Design-Time Quantification of Integrity in Cyber-Physical-Systems

In a software system it is possible to quantify the amount of information that is leaked or corrupted by analysing the flows of information present in the source code. In a cyber-physical system, information flows are not only present at the digital level, but also at a physical level, and to and fro the two levels. In this work, we provide a methodology to formally analyse a Cyber-Physical System composite model (combining physics and control) using an information flow-theoretic approach. We use this approach to quantify the level of vulnerability of a system with respect to attackers with different capabilities. We illustrate our approach by means of a water distribution case study

Improvement and analysis of a pseudo random bit generator by means of cellular automata

In this paper, we implement a revised pseudo random bit generator based on a rule-90 cellular automaton. For this purpose, we introduce a sequence matrix H_N with the aim of calculating the pseudo random sequences of N bits employing the algorithm related to the automaton backward evolution. In addition, a multifractal structure of the matrix H_N is revealed and quantified according to the multifractal formalism. The latter analysis could help to disentangle what kind of automaton rule is used in the randomization process and therefore it could be useful in cryptanalysis. Moreover, the conditions are found under which this pseudo random generator passes all the statistical tests provided by the National Institute of Standards and Technology (NIST)Comment: 20 pages, 12 figure

Prototipo de Cámara Infrarroja para obtener el Índice NDVI en Agricultura de Precisión

Las Tecnologías de la Información y Comunicación (TICs) y el uso de dispositivos móviles han revolucionado prácticamente todas las áreas del quehacer humano, dando a los usuarios de estos dispositivos las habilidades para realizar tareas que antes solo eran posibles a través de equipos de escritorio. Una de las áreas que han sido beneficiadas por estas tecnologías es la agricultura creando el término “Agricultura de Precisión (AP)”. En este artículo se presenta un prototipo de cámara infrarroja de bajo costo para obtener el Índice Diferencial de Vegetación Normalizado (NDVI: Normalized Difference Vegetation Index) el cual es usado para estimar la cantidad, calidad y desarrollo de la vegetación con base a la medición (por medio de sensores remotos) de la intensidad de la radiación de ciertas bandas del espectro electromagnético que la vegetación refleja. Este prototipo se basa en imágenes tomadas a cultivos en ambientes controlados, se realizan dos tomas del mismo objetivo (una imagen en el espectro de colores normal y una segunda foto en el espectro infrarrojo, procesando ambas imágenes es como se obtiene el índice NDVI. Asimismo, se presenta un caso de estudio con aplicabilidad para la agronomía donde usuarios sin experiencia en TICs puedan hacer uso de estas tecnologías en cualquier tipo de dispositivo (en especial los teléfonos inteligentes) para determinar los niveles de salud de plantas en el mismo lugar sin tener que esperar para su procesamiento o tener que llevar las imágenes a un centro de procesamiento especializado

Involvement of the exomer complex in the polarized transport of Ena1 required for Saccharomyces cerevisiae survival against toxic cations

