208 research outputs found
Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell
No full text19 páginas, 3 figurasThe regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.This work was funded by Ministerio de Ciencia, Innovación y Universidades, grant
number BFU2016-75792-R.Peer reviewe
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"BRÜDERLICHE EGOISTEN". DIE GEDICHTÜBERSETZUNGEN AUS DEM SPANISCHEN VON ERICH ARENDT UND HANS MAGNUS ENZENSBERGER
No full textThe authors and translators Erich Arendt and Hans Magnus Enzensberger are two key figures in German literature after 1945, known especially for their appropriation of foreign literatures. They both contributed extensively to the reception of Modern Latin American and Spanish Poetry in East and West Germany by translating poets such as Pablo Neruda, César Vallejo and Rafael Alberti. This is the first study to explore the asymmetrically intertwined literary conditions of the two author-translator figures with regard to the ways in which engaging with a foreign text opens up a perspective on the author-translator’s own poetology.Dissertation not available (per author's request)Dissertation restricted upon deposit / 10-Sep-2015, Kimberl
The use of a real-time luciferase assay to quantify gene expression dynamics in the living yeast cell
No full text[EN] A destabilized version of firefly luciferase was used in living yeast cells as a real-time reporter for gene expression. This highly sensitive and non-invasive system can be simultaneously used upon many different experimental conditions in small culture aliquots. This allows the dose-response behaviour of gene expression driven by any yeast promoter to be reported and can be used to quantify important parameters, such as the threshold, sensitivity, response time, maximal activity and synthesis rate for a given stimulus. We applied the luciferase assay to the nutrient-regulated GAL1 promoter and the stress-responsive GRE2 promoter. We find that luciferase expression driven by the GAL1 promoter responds dynamically to growing galactose concentrations, with increasing synthesis rates determined by the light increment in the initial linear phase of activation. In the case of the GRE2 promoter, we demonstrate that the very short-lived version of luciferase used here is an excellent tool to quantitatively describe transient transcriptional activation. The luciferase expression controlled by the GRE2 promoter responds dynamically to a gradual increase of osmotic or oxidative stress stimuli, which is mainly based on the progressive increase of the time the promoter remains active. Finally, we determined the dose-response behaviour of a single transcription factor binding site in a synthetic promoter context, using the stress response element (STRE) as an example. Taken together, the luciferase assay described here is an attractive tool to rapidly and precisely determine and compare kinetic parameters of gene expression. Copyright (c) 2012 John Wiley & Sons, Ltd.We thank Takayoshi Kuno for the kind gift of plasmid pGL3, containing the destabilized firefly luciferase gene. This study was supported by the Ministerio de Ciencia e Innovacion (Grant Nos BFU2008-00271 and BFU2011-23326). A.R. is the recipient of an FPI predoctoral fellowship from the Ministerio de Ciencia e Innovacion.Rienzo, A.; Pascual-Ahuir Giner, MD.; Proft, MH. (2012). The use of a real-time luciferase assay to quantify gene expression dynamics in the living yeast cell. Yeast. 29(6):219-231. doi:10.1002/yea.2905S219231296Alberti, S., Gitler, A. D., & Lindquist, S. (2007). A suite of Gateway®cloning vectors for high-throughput genetic analysis inSaccharomyces cerevisiae. Yeast, 24(10), 913-919. doi:10.1002/yea.1502Cormack, B. (1998). Green fluorescent protein as a reporter of transcription and protein localization in fungi. Current Opinion in Microbiology, 1(4), 406-410. doi:10.1016/s1369-5274(98)80057-xDeng, L., Sugiura, R., Takeuchi, M., Suzuki, M., Ebina, H., Takami, T., … Kuno, T. (2006). Real-Time Monitoring of Calcineurin Activity in Living Cells: Evidence for Two Distinct Ca2+-dependent Pathways in Fission Yeast. Molecular Biology of the Cell, 17(11), 4790-4800. doi:10.1091/mbc.e06-06-0526Gasch, A. P. (2007). Comparative genomics of the environmental stress response in ascomycete fungi. Yeast, 24(11), 961-976. doi:10.1002/yea.1512Hahn, S., & Young, E. T. (2011). Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators. Genetics, 189(3), 705-736. doi:10.1534/genetics.111.127019Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., … Young, R. A. