Functional Genomics Center Zurich

Zürich, Switzerland

Functional Genomics Center Zurich

Zürich, Switzerland
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Vanderschuren H.,ETH Zurich | Lentz E.,ETH Zurich | Zainuddin I.,ETH Zurich | Zainuddin I.,Indonesian Institute of Sciences | And 2 more authors.
Journal of Proteomics | Year: 2013

In the last decade proteomics studies have gained increasing importance in plant research. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins have been particularly instrumental to characterize proteomes and their modulation during plant development, biotic and abiotic stresses. Despite important advances, plant proteome analysis, including those of model plant species, remain constrained by limitations inherent to proteomics techniques and data interpretation. Here we review the approaches and achievements of proteomics with model plant and crop species (i.e. Arabidopsis and rice) and discuss the current limitations of crop proteomics. We anticipate future directions that could advance the contribution of plant proteomics to crop improvement.This article is part of a Special Issue entitled: Translational Plant Proteomics. © 2013 Elsevier B.V.

Casutt M.S.,Albert Ludwigs University of Freiburg | Huber T.,University of Zürich | Brunisholz R.,Functional Genomics Center Zurich | Tao M.,University of Zürich | And 2 more authors.
Journal of Biological Chemistry | Year: 2010

The sodium ion-translocating NADH:quinone oxidoreductase (Na +-NQR) from the human pathogen Vibrio cholerae is a respiratory membrane protein complex that couples the oxidation of NADH to the transport of Na+ across the bacterial membrane. The Na+-NQR comprises the six subunits NqrABCDEF, but the stoichiometry and arrangement of these subunits are unknown. Redox-active cofactors are FAD and a 2Fe-2S cluster on NqrF, covalently attached FMNs on NqrB and NqrC, and riboflavin and ubiquinone-8 with unknown localization in the complex. By analyzing the cofactor content and NADH oxidation activity of subcomplexes of the Na+-NQR lacking individual subunits, the riboflavin cofactor was unequivocally assigned to the membrane-bound NqrB subunit. Quantitative analysis of the N-terminal amino acids of the holo-complex revealed that NqrB is present in a single copy in the holo-complex. It is concluded that the hydrophobic NqrB harbors one riboflavin in addition to its covalently attached FMN. The catalytic role of two flavins in subunit NqrB during the reduction of ubiquinone to ubiquinol by the Na +-NQR is discussed. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

Bischof S.,ETH Zurich | Bischof S.,University of California at Los Angeles | Umhang M.,ETH Zurich | Eicke S.,ETH Zurich | And 3 more authors.
Plant Cell | Year: 2013

The branched glucans glycogen and starch are the most widespread storage carbohydrates in living organisms. The production of semicrystalline starch granules in plants is more complex than that of small, soluble glycogen particles in microbes and animals. However, the factors determining whether glycogen or starch is formed are not fully understood. The tropical tree Cecropia peltata is a rare example of an organism able to make either polymer type. Electron micrographs and quantitative measurements show that glycogen accumulates to very high levels in specialized myrmecophytic structures (Müllerian bodies), whereas starch accumulates in leaves. Compared with polymers comprising leaf starch, glycogen is more highly branched and has shorter branches-factors that prevent crystallization and explain its solubility. RNA sequencing and quantitative shotgun proteomics reveal that isoforms of all three classes of glucan biosynthetic enzyme (starch/glycogen synthases, branching enzymes, and debranching enzymes) are differentially expressed in Müllerian bodies and leaves, providing a system-wide view of the quantitative programming of storage carbohydrate metabolism. This work will prompt targeted analysis in model organisms and cross-species comparisons. Finally, as starch is the major carbohydrate used for food and industrial applications worldwide, these data provide a basis for manipulating starch biosynthesis in crops to synthesize tailor-made polyglucans. © 2013 American Society of Plant Biologists. All rights reserved.

Schicht S.,University of Veterinary Medicine Hannover | Qi W.,Functional Genomics Center Zurich | Poveda L.,Functional Genomics Center Zurich | Strube C.,University of Veterinary Medicine Hannover
Parasites and Vectors | Year: 2013