[EN] Exomer is an adaptor complex required for the direct transport of a selected number of cargoes from the trans-Golgi network (TGN) to the plasma membrane in Saccharomyces cerevisiae However, exomer mutants are highly sensitive to increased concentrations of alkali metal cations, a situation that remains unexplained by the lack of transport of any known cargoes. Here we identify several HAL genes that act as multicopy suppressors of this sensitivity and are connected to the reduced function of the sodium ATPase Ena1. Furthermore, we find that Ena1 is dependent on exomer function. Even though Ena1 can reach the plasma membrane independently of exomer, polarized delivery of Ena1 to the bud requires functional exomer. Moreover, exomer is required for full induction of Ena1 expression after cationic stress by facilitating the plasma membrane recruitment of the molecular machinery involved in Rim101 processing and activation of the RIM101 pathway in response to stress. Both the defective localization and the reduced levels of Ena1 contribute to the sensitivity of exomer mutants to alkali metal cations. Our work thus expands the spectrum of exomer-dependent proteins and provides a link to a more general role of exomer in TGN organization.We acknowledge Emma Keck for English language revision. We also thank members of the Translucent group, J. Arino, J. Ramos, and L. Yenush, for many useful discussions throughout this work and especially L. Yenush for her generous gift of strains and reagents. The help of O. Vincent was essential for developing the work involving RIM101. We also thank R. Valle for her technical assistance at the CR Laboratory. M. Trautwein is acknowledged for data acquisition and discussions during the early stages of the project. C.A. is supported by a USAL predoctoral fellowship. Work at the Spang laboratory was supported by the University of Basel and the Swiss National Science Foundation (31003A-141207 and 310030B-163480). C.R. was supported by grant SA073U14 from the Regional Government of Castilla y Leon and by grant BFU2013-48582-C2-1-P from the CICYT/FEDER Spanish program. J.M.M. acknowledges the financial support from Universitat Politecnica de Valencia project PAID-06-10-1496.Anton, C.; Zanolari, B.; Arcones, I.; Wang, C.; Mulet, JM.; Spang, A.; Roncero, C. (2017). Involvement of the exomer complex in the polarized transport of Ena1 required for Saccharomyces cerevisiae survival against toxic cations. Molecular Biology of the Cell. 28(25):3672-3685. https://doi.org/10.1091/mbc.E17-09-0549S367236852825Ariño, J., Ramos, J., & Sychrová, H. (2010). Alkali Metal Cation Transport and Homeostasis in Yeasts. Microbiology and Molecular Biology Reviews, 74(1), 95-120. doi:10.1128/mmbr.00042-09Bard, F., & Malhotra, V. (2006). The Formation of TGN-to-Plasma-Membrane Transport Carriers. Annual Review of Cell and Developmental Biology, 22(1), 439-455. doi:10.1146/annurev.cellbio.21.012704.133126Barfield, R. M., Fromme, J. C., & Schekman, R. (2009). The Exomer Coat Complex Transports Fus1p to the Plasma Membrane via a Novel Plasma Membrane Sorting Signal in Yeast. Molecular Biology of the Cell, 20(23), 4985-4996. doi:10.1091/mbc.e09-04-0324Bonifacino, J. S. (2014). Adaptor proteins involved in polarized sorting. Journal of Cell Biology, 204(1), 7-17. doi:10.1083/jcb.201310021Bonifacino, J. S., & Glick, B. S. (2004). The Mechanisms of Vesicle Budding and Fusion. Cell, 116(2), 153-166. doi:10.1016/s0092-8674(03)01079-1Bonifacino, J. S., & Lippincott-Schwartz, J. (2003). Coat proteins: shaping membrane transport. Nature Reviews Molecular Cell Biology, 4(5), 409-414. doi:10.1038/nrm1099Carlson, M., & Botstein, D. (1982). Two differentially regulated mRNAs with different 5′ ends encode secreted and intracellular forms of yeast invertase. Cell, 28(1), 145-154. doi:10.1016/0092-8674(82)90384-1Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., … Mostafavi, S. (2010). The Genetic Landscape of a Cell. Science, 327(5964), 425-431. doi:10.1126/science.1180823De Matteis, M. A., & Luini, A. (2008). Exiting the Golgi complex. Nature Reviews Molecular Cell Biology, 9(4), 273-284. doi:10.1038/nrm2378De Nadal, E., Clotet, J., Posas, F., Serrano, R., Gomez, N., & Arino, J. (1998). The yeast halotolerance determinant Hal3p is an inhibitory subunit of the Ppz1p Ser/Thr protein phosphatase. Proceedings of the National Academy of Sciences, 95(13), 