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431(7004), 99-104. doi:10.1038/nature02800Kuge, S. (1997). Regulation of yAP-1 nuclear localization in response to oxidative stress. The EMBO Journal, 16(7), 1710-1720. doi:10.1093/emboj/16.7.1710Kundu, S., & Peterson, C. L. (2010). Dominant Role for Signal Transduction in the Transcriptional Memory of Yeast GAL Genes. Molecular and Cellular Biology, 30(10), 2330-2340. doi:10.1128/mcb.01675-09Marchler, G., Schüller, C., Adam, G., & Ruis, H. (1993). A Saccharomyces cerevisiae UAS element controlled by protein kinase A activates transcription in response to a variety of stress conditions. The EMBO Journal, 12(5), 1997-2003. doi:10.1002/j.1460-2075.1993.tb05849.xMartínez-Montañés, F., Pascual-Ahuir, A., & Proft, M. (2010). Toward a Genomic View of the Gene Expression Program Regulated by Osmostress in Yeast. OMICS: A Journal of Integrative Biology, 14(6), 619-627. doi:10.1089/omi.2010.0046Martínez-Pastor, M. T., Marchler, G., Schüller, C., Marchler-Bauer, A., Ruis, H., & Estruch, F. (1996). The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). The EMBO Journal, 15(9), 2227-2235. doi:10.1002/j.1460-2075.1996.tb00576.xMateus, C., & Avery, S. V. (2000). Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. Yeast, 16(14), 1313-1323. doi:10.1002/1097-0061(200010)16:143.0.co;2-oJ. Miraglia, L., J. King, F., & Damoiseaux, R. (2011). Seeing the Light: Luminescent Reporter Gene Assays. Combinatorial Chemistry & High Throughput Screening, 14(8), 648-657. doi:10.2174/138620711796504389Ni, L., Bruce, C., Hart, C., Leigh-Bell, J., Gelperin, D., Umansky, L., … Snyder, M. (2009). Dynamic and complex transcription factor binding during an inducible response in yeast. Genes & Development, 23(11), 1351-1363. doi:10.1101/gad.1781909Pelet, S., Rudolf, F., Nadal-Ribelles, M., de Nadal, E., Posas, F., & Peter, M. (2011). Transient Activation of the HOG MAPK Pathway Regulates Bimodal Gene Expression. Science, 332(6030), 732-735. doi:10.1126/science.1198851Proft, M. (2001). Regulation of the Sko1 transcriptional repressor by the Hog1 MAP kinase in response to osmotic stress. The EMBO Journal, 20(5), 1123-1133. doi:10.1093/emboj/20.5.1123Proft, M., & Struhl, K. (2004). MAP Kinase-Mediated Stress Relief that Precedes and Regulates the Timing of Transcriptional Induction. Cell, 118(3), 351-361. doi:10.1016/j.cell.2004.07.016Rep, M., Proft, M., Remize, F., Tamas, M., Serrano, R., Thevelein, J. M., & Hohmann, S. (2001). The Saccharomyces cerevisiae Sko1p transcription factor mediates HOG pathway-dependent osmotic regulation of a set of genes encoding enzymes implicated in protection from oxidative damage. Molecular Microbiology, 40(5), 1067-1083. doi:10.1046/j.1365-2958.2001.02384.xRobertson, J. B., & Johnson, C. H. (2011). Luminescence as a Continuous Real-Time Reporter of Promoter Activity in Yeast Undergoing Respiratory Oscillations or Cell Division Rhythms. Yeast Genetic Networks, 63-79. doi:10.1007/978-1-61779-086-7_4Robertson, J. B., Stowers, C. C., Boczko, E., & Hirschie Johnson, C. (2008). Real-time luminescence monitoring of cell-cycle and respiratory oscillations in yeast. Proceedings of the National Academy of Sciences, 105(46), 17988-17993. doi:10.1073/pnas.0809482105Varela, J. C., Praekelt, U. M., Meacock, P. A., Planta, R. J., & Mager, W. H. (1995). The Saccharomyces cerevisiae HSP12 gene is activated by the high-osmolarity glycerol pathway and negatively regulated by protein kinase A. Molecular and Cellular Biology, 15(11), 6232-6245. doi:10.1128/mcb.15.11.6232Yosef, N., & Regev, A. (2011). Impulse Control: Temporal Dynamics in Gene Transcription. Cell, 144(6), 886-896. doi:10.1016/j.cell.2011.02.01
Repression of ergosterol biosynthesis is essential for stress resistance and is mediated by the Hog1 MAP kinase and the Mot3 and Rox1 transcription factors
No full text[EN] Hyperosmotic stress triggers a complex adaptive response that is dominantly regulated by the Hog1 MAP kinase in yeast. Here we characterize a novel physiological determinant of osmostress tolerance, which involves the Hog1-dependent transcriptional downregulation of ergosterol biosynthesis genes (ERG). Yeast cells considerably lower their sterol content in response to high osmolarity. The transcriptional repressors Mot3 and Rox1 are essential for this response. Both factors together with Hog1 are required to rapidly and transiently shut down transcription of ERG2 and ERG11 upon osmoshock. Mot3 abundance and its binding to the ERG2 promoter is stimulated by osmostress in a Hog1-dependent manner. As an additional layer of control, the expression