A proteomics approach to decipher the molecular nature of planarian stem cells

Background In recent years, planaria have emerged as an important model system for research into stem cells and regeneration. Attention is focused on their unique stem cells, the neoblasts, which can differentiate into any cell type present in the adult organism. Sequencing of the Schmidtea mediterranea genome and some expressed sequence tag projects have generated extensive data on the genetic profile of these cells. However, little information is available on their protein dynamics. Results We developed a proteomic strategy to identify neoblast-specific proteins. Here we describe the method and discuss the results in comparison to the genomic high-throughput analyses carried out in planaria and to proteomic studies using other stem cell systems. We also show functional data for some of the candidate genes selected in our proteomic approach. Conclusions We have developed an accurate and reliable mass-spectra-based proteomics approach to complement previous genomic studies and to further achieve a more accurate understanding and description of the molecular and cellular processes related to the neoblasts

Microwave Guiding of Electrons on a Chip

Electrons travelling in free space have allowed to explore fundamental physics like the wave nature of matter, the Aharonov-Bohm and the Hanbury Brown-Twiss effect. Complementarily, the precise control over the external degrees of freedom of electrons has proven pivotal for wholly new types of experiments such as high precision measurements of the electron's mass and magnetic moment in Penning traps. Interestingly, the confinement of electrons in the purely electric field of an alternating quadrupole has rarely been considered. Recent advances in the development of planar chip-based ion traps suggest that this technology can be applied to enable entirely new experiments with electron beams guided in versatile potentials. Here we demonstrate the transverse confinement of a low energy electron beam in a linear quadrupole guide based on microstructured planar electrodes and driven at microwave frequencies. A new guided matter-wave system will result, with applications ranging from electron interferometry to novel non-invasive electron microscopy

Integrative analysis of DNA methylation and gene expression in butyrate-treated CHO cells

The cellular mechanisms responsible for the versatile properties of CHO cells as the major production cell line for biopharmaceutical molecules are not entirely understood yet, although several 'omics' data facilitate the understanding of CHO cells and their reactions to environmental conditions. However, genome-wide studies of epigenetic processes such as DNA methylation are still limited. To prove the applicability and usefulness of integrating DNA methylation and gene expression data in a biotechnological context, we exemplarily analyzed the time course of cellular reactions upon butyrate addition in antibody-producing CHO cells by whole-genome bisulfite sequencing and CHO-specific cDNA microarrays. Gene expression and DNA methylation analyses showed that pathways known to be affected by butyrate, including cell cycle and apoptosis, as well as pathways potentially involved in butyrate-induced hyperproductivity such as central energy metabolism and protein biosynthesi s were affected. Differentially methylated regions were furthermore found to contain binding-site motifs of specific transcription factors and were hypothesized to represent regulatory regions closely connected to the cellular response to butyrate. Generally, our experiment underlines the benefit of integrating DNA methylation and gene expression data, as it provided potential novel candidate genes for rational cell line development and allowed for new insights into the butyrate effect on CHO cells

3-Hydroxy-3-methylglutaryl coenzyme A reductase inhibitor Atorvastatin mediated effects depend on the activation status of target cells in PLP-EAE

Mix E, Ibrahim SM, Pahnke J, et al. 3-Hydroxy-3-methylglutaryl coenzyme A reductase inhibitor Atorvastatin mediated effects depend on the activation status of target cells in PLP-EAE. Journal of Autoimmunity. 2006;27(4):251-265