7357-7362. doi:10.1073/pnas.95.13.7357Drubin, D. G., & Nelson, W. J. (1996). Origins of Cell Polarity. Cell, 84(3), 335-344. doi:10.1016/s0092-8674(00)81278-7Fell, G. L., Munson, A. M., Croston, M. A., & Rosenwald, A. G. (2011). Identification of Yeast Genes Involved in K+Homeostasis: Loss of Membrane Traffic Genes Affects K+Uptake. G3: Genes|Genomes|Genetics, 1(1), 43-56. doi:10.1534/g3.111.000166Ferrando, A., Kron, S. J., Rios, G., Fink, G. R., & Serrano, R. (1995). Regulation of cation transport in Saccharomyces cerevisiae by the salt tolerance gene HAL3. Molecular and Cellular Biology, 15(10), 5470-5481. doi:10.1128/mcb.15.10.5470Forsmark, A., Rossi, G., Wadskog, I., Brennwald, P., Warringer, J., & Adler, L. (2011). Quantitative Proteomics of Yeast Post-Golgi Vesicles Reveals a Discriminating Role for Sro7p in Protein Secretion. Traffic, 12(6), 740-753. doi:10.1111/j.1600-0854.2011.01186.xGaber, R. F., Styles, C. A., & Fink, G. R. (1988). TRK1 encodes a plasma membrane protein required for high-affinity potassium transport in Saccharomyces cerevisiae. Molecular and Cellular Biology, 8(7), 2848-2859. doi:10.1128/mcb.8.7.2848Galindo, A., Calcagno-Pizarelli, A. M., Arst, H. N., & Penalva, M. A. (2012). An ordered pathway for the assembly of fungal ESCRT-containing ambient pH signalling complexes at the plasma membrane. Journal of Cell Science, 125(7), 1784-1795. doi:10.1242/jcs.098897Goldstein, A. L., & McCusker, J. H. (1999). Three new dominant drug resistance cassettes for gene disruption inSaccharomyces cerevisiae. Yeast, 15(14), 1541-1553. doi:10.1002/(sici)1097-0061(199910)15:143.0.co;2-kHayashi, M., Fukuzawa, T., Sorimachi, H., & Maeda, T. (2005). Constitutive Activation of the pH-Responsive Rim101 Pathway in Yeast Mutants Defective in Late Steps of the MVB/ESCRT Pathway. Molecular and Cellular Biology, 25(21), 9478-9490. doi:10.1128/mcb.25.21.9478-9490.2005Herrador, A., Herranz, S., Lara, D., & Vincent, O. (2009). Recruitment of the ESCRT Machinery to a Putative Seven-Transmembrane-Domain Receptor Is Mediated by an Arrestin-Related Protein. Molecular and Cellular Biology, 30(4), 897-907. doi:10.1128/mcb.00132-09Herrador, A., Livas, D., Soletto, L., Becuwe, M., Léon, S., & Vincent, O. (2015). Casein kinase 1 controls the activation threshold of an α-arrestin by multisite phosphorylation of the interdomain hinge. Molecular Biology of the Cell, 26(11), 2128-2138. doi:10.1091/mbc.e14-11-1552Herranz, S., Rodriguez, J. M., Bussink, H.-J., Sanchez-Ferrero, J. C., Arst, H. N., Penalva, M. A., & Vincent, O. (2005). Arrestin-related proteins mediate pH signaling in fungi. Proceedings of the National Academy of Sciences, 102(34), 12141-12146. doi:10.1073/pnas.0504776102Hoya, M., Yanguas, F., Moro, S., Prescianotto-Baschong, C., Doncel, C., de León, N., … Valdivieso, M.-H. (2016). Traffic Through theTrans-Golgi Network and the Endosomal System Requires Collaboration Between Exomer and Clathrin Adaptors in Fission Yeast. Genetics, 205(2), 673-690. doi:10.1534/genetics.116.193458Huranova, M., Muruganandam, G., Weiss, M., & Spang, A. (2016). Dynamic assembly of the exomer secretory vesicle cargo adaptor subunits. EMBO reports, 17(2), 202-219. doi:10.15252/embr.201540795Kung, L. F., Pagant, S., Futai, E., D’Arcangelo, J. G., Buchanan, R., Dittmar, J. C., … Miller, E. A. (2011). Sec24p and Sec16p cooperate to regulate the GTP cycle of the COPII coat. The EMBO Journal, 31(4), 1014-1027. doi:10.1038/emboj.2011.444Lamb, T. M., & Mitchell, A. P. (2003). The Transcription Factor Rim101p Governs Ion Tolerance and Cell Differentiation by Direct Repression of the Regulatory Genes NRG1 and SMP1 in Saccharomyces cerevisiae. Molecular and Cellular Biology, 23(2), 677-686. doi:10.1128/mcb.23.2.677-686.2003Lamb, T. M., Xu, W., Diamond, A., & Mitchell, A. P. (2000). Alkaline Response Genes ofSaccharomyces cerevisiaeand Their Relationship to theRIM101Pathway. Journal of