of the main transcriptional activator of ERG gene expression, Ecm22, is negatively regulated by Hog1 and Mot3/Rox1 upon salt shock. Oxidative stress also triggers repression of ERG2, 11 transcription and a profound decrease in total sterol levels. However, this response was only partially dependent on Mot3/Rox1 and Hog1. Finally, we show that the upc2-1 mutation confers stress insensitive hyperaccumulation of ergosterol, overexpression of ERG2, 11 and severe sensitivity to salt and oxidative stress. Our results indicate that transcriptional control of ergosterol biosynthesis is an important physiological target of stress signalling.We thank J.M. Mulet for his help with the quantification of intracellular ion concentrations, W.A. Prinz (NIH, Bethesda, MD) and A.K. Menon (Weill Cornell Medical College, New York) for the kind gift of the upc2-1 strain, F. Winston (Harvard Medical School, Boston) for the kind gift of the MOT3-18myc strain, and Avelino Corma (Instituto de Tecnologia Quimica, Valencia, Spain) for making available an ICP optical emission spectrometer for ion content determination. This work was supported by grants from Ministerio de Educacion y Ciencia (BFU2005-01714), from Ministerio de Ciencia e Innovacion (BFU2008-00271) and from Consejo Superior de Investigaciones Cientificas (200820I019). F.M. is recipient of an FPI predoctoral fellowship from Ministerio de Educacion y Ciencia.Martínez Montañés, FV.; Pascual-Ahuir Giner, MD.; Proft ., MH. (2010). Repression of ergosterol biosynthesis is essential for stress resistance and is mediated by the Hog1 MAP kinase and the Mot3 and Rox1 transcription factors. Molecular Microbiology. 79(4):1008-1023. https://doi.org/10.1111/j.1365-2958.2010.07502.xS1008102379
Ask yeast how to burn your fats: lessons learned from the metabolic adaptation to salt stress
No full text7 páginas, 3 figurasHere, we review and update the recent advances in the metabolic control during the adaptive response of budding yeast to hyperosmotic and salt stress, which is one of the best understood signaling events at the molecular level. This environmental stress can be easily applied and hence has been exploited in the past to generate an impressively detailed and comprehensive model of cellular adaptation. It is clear now that this stress modulates a great number of different physiological functions of the cell, which altogether contribute to cellular survival and adaptation. Primary defense mechanisms are the massive induction of stress tolerance genes in the nucleus, the activation of cation transport at the plasma membrane, or the production and intracellular accumulation of osmolytes. At the same time and in a coordinated manner, the cell shuts down the expression of housekeeping genes, delays the progression of the cell cycle, inhibits genomic replication, and modulates translation efficiency to optimize the response and to avoid cellular damage. To this fascinating interplay of cellular functions directly regulated by the stress, we have to add yet another layer of control, which is physiologically relevant for stress tolerance. Salt stress induces an immediate metabolic readjustment, which includes the up-regulation of peroxisomal biomass and activity in a coordinated manner with the reinforcement of mitochondrial respiratory metabolism. Our recent findings are consistent with a model, where salt stress triggers a metabolic shift from fermentation to respiration fueled by the enhanced peroxisomal oxidation of fatty acids. We discuss here the regulatory details of this stress-induced metabolic shift and its possible roles in the context of the previously known adaptive functions.The work of the authors was supported by grants from Ministerio de Economía y Competitividad (BFU2011-23326 and BFU2016-75792-R).Peer reviewe
Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast
No full text[EN] Optimized nutrient utilization is crucial for the progression of microorganisms in competing communities. Here we investigate how different budding yeast species and ecological isolates have established divergent preferences for two alternative sugar substrates: Glucose, which is fermented preferentially by yeast, and galactose, which is alternatively used upon induction of the relevant GAL metabolic genes. We quantified the dose-dependent induction of the GAL1 gene encoding the central galactokinase enzyme and found that a very large diversification exists between different yeast ecotypes and species. The sensitivity of GAL1 induction correlates with the growth performance of the respective yeasts with the alternative