Christian Schudoma | Earlham Institute (original) (raw)

Papers by Christian Schudoma

Research paper thumbnail of Assessment of drought tolerance and its potential yield penalty in potato

Functional Plant Biology, 2015

ABSTRACT Climate models predict an increased likelihood of seasonal droughts for many areas of th... more ABSTRACT Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied genetic variance, predictability of field performance, and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial data set, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified DRYM (deviation of relative starch yield from its experimental median) as the most efficient index. DRYM corresponded qualitatively to the partial least square-model based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials, but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding.

Research paper thumbnail of Data management pipeline for plant phenotyping in a multisite project

Functional Plant Biology, 2012

In plant breeding, plants have to be characterised precisely, consistently and rapidly by differe... more In plant breeding, plants have to be characterised precisely, consistently and rapidly by different people at several field sites within defined time spans. For a meaningful data evaluation and statistical analysis, standardised data storage is required. Data access must be provided on a long-term basis and be independent of organisational barriers without endangering data integrity or intellectual property rights. We discuss the associated technical challenges and demonstrate adequate solutions exemplified in a data management pipeline for a project to identify markers for drought tolerance in potato. This project involves 11 groups from academia and breeding companies, 11 sites and four analytical platforms. Our data warehouse concept combines central data storage in databases and a file server and integrates existing and specialised database solutions for particular data types with new, project-specific databases. The strict use of controlled vocabularies and the application of web-access technologies proved vital to the successful data exchange between diverse institutes and data management concepts and infrastructures. By presenting our data management system and making the software available, we aim to support related phenotyping projects.

Research paper thumbnail of Conducting molecular biomarker discovery studies in plants

Molecular biomarkers are molecules whose concentrations in a biological system inform about the c... more Molecular biomarkers are molecules whose concentrations in a biological system inform about the current phenotypical state and, more importantly, may also be predictive of future phenotypic trait endpoints. The identification of biomarkers has gained much attention in targeted plant breeding since technologies have become available that measure many molecules across different levels of molecular organization and at decreasing costs. In this chapter, we outline the general strategy and workflow of conducting biomarker discovery studies. Critical aspects of study design as well as the statistical data analysis and model building will be highlighted.

Research paper thumbnail of It's a loop world – single strands in RNA as structural and functional elements

BioMolecular Concepts, 2011

Unpaired regions in RNA molecules - loops - are centrally involved in defining the characteristic... more Unpaired regions in RNA molecules - loops - are centrally involved in defining the characteristic three-dimensional (3D) architecture of RNAs and are of high interest in RNA engineering and design. Loops adopt diverse, but specific conformations stabilised by complex tertiary structural interactions that provide structural flexibility to RNA structures that would otherwise not be possible if they only consisted of the rigid A-helical shapes usually formed by canonical base pairing. By participating in sequence-non-local contacts, they furthermore contribute to stabilising the overall fold of RNA molecules. Interactions between RNAs and other nucleic acids, proteins, or small molecules are also generally mediated by RNA loop structures. Therefore, the function of an RNA molecule is generally dependent on its loops. Examples include intermolecular interactions between RNAs as part of the microRNA processing pathways, ribozymatic activity, or riboswitch-ligand interactions. Bioinformatics approaches have been successfully applied to the identification of novel RNA structural motifs including loops, local and global RNA 3D structure prediction, and structural and conformational analysis of RNAs and have contributed to a better understanding of the sequence-structure-function relationships in RNA loops.

Research paper thumbnail of 3D-Modeling approaches for the detection of RNA-regulatory elements–2nd Progress Report

Research paper thumbnail of Bioinformatic Approaches to Sequence Structure Relationships in RNA Loops

Research paper thumbnail of Application of a Combined Sequence and Structure Alignment for RNA 3D Modeling

The prediction of RNA structure is a major field of bioinformatics research. A framework for mode... more The prediction of RNA structure is a major field of bioinformatics research. A framework for modeling RNA 3D structures based on sequence-to-structure alignment via genetic algorithm (RAGA) has been designed in a previous work. Due to performance and robustness problems with the RAGA algorithm it has to be exchanged with a newly developed method: Lagrangian Relaxed RNA structure alignment (LR-RSA). This thesis describes the necessary modifications which had to be applied to the framework to embed the new alignment and restore the operative status of the RNA Threading Framework. Also a validation is given whether the new algorithm is an acceptable replacement within the RNA 3D structure prediction.