Biological Chemistry, 276(3), 1850-1856. doi:10.1074/jbc.m008381200Madrid, R., Gómez, M. J., Ramos, J., & Rodrı́guez-Navarro, A. (1998). Ectopic Potassium Uptake intrk1 trk2Mutants ofSaccharomyces cerevisiaeCorrelates with a Highly Hyperpolarized Membrane Potential. Journal of Biological Chemistry, 273(24), 14838-14844. doi:10.1074/jbc.273.24.14838Maresova, L., & Sychrova, H. (2004). Physiological characterization of Saccharomyces cerevisiae kha1 deletion mutants. Molecular Microbiology, 55(2), 588-600. doi:10.1111/j.1365-2958.2004.04410.xMarqués, M. C., Zamarbide-Forés, S., Pedelini, L., Llopis-Torregrosa, V., & Yenush, L. (2015). A functional Rim101 complex is required for proper accumulation of the Ena1 Na+-ATPase protein in response to salt stress in Saccharomyces cerevisiae. FEMS Yeast Research, 15(4). doi:10.1093/femsyr/fov017Mulet, J. M., Leube, M. P., Kron, S. J., Rios, G., Fink, G. R., & Serrano, R. (1999). A Novel Mechanism of Ion Homeostasis and Salt Tolerance in Yeast: the Hal4 and Hal5 Protein Kinases Modulate the Trk1-Trk2 Potassium Transporter. Molecular and Cellular Biology, 19(5), 3328-3337. doi:10.1128/mcb.19.5.3328Mulet, J. M., & Serrano, R. (2002). Simultaneous determination of potassium and rubidium content in yeast. Yeast, 19(15), 1295-1298. doi:10.1002/yea.909Murguía, J. R., Bellés, J. M., & Serrano, R. (1996). The YeastHAL2Nucleotidase Is anin VivoTarget of Salt Toxicity. Journal of Biological Chemistry, 271(46), 29029-29033. doi:10.1074/jbc.271.46.29029Obara, K., & Kihara, A. (2014). Signaling Events of the Rim101 Pathway Occur at the Plasma Membrane in a Ubiquitination-Dependent Manner. Molecular and Cellular Biology, 34(18), 3525-3534. doi:10.1128/mcb.00408-14Paczkowski, J. E., & Fromme, J. C. (2014). Structural Basis for Membrane Binding and Remodeling by the Exomer Secretory Vesicle Cargo Adaptor. Developmental Cell, 30(5), 610-624. doi:10.1016/j.devcel.2014.07.014Paczkowski, J. E., Richardson, B. C., & Fromme, J. C. (2015). Cargo adaptors: structures illuminate mechanisms regulating vesicle biogenesis. Trends in Cell Biology, 25(7), 408-416. doi:10.1016/j.tcb.2015.02.005Paczkowski, J. E., Richardson, B. C., Strassner, A. M., & Fromme, J. C. (2012). The exomer cargo adaptor structure reveals a novel GTPase-binding domain. The EMBO Journal, 31(21), 4191-4203. doi:10.1038/emboj.2012.268Parsons, A. B., Brost, R. L., Ding, H., Li, Z., Zhang, C., Sheikh, B., … Boone, C. (2003). Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nature Biotechnology, 22(1), 62-69. doi:10.1038/nbt919Peñalva, M. A., Lucena-Agell, D., & Arst, H. N. (2014). Liaison alcaline: Pals entice non-endosomal ESCRTs to the plasma membrane for pH signaling. Current Opinion in Microbiology, 22, 49-59. doi:10.1016/j.mib.2014.09.005Ríos, G., Cabedo, M., Rull, B., Yenush, L., Serrano, R., & Mulet, J. M. (2013). Role of the yeast multidrug transporter Qdr2 in cation homeostasis and the oxidative stress response. FEMS Yeast Research, 13(1), 97-106. doi:10.1111/1567-1364.12013RIOS, G., FERRANDO, A., & SERRANO, R. (1997). Mechanisms of Salt Tolerance Conferred by Overexpression of theHAL1 Gene inSaccharomyces cerevisiae. Yeast, 13(6), 515-528. doi:10.1002/(sici)1097-0061(199705)13:63.0.co;2-xRitz, A. M., Trautwein, M., Grassinger, F., & Spang, A. (2014). The Prion-like Domain in the Exomer-Dependent Cargo Pin2 Serves as a trans-Golgi Retention Motif. Cell Reports, 7(1), 249-260. doi:10.1016/j.celrep.2014.02.026Rockenbauch, U., Ritz, A. M., Sacristan, C., Roncero, C., & Spang, A. (2012). The complex interactions of Chs5p, the ChAPs, and the cargo Chs3p. Molecular Biology of the Cell, 23(22), 4402-4415. doi:10.1091/mbc.e11-12-1015Roncero, C. (2002). The genetic complexity of chitin synthesis in fungi. Current Genetics, 41(6), 367-378. doi:10.1007/s00294-002-0318-7Rothfels, K., Tanny, J. C., Molnar, E., Friesen, H., Commisso, C., & Segall, J. (2005). Components of