseq data. We introduce an extension for gene selection that provides a tissue-wise context for every gene and can be flexibly combined with any existing gene selection approach. We suggest to expand conventional evaluation by additional metrics that are sensitive to the tissue-related bias. Evaluations show that especially low complexity gene selection approaches profit from introducing tissue-awareness.
KW  - RNAseq
KW  - gene selection
KW  - tissue-awareness
KW  - TCGA
KW  - GTEx
Y1  - 2018
SN  - 978-1-5386-5488-0
U6  - https://doi.org/10.1109/BIBM.2018.8621189
SN  - 2156-1125
SN  - 2156-1133
SP  - 2159
EP  - 2166
PB  - IEEE
CY  - New York
ER  -