Research paper thumbnail of blastjs: a BLAST+ wrapper for Node.js

BMC research notes, 2016

To cope with the ever-increasing amount of sequence data generated in the field of genomics, the ... more To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase. We developed blastjs, a Node.js library that wraps the search tools of the BLAST+ suite and thus allows to easily add significant functionality to any Node.js-based application. blastjs is a library that allows the incorporation of BLAST+ functionality into bioinformatics applications based on JavaScript and Node.js. The library was designed to be as user-friendly as possibl...

Research paper thumbnail of Corrigendum: Endogenous Arabidopsis messenger RNAs transported to distant tissues

Research paper thumbnail of A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads

Plant methods, 2015

The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of ... more The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of parasitization starts with a Cuscuta plant coiling around the host stem. The parasite's haustorial organs then establish a vascular connection allowing for access to the phloem content. The host and the parasite form new cellular connections, suggesting coordination of developmental and biochemical processes. Simultaneous monitoring of gene expression in the parasite's and host's tissues may shed light on the complex events occurring between the parasitic and host cells and may help to overcome experimental limitations (i.e. how to separate host tissue from Cuscuta tissue at the haustorial connection). A novel approach is to use bioinformatic analysis to classify sequencing reads as either belonging to the host or to the parasite and to characterize the expression patterns. Owing to the lack of a comprehensive genomic dataset from Cuscuta spp., such a classification has not b...

Research paper thumbnail of Assessment of drought tolerance and its potential yield penalty in potato

Functional Plant Biology, 2015

ABSTRACT Climate models predict an increased likelihood of seasonal droughts for many areas of th... more ABSTRACT Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied genetic variance, predictability of field performance, and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial data set, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified DRYM (deviation of relative starch yield from its experimental median) as the most efficient index. DRYM corresponded qualitatively to the partial least square-model based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials, but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding.

Research paper thumbnail of The influence of the local sequence environment on RNA loop structures

RNA (New York, N.Y.), 2011

RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, ... more RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotid...

Research paper thumbnail of Give It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone

Frontiers in plant science, 2012

The specific recognition of miRNAs by Argonaute (AGO) proteins, the effector proteins of the RNA-... 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...

Research paper thumbnail of Endogenous Arabidopsis messenger RNAs transported to distant tissues

Nature Plants, 2015

ABSTRACT The concept that proteins and small RNAs can move to and function in distant body parts ... more ABSTRACT The concept that proteins and small RNAs can move to and function in distant body parts is well established. However, non-cell-autonomy of small RNA molecules raises the question: To what extent are protein-coding messenger RNAs (mRNAs) exchanged between tissues in plants? Here we report the comprehensive identification of 2,006 genes producing mobile RNAs in Arabidopsis thaliana. The analysis of variant ecotype transcripts that were present in heterografted plants allowed the identification of mRNAs moving between various organs under normal or nutrient-limiting conditions. Most of these mobile transcripts seem to follow the phloem-dependent allocation pathway transporting sugars from photosynthetic tissues to roots via the vasculature. Notably, a high number of transcripts also move in the opposite, root-to-shoot direction and are transported to specific tissues including flowers. Proteomic data on grafted plants indicate the presence of proteins from mobile RNAs, allowing the possibility that they may be translated at their destination site. The mobility of a high number of mRNAs suggests that a postulated tissue-specific gene expression profile might not be predictive for the actual plant body part in which a transcript exerts its function.

Research paper thumbnail of Cracking the elusive alignment hypothesis: the microtubule–cellulose synthase nexus unraveled

Trends in Plant Science, 2012

Directed plant cell growth is governed by deposition and alterations of cell wall components unde... more Directed plant cell growth is governed by deposition and alterations of cell wall components under turgor pressure. A key regulatory element of anisotropic growth, and hence cell shape, is the directional deposition of cellulose microfibrils. The microfibrils are synthesized by plasma membrane-located cellulose synthase complexes that co-align with and move along cortical microtubules. That the parallel relation between cortical microtubules and extracellular microfibrils is causal has been named the alignment hypothesis. Three recent studies revealed that the previously identified pom2 mutant codes for a large cellulose synthases interacting (CSI1) protein which also binds cortical microtubules. This review summarizes these findings, provides structure-function models and discusses the inferred mechanisms in the context of plant growth.

