TY - JOUR A1 - Hilson, Pierre A1 - Allemeersch, Joke A1 - Altmann, Thomas A1 - Aubourg, Sebastien A1 - Avon, Alexandra A1 - Beynon, Jim A1 - Bhalerao, Rishikesh P. A1 - Bitton, Frederique A1 - Caboche, Michel A1 - Cannoot, Bernard A1 - Chardakov, Vasil A1 - Cognet-Holliger, Cecile A1 - Colot, Vincent A1 - Crowe, Mark A1 - Darimont, Caroline A1 - Durinck, Steffen A1 - Eickhoff, Holger A1 - deLongevialle, Andeol Falcon A1 - Farmer, Edward E. A1 - Grant, Murray A1 - Kuiper, Martin T. R. A1 - Lehrach, Hans A1 - Leon, Celine A1 - Leyva, Antonio A1 - Lundeberg, Joakim A1 - Lurin, Claire A1 - Moreau, Yves T1 - Versatile gene-specific sequence tags for arabidopsis functional genomics : transcript profiling and reserve genetics applications N2 - Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics Y1 - 2004 ER - TY - JOUR A1 - Altmann, Thomas A1 - Brandt, Stephan Peter A1 - Kloska, Sebastian A1 - Kehr, Julia T1 - Using array hybridization to monitore gene expression at the single cell level Y1 - 2002 ER - TY - GEN A1 - Andorf, Sandra A1 - Gärtner, Tanja A1 - Steinfath, Matthias A1 - Witucka-Wall, Hanna A1 - Altmann, Thomas A1 - Repsilber, Dirk T1 - Towards systems biology of heterosis BT - a hypothesis about molecular network structure applied for the Arabidopsis metabolome T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 949 KW - partial correlation KW - biological network KW - metabolite profile KW - molecular network KW - significant edge Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436274 SN - 1866-8372 IS - 949 ER - TY - JOUR A1 - Altmann, Thomas A1 - von Groll, Uritza A1 - Berger, Dieter T1 - The subtilisin-like serine protease SDD1 mediates cell-cell signaling during Arabidopsis stomatal development Y1 - 2002 ER - TY - JOUR A1 - Lisso, Janina A1 - Altmann, Thomas A1 - Müssig, Carsten T1 - The AtNFXL1 gene encodes a NF-X1 type zinc finger protein required for growth under salt stress JF - FEBS letters : the journal for rapid publication of short reports in molecular biosciences N2 - The human NF-X1 protein and homologous proteins in eukaryotes represent a class of transcription factors which are characterised. by NF-X1 type zinc finger motifs. The Arabidopsis genome encodes two NF-X1 homologs, which we termed AtNFXL1 and AtNFXL2. Growth and survival was impaired in atnfxl1 knock-out mutants and AtNFXL1-antisense plants under salt stress in comparison to wild-type plants. In contrast, 35S: :AtNFXL1 plants showed higher survival rates. The AtNFXL2 protein potentially plays an antagonistic role. The Arabidopsis NF-X1 type zinc finger proteins likely are part of regulatory mechanisms, which protect major processes such as photosynthesis. KW - Arabidopsis thaliana KW - NF-X1 KW - salt stress Y1 - 2006 U6 - https://doi.org/10.1016/j.febslet.2006.07.079 SN - 0014-5793 VL - 580 IS - 22 SP - 4851 EP - 4856 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Altmann, Thomas A1 - von Groll, Uritza T1 - Stomatal cell biology Y1 - 2003 ER - TY - JOUR A1 - Sulpice, Ronan A1 - Pyl, Eva-Theresa A1 - Ishihara, Hirofumi A1 - Trenkamp, Sandra A1 - Steinfath, Matthias A1 - Witucka-Wall, Hanna A1 - Gibon, Yves A1 - Usadel, Björn A1 - Poree, Fabien A1 - Piques, Maria Conceicao A1 - von Korff, Maria A1 - Steinhauser, Marie Caroline A1 - Keurentjes, Joost J. B. A1 - Guenther, Manuela A1 - Hoehne, Melanie A1 - Selbig, Joachim A1 - Fernie, Alisdair R. A1 - Altmann, Thomas A1 - Stitt, Mark T1 - Starch as a major integrator in the regulation of plant growth N2 - Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light and is degraded at night to provide a sustained supply of carbon for growth. Multivariate analysis revealed that starch is an integrator of the overall metabolic response. We hypothesized that this reflects variation in a regulatory network that balances growth with the carbon supply. Transcript profiling in 21 accessions revealed coordinated changes of transcripts of more than 70 carbon-regulated genes and identified 2 genes (myo-inositol-1- phosphate synthase, a Kelch-domain protein) whose transcripts correlate with biomass. The impact of allelic variation at these 2 loci was shown by association mapping, identifying them as candidate lead genes with the potential to increase biomass production. Y1 - 2009 UR - http://www.pnas.org/ U6 - https://doi.org/10.1073/pnas.0903478106 SN - 0027-8424 ER - TY - JOUR A1 - Childs, Liam H. A1 - Witucka-Wall, Hanna A1 - Guenther, Torsten A1 - Sulpice, Ronan A1 - Korff, Maria V. A1 - Stitt, Mark A1 - Walther, Dirk A1 - Schmid, Karl J. A1 - Altmann, Thomas T1 - Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth- related metabolic traits in Arabidopsis thaliana N2 - Background: Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits. Results: A total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non- repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait. Conclusions: We generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation. Y1 - 2010 UR - http://www.biomedcentral.com/1471-2164/ U6 - https://doi.org/10.1186/1471-2164-11-188 SN - 1471-2164 ER - TY - JOUR A1 - Torjek, Otto A1 - Witucka-Wall, Hanna A1 - Meyer, Rhonda C. A1 - von Korff, Maria A1 - Kusterer, Barbara A1 - Rautengarten, Carsten A1 - Altmann, Thomas T1 - Segregation distortion in Arabidopsis C24/Col-0 and Col-0/C24 recombinant inbred line populations is due to reduced fertility caused by epistatic interaction of two loci JF - Theoretical and applied genetics N2 - A new large set of reciprocal recombinant inbred lines (RILs) was created between the Arabidopsis accessions Col-0 and C24 for quantitative trait mapping approaches, consisting of 209 Col-0 x C24 and 214 C24 x Col-0 F-7 RI lines. Genotyping was performed using 110 evenly distributed framework single nucleotide polymorphism markers, yielding a genetic map of 425.70 cM, with an average interval of 3.87 cM. Segregation distortion (SD) was observed in several genomic regions during the construction of the genetic map. Linkage disequilibrium analysis revealed an association between a distorted region at the bottom of chromosome V and a non-distorted region on chromosome IV. A detailed analysis of the RILs for these two regions showed that an SD occurred when homozygous Col-0 alleles on chromosome IV coincided with homozygous C24 alleles at the bottom of chromosome V. Using nearly isogenic lines segregating for the distorted region we confirmed that this genotypic composition leads to reduced fertility and fitness. Y1 - 2006 U6 - https://doi.org/10.1007/s00122-006-0402-3 SN - 0040-5752 VL - 113 SP - 1551 EP - 1561 PB - Springer CY - Berlin ER - TY - JOUR A1 - Altmann, Thomas A1 - Thimm, O. A1 - Essigmann, B. A1 - Kloska, Sebastian A1 - Buckhout, Thomas J. T1 - Response of arabidopsis to iron deficiency stress as revealed by microarray analysis Y1 - 2001 ER -