sugar. We further define some of the mechanisms, which have established different glucose/galactose consumption strategies in representative yeast strains by modulating the activity of the Gal3 inducer. (1) Optimal galactose consumers, such as Saccharomyces uvarum, contain a hyperactive GAL3 promoter, sustaining highly sensitive GAL1 expression, which is not further improved upon repetitive galactose encounters. (2) Desensitized galactose consumers, such as S. cerevisiae Y12, contain a less sensitive Gal3 sensor, causing a shift of the galactose response towards higher sugar concentrations even in galactose experienced cells. (3) Galactose insensitive sugar consumers, such as S. cerevisiae DBVPG6044, contain an interrupted GAL3 gene, causing extremely reluctant galactose consumption, which is, however, improved upon repeated galactose availability. In summary, different yeast strains and natural isolates have evolved galactose utilization strategies, which cover the whole range of possible sensitivities by modulating the expression and/or activity of the inducible galactose sensor Gal3.Ahmedabad University, Grant/Award Number: AU/SUG/SAS/DBLS/2019-20/01; DBT- Ramalinagaswami, Grant/Award Number: AU/SAS/DBT-RLS/20-21/04_KS_03.25; Ministerio de Ciencia e Innovacion, Grant/Award Number: PID2019-104214RB-I00Fita-Torró, J.; Swamy, KBS.; Pascual-Ahuir Giner, MD.; Proft, MH. (2023). Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast. Molecular Ecology (Online). 32(13):3557-3574. https://doi.org/10.1111/mec.16954S35573574321
Deciphering dynamic dose responses of natural promoters and single cis elements upon osmotic and oxidative stress in yeast
No full text[EN] Fine-tuned activation of gene expression in response to stress is the result of dynamic interactions of transcription factors with specific promoter binding sites. In the study described here we used a time-resolved luciferase reporter assay in living Saccharomyces cerevisiae yeast cells to gain insights into how osmotic and oxidative stress signals modulate gene expression in a dose-sensitive manner. Specifically, the dose-response behavior of four different natural promoters (GRE2, CTT1, SOD2, and CCP1) reveals differences in their sensitivity and dynamics in response to different salt and oxidative stimuli. Characteristic dose-response profiles were also obtained for artificial promoters driven by only one type of stress-regulated consensus element, such as the cyclic AMP-responsive element, stress response element, or AP-1 site. Oxidative and osmotic stress signals activate these elements separately and with different sensitivities through different signaling molecules. Combination of stress-activated cis elements does not, in general, enhance the absolute expression levels; however, specific combinations can increase the inducibility of the promoter in response to different stress doses. Finally, we show that the stress tolerance of the cell critically modulates the dynamics of its transcriptional response in the case of oxidative stress.This work was supported by the Ministerio de Economa y Competitividad (grant BFU2011-23326 to M.P.) and the Ministerio de Ciencia e Innovacion (predoctoral FPI grant to A.R.).Dolz Edo, L.; Rienzo, A.; Poveda Huertes, D.; Pascual-Ahuir Giner, MD.; Proft, MH. (2013). Deciphering dynamic dose responses of natural promoters and single cis elements upon osmotic and oxidative stress in yeast. Molecular and Cellular Biology. 33(11):2228-2240. https://doi.org/10.1128/MCB.00240-13S222822403311Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., … Brown, P. O. (2000). Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Molecular Biology of the Cell, 11(12), 4241-4257. doi:10.1091/mbc.11.12.4241Ni, L., Bruce, C., Hart, C., Leigh-Bell, J., Gelperin, D., Umansky, L., … Snyder, M. (2009). Dynamic and complex transcription factor binding during an inducible response in yeast. Genes & Development, 23(11), 1351-1363. doi:10.1101/gad.1781909Posas, F., Chambers, J. R., Heyman, J. A., Hoeffler, J. P., de Nadal, E., & Ariño, J. (2000). The Transcriptional Response of Yeast to Saline Stress. Journal of Biological Chemistry, 275(23), 17249-17255. doi:10.1074/jbc.m910016199Rep, M., Krantz, M., Thevelein, J. M., & Hohmann, S. (2000). The Transcriptional Response ofSaccharomyces cerevisiaeto Osmotic Shock. 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Computational Worlds: An Information Ontology