Research paper thumbnail of Conducting molecular biomarker discovery studies in plants

Molecular biomarkers are molecules whose concentrations in a biological system inform about the c... more Molecular biomarkers are molecules whose concentrations in a biological system inform about the current phenotypical state and, more importantly, may also be predictive of future phenotypic trait endpoints. The identification of biomarkers has gained much attention in targeted plant breeding since technologies have become available that measure many molecules across different levels of molecular organization and at decreasing costs. In this chapter, we outline the general strategy and workflow of conducting biomarker discovery studies. Critical aspects of study design as well as the statistical data analysis and model building will be highlighted.

Research paper thumbnail of Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling

Nucleic Acids Research, 2010

Research paper thumbnail of Use of TILLING and robotised enzyme assays to generate an allelic series of Arabidopsis thaliana mutants with altered ADP-glucose pyrophosphorylase activity

Journal of Plant Physiology, 2011

ADP-glucose pyrophosphorylase (AGPase) catalyses the synthesis of ADP-glucose, and is a highly re... more ADP-glucose pyrophosphorylase (AGPase) catalyses the synthesis of ADP-glucose, and is a highly regulated enzyme in the pathway of starch synthesis. In Arabidopsis thaliana, the enzyme is a heterotetramer, containing two small subunits encoded by the APS1 gene and two large subunits encoded by the APL1-4 genes. TILLING (Targeting Induced Local Lesions IN Genomes) of a chemically mutagenised population of A. thaliana plants identified 33 novel mutations in the APS1 gene, including 21 missense mutations in the protein coding region. High throughput measurements using a robotised cycling assay showed that maximal AGPase activity in the aps1 mutants varied from <15 to 117% of wild type (WT), and that the kinetic properties of the enzyme were altered in several lines, indicating a role for the substituted amino acid residues in catalysis or substrate binding. These results validate the concept of using such a platform for efficient high-throughput screening of very large populations of mutants, natural accessions or introgression lines. AGPase was estimated to have a flux control coefficient of 0.20, indicating that the enzyme exerted only modest control over the rate of starch synthesis in plants grown under short day conditions (8 h light/16 h dark) with an irradiance of 150 μmol quanta m(-2)s(-1). Redox activation of the enzyme, via reduction of the intermolecular disulphide bridge between the two small subunits, was increased in several lines. This was sometimes, but not always, associated with a decrease in the abundance of the APS1 protein. In conclusion, the TILLING technique was used to generate an allelic series of aps1 mutants in A. thaliana that revealed new insights into the multi-layered regulation of AGPase. These mutants offer some advantages over the available loss-of-function mutants, e.g. adg1, for investigating the effects of subtle changes in the enzyme's activity on the rate of starch synthesis.

Research paper thumbnail of Data management pipeline for plant phenotyping in a multisite project

Functional Plant Biology, 2012

In plant breeding, plants have to be characterised precisely, consistently and rapidly by differe... more In plant breeding, plants have to be characterised precisely, consistently and rapidly by different people at several field sites within defined time spans. For a meaningful data evaluation and statistical analysis, standardised data storage is required. Data access must be provided on a long-term basis and be independent of organisational barriers without endangering data integrity or intellectual property rights. We discuss the associated technical challenges and demonstrate adequate solutions exemplified in a data management pipeline for a project to identify markers for drought tolerance in potato. This project involves 11 groups from academia and breeding companies, 11 sites and four analytical platforms. Our data warehouse concept combines central data storage in databases and a file server and integrates existing and specialised database solutions for particular data types with new, project-specific databases. The strict use of controlled vocabularies and the application of web-access technologies proved vital to the successful data exchange between diverse institutes and data management concepts and infrastructures. By presenting our data management system and making the software available, we aim to support related phenotyping projects.