Background: The worldwide distributed hematophagous poultry red mite Dermanyssus gallinae (De Geer, 1778) is one of the most important pests of poultry. Even though 35 acaricide compounds are available, control of D. gallinae remains difficult due to acaricide resistances as well as food safety regulations. The current study was carried out to identify putative excretory/secretory (pES) proteins of D. gallinae since these proteins play an important role in the host-parasite interaction and therefore represent potential targets for the development of novel intervention strategies. Additionally, putative transmembrane proteins (pTM) of D. gallinae were analyzed as representatives of this protein group also serve as promising targets for new control strategies. Methods. D. gallinae pES and pTM protein prediction was based on putative protein sequences of whole transcriptome data which was parsed to different bioinformatical servers (SignalP, SecretomeP, TMHMM and TargetP). Subsequently, pES and pTM protein sequences were functionally annotated by different computational tools. Results: Computational analysis of the D. gallinae proteins identified 3,091 pES (5.6%) and 7,361 pTM proteins (13.4%). A significant proportion of pES proteins are considered to be involved in blood feeding and digestion such as salivary proteins, proteases, lipases and carbohydrases. The cysteine proteases cathepsin D and L as well as legumain, enzymes that cleave hemoglobin during blood digestion of the near related ticks, represented 6 of the top-30 BLASTP matches of the poultry red mite's secretome. Identified pTM proteins may be involved in many important biological processes including cell signaling, transport of membrane-impermeable molecules and cell recognition. Ninjurin-like proteins, whose functions in mites are still unknown, represent the most frequently occurring pTM. Conclusion: The current study is the first providing a mite's secretome as well as transmembranome and provides valuable insights into D. gallinae pES and pTM proteins operating in different metabolic pathways. Identifying a variety of molecules putatively involved in blood feeding may significantly contribute to the development of new therapeutic targets or vaccines against this poultry pest. © 2013 Schicht et al.; licensee BioMed Central Ltd.

Wollenick K.,University of Zürich | Hu J.,University of Duisburg - Essen | Kristiansen G.,University of Bonn | Schraml P.,University of Zürich | And 5 more authors.
Nucleic Acids Research | Year: 2012

The human prolyl-4-hydroxylase domain (PHD) proteins 1-3 are known as cellular oxygen sensors, acting via the degradation of hypoxia-inducible factor (HIF) α-subunits. PHD2 and PHD3 genes are inducible by HIFs themselves, suggesting a negative feedback loop that involves PHD abundance. To identify novel regulators of the PHD2 gene, an expression array of 704 transcription factors was screened by a method that allows distinguishing between HIF-dependent and HIF-independent promoter regulation. Among others, the E-twenty six transcription factor ETS translocation variant 4 (ETV4) was found to contribute to PHD2 gene expression particularly under hypoxic conditions. Mechanistically, complex formation between ETV4 and HIF-1/2α was observed by mammalian two-hybrid and fluorescence resonance energy transfer analysis. HIF-1α domain mapping, CITED2 overexpression and factor inhibiting HIF depletion experiments provided evidence for cooperation between HIF-1α and p300/CBP in ETV4 binding. Chromatin immunoprecipitation confirmed ETV4 and HIF-1α corecruitment to the PHD2 promoter. Of 608 hypoxically induced transcripts found by genome-wide expression profiling, 7.7 required ETV4 for efficient hypoxic induction, suggesting a broad role of ETV4 in hypoxic gene regulation. Endogenous ETV4 highly correlated with PHD2, HIF-1/2α and several established markers of tissue hypoxia in 282 human breast cancer tissue samples, corroborating a functional interplay between the ETV4 and HIF pathways. © 2011 The Author(s).

Kaufmann S.,ETH Zurich | Sobek J.,Functional Genomics Center Zurich | Textor M.,ETH Zurich | Reimhult E.,University of Natural Resources and Life Sciences, Vienna
Lab on a Chip - Miniaturisation for Chemistry and Biology | Year: 2011

Arrays of supported lipid bilayers (SLBs) provide great potential for future drug development and multiplexed biological research, but are difficult to prepare due to the sensitivity of both the lipid and protein structural arrangement to air exposure. A novel way to produce arrays of SLBs is presented based on non-contact dispensing of vesicles to a substrate through a thin surface confined water film. The approach presents many degrees of freedom since it is not limited to a specific substrate, lipid composition, linker or controlled environment. The method allows adjustment of spot size (180-360 μm) by repeated dispensing as well as control over the composition of the spots and subsequent analytes. SLB formation by vesicle adsorption and rupture allows for incorporation of membrane proteins through pre-formed proteoliposomes. Dispensing through a dip-and-rinse water film avoids contamination, disruptive drying and the need for complex buffer compositions. Furthermore, no humidity control is necessary which simplifies the production step and prolongs the life-time of the spotting system. We characterize the method with respect to control over spot size, bilayer mobility and the formation process as well as demonstrate the possibility to fuse bilayer spots with subsequently added vesicles. Since complex lipid compositions and multiple spotting nozzles can be used, this novel technique is expected to be a promising platform for future applications, e.g. patterning to monitor peptide/protein-lipid interactions, for glycomics using glycolipids or lipopolysaccharides, and to study mixing of spatially confined lipid membranes. © 2011 The Royal Society of Chemistry.

