Professional Education

  • Master of Science, Unlisted School (2006)
  • Doctor of Philosophy, University Of Helsinki (2012)

Stanford Advisors

All Publications

  • Transcriptome Dynamics of the Stomatal Lineage: Birth, Amplification, and Termination of a Self-Renewing Population DEVELOPMENTAL CELL Adrian, J., Chang, J., Ballenger, C. E., Bargmann, B. O., Alassimone, J., Davies, K. A., Lau, O. S., Matos, J. L., Hachez, C., Lanctot, A., Vaten, A., Birnbaum, K. D., Bergmann, D. C. 2015; 33 (1): 107-118


    Developmental transitions can be described in terms of morphology and the roles of individual genes, but also in terms of global transcriptional and epigenetic changes. Temporal dissections of transcriptome changes, however, are rare for intact, developing tissues. We used RNA sequencing and microarray platforms to quantify gene expression from labeled cells isolated by fluorescence-activated cell sorting to generate cell-type-specific transcriptomes during development of an adult stem-cell lineage in the Arabidopsis leaf. We show that regulatory modules in this early lineage link cell types that had previously been considered to be under separate control and provide evidence for recruitment of individual members of gene families for different developmental decisions. Because stomata are physiologically important and because stomatal lineage cells exhibit exemplary division, cell fate, and cell signaling behaviors, this dataset serves as a valuable resource for further investigations of fundamental developmental processes.

    View details for DOI 10.1016/j.devcel.2015.01.025

    View details for Web of Science ID 000352454200011

    View details for PubMedID 25850675

    View details for PubMedCentralID PMC4390738

  • Tryptophan-dependent auxin biosynthesis is required for HD-ZIP III-mediated xylem patterning DEVELOPMENT Ursache, R., Miyashima, S., Chen, Q., Vaten, A., Nakajima, K., Carlsbecker, A., Zhao, Y., Helariutta, Y., Dettmer, J. 2014; 141 (6): 1250-1260


    The development and growth of higher plants is highly dependent on the conduction of water and minerals throughout the plant by xylem vessels. In Arabidopsis roots the xylem is organized as an axis of cell files with two distinct cell fates: the central metaxylem and the peripheral protoxylem. During vascular development, high and low expression levels of the class III HD-ZIP transcription factors promote metaxylem and protoxylem identities, respectively. Protoxylem specification is determined by both mobile, ground tissue-emanating miRNA165/6 species, which downregulate, and auxin concentrated by polar transport, which promotes HD-ZIP III expression. However, the factors promoting high HD-ZIP III expression for metaxylem identity have remained elusive. We show here that auxin biosynthesis promotes HD-ZIP III expression and metaxylem specification. Several auxin biosynthesis genes are expressed in the outer layers surrounding the vascular tissue in Arabidopsis root and downregulation of HD-ZIP III expression accompanied by specific defects in metaxylem development is seen in auxin biosynthesis mutants, such as trp2-12, wei8 tar2 or a quintuple yucca mutant, and in plants treated with L-kynurenine, a pharmacological inhibitor of auxin biosynthesis. Some of the patterning defects can be suppressed by synthetically elevated HD-ZIP III expression. Taken together, our results indicate that polar auxin transport, which was earlier shown to be required for protoxylem formation, is not sufficient to establish a proper xylem axis but that root-based auxin biosynthesis is additionally required.

    View details for DOI 10.1242/dev.103473

    View details for Web of Science ID 000332535400009

    View details for PubMedID 24595288

  • Mechanisms of stomatal development: an evolutionary view EVODEVO Vaten, A., Bergmann, D. C. 2012; 3


    Plant development has a significant postembryonic phase that is guided heavily by interactions between the plant and the outside environment. This interplay is particularly evident in the development, pattern and function of stomata, epidermal pores on the aerial surfaces of land plants. Stomata have been found in fossils dating from more than 400 million years ago. Strikingly, the morphology of the individual stomatal complex is largely unchanged, but the sizes, numbers and arrangements of stomata and their surrounding cells have diversified tremendously. In many plants, stomata arise from specialized and transient stem-cell like compartments on the leaf. Studies in the flowering plant Arabidopsis thaliana have established a basic molecular framework for the acquisition of cell fate and generation of cell polarity in these compartments, as well as describing some of the key signals and receptors required to produce stomata in organized patterns and in environmentally optimized numbers. Here we present parallel analyses of stomatal developmental pathways at morphological and molecular levels and describe the innovations made by particular clades of plants.

    View details for DOI 10.1186/2041-9139-3-11

    View details for Web of Science ID 000310696500001

    View details for PubMedID 22691547