No full textRyan D. Mullins Computational Worlds: An Information Ontology Abstract of the Master-Thesis In this thesis, 'the world', that unified, all-encompassing domain about which we speak and make apparent discoveries every day will be declared another mythology. Instead, reality will look radically different. Reality comprises distortive, aesthetic simulations. The reality that will emerge will be a computational reality, a metaphysical pluralism in which actuality and possibility vie and vex, ultimately 'collapsing' into unified information states. This is a philosophy of the transfinite; more negatively, an anti-Kantian, anti-monistic philosophy. The author seeks nothing less than a new prism through which to view traditional philosophical problems and, in the best-case scenario, create possible solutions
Structure and Dynamics of Confined Liquids: Challenges and Perspectives for the X-ray Surface Forces Apparatus
No full textThe molecular-scale structure and dynamics of confined liquids has increasingly gained relevance for applications in nanotechnology. Thus, a detailed knowledge of the structure of confined liquids on molecular length scales is of great interest for fundamental and applied sciences. To study confined structures under dynamic conditions, we constructed an in situ X-ray surface forces apparatus (X-SFA). This novel device can create a precisely controlled slit-pore confinement down to dimensions on the 10 nm scale by using a cylinder-on-flat geometry for the first time. Complementary structural information can be obtained by simultaneous force measurements and X-ray scattering experiments. The in-plane structure of liquids parallel to the slit pore and density profiles perpendicular to the confining interfaces are studied by X-ray scattering and reflectivity. The normal load between the opposing interfaces can be modulated to study the structural dynamics of confined liquids. The confinement gap distance is tracked simultaneously with nanometer precision by analyzing optical interference fringes of equal chromatic order. Relaxation processes can be studied by driving the system out of equilibrium by shear stress or compression/decompression cycles of the slit pore. The capability of the new device is demonstrated on the liquid crystal 4'-octyl-4-cyano-biphenyl (8CB) in its smectic A (SmA) mesophase. Its molecular-scale structure and orientation confined in 100 nm to 1.7 mu m slit pores was studied under static and dynamic nonequilibrium conditions.The authors acknowledge the help of Thomas Buslaps (ESRF) at beamline ID31, Marie Ruat (ESRF) for support on the CdTe MAXIPIX detector, and Michael Kappl (MPI-P) for AFM measurements and thank Harald Reichert (ESRF), Milena Lippmann (PETRA III), and Hans-Jürgen Butt (MPI-P) for helpful discussions. J.M. and M.M. acknowledge the MAINZ Graduate School of Excellence, funded through the Excellence Initiative (DFG/GSC 266). M.V. was supported by an ERC Starting Grant (no. 677663), and H.L., by the China Scholarship Council.Mezger, M (reprint author), Max Planck Inst Polymer Res, Ackermannweg 10, D-55128 Mainz, Germany, Johannes Gutenberg Univ Mainz, Inst Phys, D-55128 Mainz, Germany.
Valtiner, M (reprint author), Vienna Inst Technol, Inst Appl Phys, Wiedner Hauptstr 8-10-E134, A-1040 Vienna, Austria, Max Planck Inst Eisenforsch GmbH, Max Planck Str 1, D-40237 Dusseldorf, Germa
Verstehen, was Markus erzählt: philologisch-hermeneutische Reflexionen zum Übersetzen von Markus 3,1–6
No full textThe thesis reflects translation as a paradigm of interpretation. The exegesis of a text depends on how we understand its language, and we try to un-derstand the text in our own language. Thus translation is closely related to fundamental questions of interpretation. Starting from a philological point of view and hermeneutical considerations, the author discusses problems of translation in a Markan narrative. The hermeneutical approach leads to the question of the adequacy of understanding between the conflicting areas of non-arbitrariness and a variety of possible interpretations.
Die Arbeit reflektiert das Übersetzen als ein Paradigma der Interpretation. Die Auslegung eines Textes basiert auf unserem Verständnis seiner Sprache, und wir suchen, ihn in unsrer Sprache zu verstehen. Insofern spiegelt das Anliegen einer Übersetzung Grundfragen der Interpretation. Ausgehend von einer philologischen Orientierung und hermeneutischen Überlegungen diskutiert der Autor Probleme des Übersetzens einer markinischen Erzählung. Sein hermeneutische Interesse gilt der Frage der Angemessenheit des Verstehens im Spannungsfeld zwischen der Vielfalt möglicher Deutungen und der Nichtbeliebigkeit der Interpretation
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