Aregger F.,Charité - Medical University of Berlin | Aregger F.,University of Bern | Uehlinger D.E.,University of Bern | Witowski J.,Charité - Medical University of Berlin | And 4 more authors.
Kidney International | Year: 2014

Early diagnosis of acute kidney injury (AKI) and accurate prognostic stratification is a prerequisite for optimal medical management. To identify novel prognostic markers of AKI, urine was collected on the first day of AKI in critically ill patients. Twelve patients with early recovery and 12 matching patients with late/non-recovery were selected and their proteome analyzed by gel electrophoresis and mass spectrometry. We identified eight prognostic candidates including α-1 microglobulin, α-1 antitrypsin, apolipoprotein D, calreticulin, cathepsin D, CD59, insulin-like growth factor-binding protein 7 (IGFBP-7), and neutrophil gelatinase-associated lipocalin (NGAL). Subsequent quantification by ELISA showed that IGFBP-7 was the most potent predictor of renal recovery. IGFBP-7 and NGAL were then chosen for further analyses in an independent verification group of 28 patients with and 12 control patients without AKI. IGFBP-7 and NGAL discriminated between early and late/non-recovery patients and patients with and without AKI. Significant upregulation of the urinary markers predicted mortality (IGFBP-7: AUC 0.68; NGAL: AUC 0.81), recovery (IGFBP-7: AUC 0.74; NGAL: AUC 0.70), and severity of AKI (IGFBP-7: AUC 0.77; NGAL: AUC 0.69), and were associated with the duration of AKI. IGFBP-7 was a more accurate predictor of renal outcome than NGAL. Thus, IGFBP-7 is a novel prognostic urinary marker that warrants further investigation. © 2013 International Society of Nephrology.

Quaroni L.,Paul Scherrer Institute | Quaroni L.,Functional Genomics Center Zurich | Zlateva T.,Paul Scherrer Institute
Analytical Chemistry | Year: 2014

In recent years, major efforts have been devoted to the application of microscopy with mid-infrared light to the study of living cells and tissue. Despite this interest, infrared (IR) microscopy has not realized its full potential in the molecular characterization of living systems. This is partly due to the fact that current approaches for data mining and analysis of IR absorption spectra have not evolved comparably to measurement technology and are not up to the interpretation of the complex spectra of living systems such as cells and tissue. In this work we show that the use of two-dimensional correlation spectroscopy coupled to IR absorption spectro-microscopy allows us to extract the spectral components of individual metabolites from time-resolved IR spectra of living cells. We call this method correlated cellular spectro-microscopy, and we implement it in the study of the glycolytic metabolism of cancer cells. We show that the method can detect intermediates of the glycolytic pathway, quantify their rate of formation, and correlate this with variations in pH, all in a single measurement. We propose the method as a useful tool for the quantitative description of metabolic processes in living cells and for the validation of drug candidates aimed at suppressing glycolysis in cancer cells. © 2014 American Chemical Society.

Quaroni L.,University of Fribourg | Quaroni L.,Functional Genomics Center Zurich | Obst M.,University of Tübingen | Nowak M.,University of Tübingen | Zobi F.,University of Fribourg
Angewandte Chemie - International Edition | Year: 2015

Microscopy in the mid-infrared spectral range provides detailed chemical information on a sample at moderate spatial resolution and is being used increasingly in the characterization of biological entities as challenging as single cells. However, a conventional cellular 2D imaging measurement is limited in its ability to associate specific compositional information to subcellular structures because of the interference from the complex topography of the sample. Herein we provide a method and protocols that overcome this challenge in which tilt-series infrared tomography is used with a standard benchtop infrared microscope. This approach gives access to the quantitative 3D distribution of molecular components based on the intrinsic contrast provided by the sample. We demonstrate the method by quantifying the distribution of an exogenous metal carbonyl complex throughout the cell and by reporting changes in its coordination sphere in different locations in the cell. ©2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim chemical imaging • infrared tomography • single-cell studies.

Shakhova O.,University of Zürich | Zingg D.,University of Zürich | Schaefer S.M.,University of Zürich | Hari L.,University of Zürich | And 12 more authors.
Nature Cell Biology | Year: 2012

Giant congenital naevi are pigmented childhood lesions that frequently lead to melanoma, the most aggressive skin cancer. The mechanisms underlying this malignancy are largely unknown, and there are no effective therapies. Here we describe a mouse model for giant congenital naevi and show that naevi and melanoma prominently express Sox10, a transcription factor crucial for the formation of melanocytes from the neural crest. Strikingly, Sox10 haploinsufficiency counteracts Nras Q61K-driven congenital naevus and melanoma formation without affecting the physiological functions of neural crest derivatives in the skin. Moreover, Sox10 is also crucial for the maintenance of neoplastic cells in vivo. In human patients, virtually all congenital naevi and melanomas are SOX10 positive. Furthermore, SOX10 silencing in human melanoma cells suppresses neural crest stem cell properties, counteracts proliferation and cell survival, and completely abolishes in vivo tumour formation. Thus, SOX10 represents a promising target for the treatment of congenital naevi and melanoma in human patients. © 2012 Macmillan Publishers Limited. All rights reserved.

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