Research paper thumbnail of Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

BMC Bioinformatics, 2009

Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of ... more Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites.

Research paper thumbnail of Assessment of drought tolerance and its potential yield penalty in potato

Functional Plant Biology, 2015

ABSTRACT Climate models predict an increased likelihood of seasonal droughts for many areas of th... more ABSTRACT Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied genetic variance, predictability of field performance, and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial data set, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified DRYM (deviation of relative starch yield from its experimental median) as the most efficient index. DRYM corresponded qualitatively to the partial least square-model based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials, but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding.

Research paper thumbnail of Data management pipeline for plant phenotyping in a multisite project

Functional Plant Biology, 2012

In plant breeding, plants have to be characterised precisely, consistently and rapidly by differe... more In plant breeding, plants have to be characterised precisely, consistently and rapidly by different people at several field sites within defined time spans. For a meaningful data evaluation and statistical analysis, standardised data storage is required. Data access must be provided on a long-term basis and be independent of organisational barriers without endangering data integrity or intellectual property rights. We discuss the associated technical challenges and demonstrate adequate solutions exemplified in a data management pipeline for a project to identify markers for drought tolerance in potato. This project involves 11 groups from academia and breeding companies, 11 sites and four analytical platforms. Our data warehouse concept combines central data storage in databases and a file server and integrates existing and specialised database solutions for particular data types with new, project-specific databases. The strict use of controlled vocabularies and the application of web-access technologies proved vital to the successful data exchange between diverse institutes and data management concepts and infrastructures. By presenting our data management system and making the software available, we aim to support related phenotyping projects.

Research paper thumbnail of Conducting molecular biomarker discovery studies in plants

Molecular biomarkers are molecules whose concentrations in a biological system inform about the c... more Molecular biomarkers are molecules whose concentrations in a biological system inform about the current phenotypical state and, more importantly, may also be predictive of future phenotypic trait endpoints. The identification of biomarkers has gained much attention in targeted plant breeding since technologies have become available that measure many molecules across different levels of molecular organization and at decreasing costs. In this chapter, we outline the general strategy and workflow of conducting biomarker discovery studies. Critical aspects of study design as well as the statistical data analysis and model building will be highlighted.

Research paper thumbnail of It's a loop world – single strands in RNA as structural and functional elements

BioMolecular Concepts, 2011

Unpaired regions in RNA molecules - loops - are centrally involved in defining the characteristic... more Unpaired regions in RNA molecules - loops - are centrally involved in defining the characteristic three-dimensional (3D) architecture of RNAs and are of high interest in RNA engineering and design. Loops adopt diverse, but specific conformations stabilised by complex tertiary structural interactions that provide structural flexibility to RNA structures that would otherwise not be possible if they only consisted of the rigid A-helical shapes usually formed by canonical base pairing. By participating in sequence-non-local contacts, they furthermore contribute to stabilising the overall fold of RNA molecules. Interactions between RNAs and other nucleic acids, proteins, or small molecules are also generally mediated by RNA loop structures. Therefore, the function of an RNA molecule is generally dependent on its loops. Examples include intermolecular interactions between RNAs as part of the microRNA processing pathways, ribozymatic activity, or riboswitch-ligand interactions. Bioinformatics approaches have been successfully applied to the identification of novel RNA structural motifs including loops, local and global RNA 3D structure prediction, and structural and conformational analysis of RNAs and have contributed to a better understanding of the sequence-structure-function relationships in RNA loops.

Research paper thumbnail of 3D-Modeling approaches for the detection of RNA-regulatory elements–2nd Progress Report

Research paper thumbnail of Bioinformatic Approaches to Sequence Structure Relationships in RNA Loops

Research paper thumbnail of Application of a Combined Sequence and Structure Alignment for RNA 3D Modeling

The prediction of RNA structure is a major field of bioinformatics research. A framework for mode... more The prediction of RNA structure is a major field of bioinformatics research. A framework for modeling RNA 3D structures based on sequence-to-structure alignment via genetic algorithm (RAGA) has been designed in a previous work. Due to performance and robustness problems with the RAGA algorithm it has to be exchanged with a newly developed method: Lagrangian Relaxed RNA structure alignment (LR-RSA). This thesis describes the necessary modifications which had to be applied to the framework to embed the new alignment and restore the operative status of the RNA Threading Framework. Also a validation is given whether the new algorithm is an acceptable replacement within the RNA 3D structure prediction.