the ESCRT Pathway, DFG16, and YGR122w Are Required for Rim101 To Act as a Corepressor with Nrg1 at the Negative Regulatory Element of the DIT1 Gene of Saccharomyces cerevisiae. Molecular and Cellular Biology, 25(15), 6772-6788. doi:10.1128/mcb.25.15.6772-6788.2005Santos, B., & Snyder, M. (1997). Targeting of Chitin Synthase 3 to Polarized Growth Sites in Yeast Requires Chs5p and Myo2p. Journal of Cell Biology, 136(1), 95-110. doi:10.1083/jcb.136.1.95Sato, M., Dhut, S., & Toda, T. (2005). New drug-resistant cassettes for gene disruption and epitope tagging inSchizosaccharomyces pombe. Yeast, 22(7), 583-591. doi:10.1002/yea.1233Schekman, R., & Orci, L. (1996). Coat Proteins and Vesicle Budding. Science, 271(5255), 1526-1533. doi:10.1126/science.271.5255.1526Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., … Andrews, B. (2006). Mapping Pathways and Phenotypes by Systematic Gene Overexpression. Molecular Cell, 21(3), 319-330. doi:10.1016/j.molcel.2005.12.011Spang, A. (2008). Membrane traffic in the secretory pathway. Cellular and Molecular Life Sciences, 65(18), 2781-2789. doi:10.1007/s00018-008-8349-yStarr, T. L., Pagant, S., Wang, C.-W., & Schekman, R. (2012). Sorting Signals That Mediate Traffic of Chitin Synthase III between the TGN/Endosomes and to the Plasma Membrane in Yeast. PLoS ONE, 7(10), e46386. doi:10.1371/journal.pone.0046386Trautwein, M., Schindler, C., Gauss, R., Dengjel, J., Hartmann, E., & Spang, A. (2006). Arf1p, Chs5p and the ChAPs are required for export of specialized cargo from the Golgi. The EMBO Journal, 25(5), 943-954. doi:10.1038/sj.emboj.7601007Trilla, J. A., Durán, A., & Roncero, C. (1999). Chs7p, a New Protein Involved in the Control of Protein Export from the Endoplasmic Reticulum that Is Specifically Engaged in the Regulation of Chitin Synthesis in Saccharomyces cerevisiae. Journal of Cell Biology, 145(6), 1153-1163. doi:10.1083/jcb.145.6.1153Valdivia, R. H., Baggott, D., Chuang, J. S., & Schekman, R. W. (2002). The Yeast Clathrin Adaptor Protein Complex 1 Is Required for the Efficient Retention of a Subset of Late Golgi Membrane Proteins. Developmental Cell, 2(3), 283-294. doi:10.1016/s1534-5807(02)00127-2Wadskog, I., Forsmark, A., Rossi, G., Konopka, C., Öyen, M., Goksör, M., … Adler, L. (2006). The Yeast Tumor Suppressor Homologue Sro7p Is Required for Targeting of the Sodium Pumping ATPase to the Cell Surface. Molecular Biology of the Cell, 17(12), 4988-5003. doi:10.1091/mbc.e05-08-0798Wang, C.-W., Hamamoto, S., Orci, L., & Schekman, R. (2006). Exomer: a coat complex for transport of select membrane proteins from the trans-Golgi network to the plasma membrane in yeast. Journal of Cell Biology, 174(7), 973-983. doi:10.1083/jcb.200605106Weiskoff, A. M., & Fromme, J. C. (2014). Distinct N-terminal regions of the exomer secretory vesicle cargo Chs3 regulate its trafficking itinerary. Frontiers in Cell and Developmental Biology, 2. doi:10.3389/fcell.2014.00047Yahara, N., Ueda, T., Sato, K., & Nakano, A. (2001). Multiple Roles of Arf1 GTPase in the Yeast Exocytic and Endocytic Pathways. Molecular Biology of the Cell, 12(1), 221-238. doi:10.1091/mbc.12.1.221Yenush, L., Merchan, S., Holmes, J., & Serrano, R. (2005). pH-Responsive, Posttranslational Regulation of the Trk1 Potassium Transporter by the Type 1-Related Ppz1 Phosphatase. Molecular and Cellular Biology, 25(19), 8683-8692. doi:10.1128/mcb.25.19.8683-8692.2005Yenush, L. (2002). The Ppz protein phosphatases are key regulators of K+ and pH homeostasis: implications for salt tolerance, cell wall integrity and cell cycle progression. The EMBO Journal, 21(5), 920-929. doi:10.1093/emboj/21.5.920Zanolari, B., Rockenbauch, U., Trautwein, M., Clay, L., Barral, Y., & Spang, A. (2011). Transport to the plasma membrane is regulated differently early and late in the cell cycle in Saccharomyces cerevisiae. Journal of Cell Science, 124(7), 1055-1066. doi:10.1242/jcs.07237