Author
Markus Schmid
Other affiliations: Technische Universität München, Salk Institute for Biological Studies, Max Planck Society ...read more
Bio: Markus Schmid is an academic researcher from Umeå University. The author has contributed to research in topics: Arabidopsis & Arabidopsis thaliana. The author has an hindex of 57, co-authored 109 publications receiving 24464 citations. Previous affiliations of Markus Schmid include Technische Universität München & Salk Institute for Biological Studies.
Topics: Arabidopsis, Arabidopsis thaliana, Meristem, Gene, Anammox
Papers published on a yearly basis
Papers
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TL;DR: Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels, and insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.
Abstract: Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.
5,227 citations
TL;DR: Examining the expression patterns of large gene families, it is found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.
Abstract: Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.
2,510 citations
TL;DR: It is demonstrated that miR172, previously thought to act primarily by translational repression, can efficiently guide mRNA cleavage, although the effects on steady-state levels of target transcripts are obscured by strong feedback regulation.
1,385 citations
TL;DR: Data suggest that FT primarily controls the timing of flowering of Arabidopsis, and that integration of temporal and spatial information is mediated in part by the bZIP transcription factor FD, which is already expressed at the shoot apex before floral induction.
Abstract: Flowering of Arabidopsis is regulated by several environmental and endogenous signals An important integrator of these inputs is the FLOWERING LOCUS T (FT) gene, which encodes a small, possibly mobile protein A primary response to floral induction is the activation of FT RNA expression in leaves Because flowers form at a distant site, the shoot apex, these data suggest that FT primarily controls the timing of flowering Integration of temporal and spatial information is mediated in part by the bZIP transcription factor FD, which is already expressed at the shoot apex before floral induction A complex of FT and FD proteins in turn can activate floral identity genes such as APETALA1 (AP1)
1,249 citations
TL;DR: The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB.
Abstract: The current perception of evolutionary relationships and the natural diversity of ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of their genes encoding the 16S rRNA and the active site polypeptide of the ammonia monooxygenase (AmoA). However, only partial 16S rRNA sequences are available for many AOB species and most AOB have not yet been analyzed on the amoA level. In this study, the 16S rDNA sequence data of 10 Nitrosomonas species and Nitrosococcus mobilis were completed. Furthermore, previously unavailable 16S rRNA sequences were determined for three Nitrosomonas sp. isolates and for the gamma-subclass proteobacterium Nitrosococcus halophilus. These data were used to revaluate the specificities of published oligonucleotide primers and probes for AOB. In addition, partial amoA sequences of 17 AOB, including the above-mentioned 15 AOB, were obtained. Comparative phylogenetic analyses suggested similar but not identical evolutionary relationships of AOB by using 16S rRNA and AmoA as marker molecules, respectively. The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB. For 16S rRNA-independent evaluation of AOB species-level diversity in environmental samples, amoA and AmoA sequence similarity threshold values were determined which can be used to tentatively identify novel species based on cloned amoA sequences. Subsequently, 122 amoA sequences were obtained from 11 nitrifying wastewater treatment plants. Phylogenetic analyses of the molecular isolates showed that in all but two plants only nitrosomonads could be detected. Although several of the obtained amoA sequences were only relatively distantly related to known AOB, none of these sequences unequivocally suggested the existence of previously unrecognized species in the wastewater treatment environments examined.
1,085 citations
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TL;DR: For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to
9,847 citations
TL;DR: A map-based, finished quality sequence that covers 95% of the 389 Mb rice genome, including virtually all of the euchromatin and two complete centromeres, and finds evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes.
Abstract: Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.
3,423 citations
TL;DR: Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions, and the developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels inArabidopsis in the future.
Abstract: Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future.
2,694 citations
TL;DR: The importance of miRNA-directed gene regulation during plant development is now particularly clear and typically at the cores of gene regulatory networks, targeting genes that are themselves regulators, such as those encoding transcription factors and F-box proteins.
Abstract: MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in plants and animals. In plants, these approximately 21-nucleotide RNAs are processed from stem-loop regions of long primary transcripts by a Dicer-like enzyme and are loaded into silencing complexes, where they generally direct cleavage of complementary mRNAs. Although plant miRNAs have some conserved functions extending beyond development, the importance of miRNA-directed gene regulation during plant development is now particularly clear. Identified in plants less than four years ago, miRNAs are already known to play numerous crucial roles at each major stage of development-typically at the cores of gene regulatory networks, targeting genes that are themselves regulators, such as those encoding transcription factors and F-box proteins.
2,560 citations
TL;DR: The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.
Abstract: Summary In conclusion, the eFP Browser is a convenient tool forinterpreting and visualizing gene expression and other data. Notonly is it valuable for its compatibility to existing resources but ithas also been loaded with several useful data sets. The variousmodes and other features allow the user to extract an array ofconclusions and/or generate useful hypotheses. We hope thatmany researchers will be able to use the eFP Browser both tounderstand particular microarray or other experimental results, aswell as to communicate their own findings. MATERIALS AND METHODS The eFP Browser is implemented in Python and makes use of thePython Imaging Library (PIL) Build 1.1.5 (www.python.org),which we modified to provide an optimized flood pixel re-placement function called replaceFill, and other Python modules,as described on the eFP Browser development homepage. Theinputs for the eFP Browser are illustrated in Figure 1. Apictographic representation of the sample collection as a Targa-based image is required, as is an XML control file, shown in detailin Figure 1B. Two other inputs are a database of gene identifiersand their appropriate microarray element lookups and annota-tions, and a database of gene expression values for the givensamples. In the case of the Arabidopsis, Cell and Mouse eFPBrowsers, we have mirrored publicly-available microarray datafrom several sources – described in the Data Sources andsubsequent two sections – in our Bio-Array Resource [10]. Theseinputs are used by the eFP Browser algorithm to generate anoutput image for a user’s gene identifier.The eFP Browser algorithm itself is programmed in an object-oriented manner. The main program, efpWeb.cgi, is responsiblefor the creation of the HTML code for the user interface andpresentation of the output image. It calls on four modules tocomplete the task. These modules are 1) efp.py, which performsmost of the functions for the generation of the output image,including the parsing of the XML control file, average andstandard deviation calculations, fold-change relative to controlvalue calculations, and image map HTML code; 2) efpDb.py,which connects to the gene expression, microarray element andannotation databases, and returns the appropriate values uponbeing called; 3) efpImg.py, which formulates the actual colourreplace calls on the Targa input image; and 4) efpXML.py, whichidentifies the XML control files that are present in the eFPBrowser’s data directory. These are displayed to the user in theData Source drop-down, thus obviating the need to have themhard-coded in the main efpWeb.cgi program.In the case of the Cell eFP Browser, data in the SUBAdatabase indicate the presence of a given protein in a particularsubcellular location, either based on computational methods or asmolecularly documented by mass spectrometric analysis ofsubcellular fractions, GFP fusions etc. [11]. We have used a simpleheuristic to turn these data into a confidence score for a given geneproduct’s presence in a given subcellular compartment:confidence~X
2,416 citations