References of "Walther, Dirk"
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See detailGive It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone.
Thieme, Christoph J.; Schudoma, Christian; May, Patrick UL et al

in Frontiers in Plant Science (2012), 3

The specific recognition of miRNAs by Argonaute (AGO) proteins, the effector proteins of the RNA-induced silencing complex, constitutes the final step of the biogenesis of miRNAs and is crucial for their ... [more ▼]

The specific recognition of miRNAs by Argonaute (AGO) proteins, the effector proteins of the RNA-induced silencing complex, constitutes the final step of the biogenesis of miRNAs and is crucial for their target interaction. In the genome of Arabidopsis thaliana (Ath), 10 different AGO proteins are encoded and the sorting decision, which miRNA associates with which AGO protein, was reported to depend exclusively on the identity of the 5'-sequence position of mature miRNAs. Hence, with only four different bases possible, a 5'-position-only sorting signal would not suffice to specifically target all 10 different AGOs individually or would suggest redundant AGO action. Alternatively, other and as of yet unidentified sorting signals may exist. We analyzed a dataset comprising 117 Ath-miRNAs with clear sorting preference to either AGO1, AGO2, or AGO5 as identified in co-immunoprecipitation experiments combined with sequencing. While mutual information analysis did not identify any other single position but the 5'-nucleotide to be informative for the sorting at sufficient statistical significance, significantly better than random classification results using Random Forests nonetheless suggest that additional positions and combinations thereof also carry information with regard to the AGO sorting. Positions 2, 6, 9, and 13 appear to be of particular importance. Furthermore, uracil bases at defined positions appear to be important for the sorting to AGO2 and AGO5, in particular. No predictive value was associated with miRNA length or base pair binding pattern in the miRNA:miRNA* duplex. From inspecting available AGO gene expression data in Arabidopsis, we conclude that the temporal and spatial expression profile may also contribute to the fine-tuning of miRNA sorting and function. [less ▲]

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See detailComparative analysis of miRNAs and their targets across four plant species.
Lenz, Dorina; May, Patrick UL; Walther, Dirk

in BMC Research Notes (2011), 4

BACKGROUND: MicroRNA (miRNA) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. We performed a comparative analysis of miRNAs ... [more ▼]

BACKGROUND: MicroRNA (miRNA) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. We performed a comparative analysis of miRNAs and their respective gene targets across four plant species: Arabidopsis thaliana (Ath), Medicago truncatula(Mtr), Brassica napus (Bna), and Chlamydomonas reinhardtii (Cre). RESULTS: miRNAs were obtained from mirBase with 218 miRNAs for Ath, 375 for Mtr, 46 for Bna, and 73 for Cre, annotated for each species respectively. miRNA targets were obtained from available database annotations, bioinformatic predictions using RNAhybrid as well as predicted from an analysis of mRNA degradation products (degradome sequencing) aimed at identifying miRNA cleavage products. On average, and considering both experimental and bioinformatic predictions together, every miRNA was associated with about 46 unique gene transcripts with considerably variation across species. We observed a positive and linear correlation between the number miRNAs and the total number of transcripts across different plant species suggesting that the repertoire of miRNAs correlates with the size of the transcriptome of an organism. Conserved miRNA-target pairs were found to be associated with developmental processes and transcriptional regulation, while species-specific (in particular, Ath) pairs are involved in signal transduction and response to stress processes. Conserved miRNAs have more targets and higher expression values than non-conserved miRNAs. We found evidence for a conservation of not only the sequence of miRNAs, but their expression levels as well. CONCLUSIONS: Our results support the notion of a high birth and death rate of miRNAs and that miRNAs serve many species specific functions, while conserved miRNA are related mainly to developmental processes and transcriptional regulation with conservation operating at both the sequence and expression level. [less ▲]

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See detailIntegration of proteomic and metabolomic profiling as well as metabolic modeling for the functional analysis of metabolic networks.
May, Patrick UL; Christian, Nils UL; Ebenhoh, Oliver et al

in Methods in Molecular Biology (Clifton, N.J.) (2011), 694

The integrated analysis of different omics-level data sets is most naturally performed in the context of common process or pathway association. In this chapter, the two basic approaches for a metabolic ... [more ▼]

The integrated analysis of different omics-level data sets is most naturally performed in the context of common process or pathway association. In this chapter, the two basic approaches for a metabolic pathway-centric integration of proteomics and metabolomics data are described: the knowledge-based approach relying on existing metabolic pathway information, and a data-driven approach that aims to deduce functional (pathway) associations directly from the data. Relevant algorithmic approaches for the generation of metabolic networks of model organisms, their functional analysis, database resources, visualization and analysis tools will be described. The use of proteomics data in the process of metabolic network reconstruction will be discussed. [less ▲]

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See detailModeling RNA loops using sequence homology and geometric constraints.
Schudoma, Christian; May, Patrick UL; Walther, Dirk

in Bioinformatics (Oxford, England) (2010), 26(13), 1671-2

SUMMARY: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling ... [more ▼]

SUMMARY: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface. AVAILABILITY AND IMPLEMENTATION: The application was implemented in Python, MySQL and Apache. A web interface to the database and loop modeling application is freely available at http://rloom.mpimp-golm.mpg.de CONTACT: schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de [less ▲]

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See detailSequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.
Schudoma, Christian; May, Patrick UL; Nikiforova, Viktoria et al

in Nucleic Acids Research (2010), 38(3), 970-80

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three ... [more ▼]

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts. [less ▲]

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See detailChlamyCyc--a comprehensive database and web-portal centered on Chlamydomonas reinhardtii
Christian, Jan-Ole; May, Patrick UL; Kempa, Stefan et al

Poster (2009)

Background – The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular ... [more ▼]

Background – The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the whole cellular system of a single organism. Results – In the framework of the German Systems Biology initiative GoFORSYS a pathway/genome database and web-portal for Chlamydomonas reinhardtii (ChlamyCyc) was established, which currently features about 270 metabolic pathways with related genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion – Chlamycyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas reinhardtii. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de. [less ▲]

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See detailIdentification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing.
Pant, Bikram Datt; Musialak-Lange, Magdalena; Nuc, Przemyslaw et al

in Plant Physiology (2009), 150(3), 1541-55

Comprehensive expression profiles of Arabidopsis (Arabidopsis thaliana) MIRNA genes and mature microRNAs (miRs) are currently not available. We established a quantitative real-time polymerase chain ... [more ▼]

Comprehensive expression profiles of Arabidopsis (Arabidopsis thaliana) MIRNA genes and mature microRNAs (miRs) are currently not available. We established a quantitative real-time polymerase chain reaction platform that allows rapid and sensitive quantification of 177 Arabidopsis primary miR transcripts (pri-miRs). The platform was used to detect phosphorus (P) or nitrogen (N) status-responsive pri-miR species. Several pri-miR169 species as well as pri-miR398a were found to be repressed during N limitation, whereas during P limitation, pri-miR778, pri-miR827, and pri-miR399 species were induced and pri-miR398a was repressed. The corresponding responses of the biologically active, mature miRs were confirmed using specific stem-loop reverse transcription primer quantitative polymerase chain reaction assays and small RNA sequencing. Interestingly, the latter approach also revealed high abundance of some miR star strands. Bioinformatic analysis of small RNA sequences with a modified miRDeep algorithm led to the identification of the novel P limitation-induced miR2111, which is encoded by two loci in the Arabidopsis genome. Furthermore, miR2111, miR169, a miR827-like sequence, and the abundances of several miR star strands were found to be strongly dependent on P or N status in rapeseed (Brassica napus) phloem sap, flagging them as candidate systemic signals. Taken together, these results reveal the existence of complex small RNA-based regulatory networks mediating plant adaptation to mineral nutrient availability. [less ▲]

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See detailIdentification and classification of ncRNA molecules using graph properties.
Childs, Liam; Nikoloski, Zoran; May, Patrick UL et al

in Nucleic Acids Research (2009), 37(9), 66

The study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA ... [more ▼]

The study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA molecules of mostly unknown function, as well as the discovery of novel non-coding RNA types and functional RNA elements. Here, we demonstrate that specific properties of graphs that represent the predicted RNA secondary structure reflect functional information. We introduce a computational algorithm and an associated web-based tool (GraPPLE) for classifying non-coding RNA molecules as functional and, furthermore, into Rfam families based on their graph properties. Unlike sequence-similarity-based methods and covariance models, GraPPLE is demonstrated to be more robust with regard to increasing sequence divergence, and when combined with existing methods, leads to a significant improvement of prediction accuracy. Furthermore, graph properties identified as most informative are shown to provide an understanding as to what particular structural features render RNA molecules functional. Thus, GraPPLE may offer a valuable computational filtering tool to identify potentially interesting RNA molecules among large candidate datasets. [less ▲]

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See detailChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.
May, Patrick UL; Christian, Jan-Ole; Kempa, Stefan et al

in BMC Genomics (2009), 10

BACKGROUND: The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput ... [more ▼]

BACKGROUND: The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. RESULTS: In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. CONCLUSION: ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de. [less ▲]

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See detailMetabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii.
May, Patrick UL; Wienkoop, Stefanie; Kempa, Stefan et al

in Genetics (2008), 179(1), 157-66

We present an integrated analysis of the molecular repertoire of Chlamydomonas reinhardtii under reference conditions. Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS ... [more ▼]

We present an integrated analysis of the molecular repertoire of Chlamydomonas reinhardtii under reference conditions. Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS-based shotgun proteomics profiling technologies have been applied to characterize abundant proteins and metabolites, resulting in the detection of 1069 proteins and 159 metabolites. Of the measured proteins, 204 currently do not have EST sequence support; thus a significant portion of the proteomics-detected proteins provide evidence for the validity of in silico gene models. Furthermore, the generated peptide data lend support to the validity of a number of proteins currently in the proposed model stage. By integrating genomic annotation information with experimentally identified metabolites and proteins, we constructed a draft metabolic network for Chlamydomonas. Computational metabolic modeling allowed an identification of missing enzymatic links. Some experimentally detected metabolites are not producible by the currently known and annotated enzyme set, thus suggesting entry points for further targeted gene discovery or biochemical pathway research. All data sets are made available as supplementary material as well as web-accessible databases and within the functional context via the Chlamydomonas-adapted MapMan annotation platform. Information of identified peptides is also available directly via the JGI-Chlamydomonas genomic resource database (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). [less ▲]

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