Research paper thumbnail of blastjs: a BLAST+ wrapper for Node.js

BMC research notes, 2016

To cope with the ever-increasing amount of sequence data generated in the field of genomics, the ... more To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase. We developed blastjs, a Node.js library that wraps the search tools of the BLAST+ suite and thus allows to easily add significant functionality to any Node.js-based application. blastjs is a library that allows the incorporation of BLAST+ functionality into bioinformatics applications based on JavaScript and Node.js. The library was designed to be as user-friendly as possibl...

Research paper thumbnail of Corrigendum: Endogenous Arabidopsis messenger RNAs transported to distant tissues

Research paper thumbnail of A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads

Plant methods, 2015

The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of ... more The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of parasitization starts with a Cuscuta plant coiling around the host stem. The parasite's haustorial organs then establish a vascular connection allowing for access to the phloem content. The host and the parasite form new cellular connections, suggesting coordination of developmental and biochemical processes. Simultaneous monitoring of gene expression in the parasite's and host's tissues may shed light on the complex events occurring between the parasitic and host cells and may help to overcome experimental limitations (i.e. how to separate host tissue from Cuscuta tissue at the haustorial connection). A novel approach is to use bioinformatic analysis to classify sequencing reads as either belonging to the host or to the parasite and to characterize the expression patterns. Owing to the lack of a comprehensive genomic dataset from Cuscuta spp., such a classification has not b...

Research paper thumbnail of Assessment of drought tolerance and its potential yield penalty in potato

Functional Plant Biology, 2015

ABSTRACT Climate models predict an increased likelihood of seasonal droughts for many areas of th... more ABSTRACT Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied genetic variance, predictability of field performance, and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial data set, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified DRYM (deviation of relative starch yield from its experimental median) as the most efficient index. DRYM corresponded qualitatively to the partial least square-model based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials, but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding.

Research paper thumbnail of The influence of the local sequence environment on RNA loop structures

RNA (New York, N.Y.), 2011

RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, ... more RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotid...

Research paper thumbnail of Give It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone

Frontiers in plant science, 2012

The specific recognition of miRNAs by Argonaute (AGO) proteins, the effector proteins of the RNA-... 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...

Research paper thumbnail of Endogenous Arabidopsis messenger RNAs transported to distant tissues

Nature Plants, 2015

ABSTRACT The concept that proteins and small RNAs can move to and function in distant body parts ... more ABSTRACT The concept that proteins and small RNAs can move to and function in distant body parts is well established. However, non-cell-autonomy of small RNA molecules raises the question: To what extent are protein-coding messenger RNAs (mRNAs) exchanged between tissues in plants? Here we report the comprehensive identification of 2,006 genes producing mobile RNAs in Arabidopsis thaliana. The analysis of variant ecotype transcripts that were present in heterografted plants allowed the identification of mRNAs moving between various organs under normal or nutrient-limiting conditions. Most of these mobile transcripts seem to follow the phloem-dependent allocation pathway transporting sugars from photosynthetic tissues to roots via the vasculature. Notably, a high number of transcripts also move in the opposite, root-to-shoot direction and are transported to specific tissues including flowers. Proteomic data on grafted plants indicate the presence of proteins from mobile RNAs, allowing the possibility that they may be translated at their destination site. The mobility of a high number of mRNAs suggests that a postulated tissue-specific gene expression profile might not be predictive for the actual plant body part in which a transcript exerts its function.

Research paper thumbnail of Cracking the elusive alignment hypothesis: the microtubule–cellulose synthase nexus unraveled

Trends in Plant Science, 2012

Directed plant cell growth is governed by deposition and alterations of cell wall components unde... more Directed plant cell growth is governed by deposition and alterations of cell wall components under turgor pressure. A key regulatory element of anisotropic growth, and hence cell shape, is the directional deposition of cellulose microfibrils. The microfibrils are synthesized by plasma membrane-located cellulose synthase complexes that co-align with and move along cortical microtubules. That the parallel relation between cortical microtubules and extracellular microfibrils is causal has been named the alignment hypothesis. Three recent studies revealed that the previously identified pom2 mutant codes for a large cellulose synthases interacting (CSI1) protein which also binds cortical microtubules. This review summarizes these findings, provides structure-function models and discusses the inferred mechanisms in the context of plant growth.

Research paper thumbnail of Conducting molecular biomarker discovery studies in plants

Molecular biomarkers are molecules whose concentrations in a biological system inform about the c... more Molecular biomarkers are molecules whose concentrations in a biological system inform about the current phenotypical state and, more importantly, may also be predictive of future phenotypic trait endpoints. The identification of biomarkers has gained much attention in targeted plant breeding since technologies have become available that measure many molecules across different levels of molecular organization and at decreasing costs. In this chapter, we outline the general strategy and workflow of conducting biomarker discovery studies. Critical aspects of study design as well as the statistical data analysis and model building will be highlighted.

Research paper thumbnail of Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling

Nucleic Acids Research, 2010

Research paper thumbnail of Use of TILLING and robotised enzyme assays to generate an allelic series of Arabidopsis thaliana mutants with altered ADP-glucose pyrophosphorylase activity

Journal of Plant Physiology, 2011

ADP-glucose pyrophosphorylase (AGPase) catalyses the synthesis of ADP-glucose, and is a highly re... more ADP-glucose pyrophosphorylase (AGPase) catalyses the synthesis of ADP-glucose, and is a highly regulated enzyme in the pathway of starch synthesis. In Arabidopsis thaliana, the enzyme is a heterotetramer, containing two small subunits encoded by the APS1 gene and two large subunits encoded by the APL1-4 genes. TILLING (Targeting Induced Local Lesions IN Genomes) of a chemically mutagenised population of A. thaliana plants identified 33 novel mutations in the APS1 gene, including 21 missense mutations in the protein coding region. High throughput measurements using a robotised cycling assay showed that maximal AGPase activity in the aps1 mutants varied from <15 to 117% of wild type (WT), and that the kinetic properties of the enzyme were altered in several lines, indicating a role for the substituted amino acid residues in catalysis or substrate binding. These results validate the concept of using such a platform for efficient high-throughput screening of very large populations of mutants, natural accessions or introgression lines. AGPase was estimated to have a flux control coefficient of 0.20, indicating that the enzyme exerted only modest control over the rate of starch synthesis in plants grown under short day conditions (8 h light/16 h dark) with an irradiance of 150 μmol quanta m(-2)s(-1). Redox activation of the enzyme, via reduction of the intermolecular disulphide bridge between the two small subunits, was increased in several lines. This was sometimes, but not always, associated with a decrease in the abundance of the APS1 protein. In conclusion, the TILLING technique was used to generate an allelic series of aps1 mutants in A. thaliana that revealed new insights into the multi-layered regulation of AGPase. These mutants offer some advantages over the available loss-of-function mutants, e.g. adg1, for investigating the effects of subtle changes in the enzyme's activity on the rate of starch synthesis.

Research paper thumbnail of Data management pipeline for plant phenotyping in a multisite project

Functional Plant Biology, 2012

In plant breeding, plants have to be characterised precisely, consistently and rapidly by differe... more In plant breeding, plants have to be characterised precisely, consistently and rapidly by different people at several field sites within defined time spans. For a meaningful data evaluation and statistical analysis, standardised data storage is required. Data access must be provided on a long-term basis and be independent of organisational barriers without endangering data integrity or intellectual property rights. We discuss the associated technical challenges and demonstrate adequate solutions exemplified in a data management pipeline for a project to identify markers for drought tolerance in potato. This project involves 11 groups from academia and breeding companies, 11 sites and four analytical platforms. Our data warehouse concept combines central data storage in databases and a file server and integrates existing and specialised database solutions for particular data types with new, project-specific databases. The strict use of controlled vocabularies and the application of web-access technologies proved vital to the successful data exchange between diverse institutes and data management concepts and infrastructures. By presenting our data management system and making the software available, we aim to support related phenotyping projects.

Research paper thumbnail of Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

BMC Bioinformatics, 2009

Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of ... more Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites.