The Impact of Exercise on Telomere Length, DNA Methylation and Metabolic Footprints

Aging as a major risk factor influences the probability of developing cancer, cardiovascular disease and diabetes, amongst others. The underlying mechanisms of disease are still not fully understood, but research suggests that delaying the aging process could ameliorate these pathologies. A key biological process in aging is cellular senescence which is associated with several stressors such as telomere shortening or enhanced DNA methylation. Telomere length as well as DNA methylation levels can be used as biological age predictors which are able to detect excessive acceleration or deceleration of aging. Analytical methods examining aging are often not suitable, expensive, time-consuming or require a high level of technical expertise. Therefore, research focusses on combining analytical methods which have the potential to simultaneously analyse epigenetic, genomic as well as metabolic changes

Face recognition based on the proximity measure clustering

In this paper problems of featureless face recognition are considered. The recognition is based on clustering the proximity measures between the distributions of brightness clusters cardinality for segmented images. As a proximity measure three types of distances are used in this work: the Euclidean, cosine and Kullback-Leibler distances. Image segmentation and proximity measure clustering are carried out by means of a software model of the recurrent neural network. Results of the experimental studies of the proposed approach are presented

Probing relaxation times in graphene quantum dots

Graphene quantum dots are attractive candidates for solid-state quantum bits. In fact, the predicted weak spin-orbit and hyperfine interaction promise spin qubits with long coherence times. Graphene quantum dot devices have been extensively investigated with respect to their excitation spectrum, spin-filling sequence, and electron-hole crossover. However their relaxation dynamics remain largely unexplored. This is mainly due to challenges in device fabrication, in particular regarding the control of carrier confinement and the tunability of the tunnelling barriers, both crucial to experimentally investigate decoherence times. Here, we report on pulsed-gate transient spectroscopy and relaxation time measurements of excited states in graphene quantum dots. This is achieved by an advanced device design, allowing to tune the tunnelling barriers individually down to the low MHz regime and to monitor their asymmetry with integrated charge sensors. Measuring the transient currents through electronic excited states, we estimate lower limit of charge relaxation times on the order of 60-100 ns.Comment: To be published in Nature Communications. The first two authors contributed equally to this work. Main article: 10 pages, 4 figures. Supplementary information: 4 pages, 4 figure

Challenges and Innovation in Steel Wire Production

Abstract. Products and manufacturing processes of long-product producers are subject to constantly changing requirements, characterized by increasing demands on product quality and the efficient use of resources in production, combined with permanent cost pressures. For these reasons steel wire producers must constantly improve their innovation capacity to be able to meet increasing customer demands more flexibly and more efficiently. This awareness has been anchored at Swiss Steel AG, part of the Schmolz + Bickenbach Group, for many years and leads to more and new solutions in all corporate divisions. This article focuses on practical examples from the areas of process and product innovation. It discusses options for and the potentials and challenges of meeting current and future market needs. The successful implementation of new solutions requires an in-depth understanding as well as the application of knowledge throughout the entire process chain from development, production, sales to further processing and actual use of a product. The technical challenges are addressed as well as the opportunities presented when new approaches are sought

Development of a Scheme and Tools to Construct a Standard Moth Brain for Neural Network Simulations

Understanding the neural mechanisms for sensing environmental information and controlling behavior in natural environments is a principal aim in neuroscience. One approach towards this goal is rebuilding neural systems by simulation. Despite their relatively simple brains compared with those of mammals, insects are capable of processing various sensory signals and generating adaptive behavior. Nevertheless, our global understanding at network system level is limited by experimental constraints. Simulations are very effective for investigating neural mechanisms when integrating both experimental data and hypotheses. However, it is still very difficult to construct a computational model at the whole brain level owing to the enormous number and complexity of the neurons. We focus on a unique behavior of the silkmoth to investigate neural mechanisms of sensory processing and behavioral control. Standard brains are used to consolidate experimental results and generate new insights through integration. In this study, we constructed a silkmoth standard brain and brain image, in which we registered segmented neuropil regions and neurons. Our original software tools for segmentation of neurons from confocal images, KNEWRiTE, and the registration module for segmented data, NeuroRegister, are shown to be very effective in neuronal registration for computational neuroscience studies

Odorant Concentration Differentiator for Intermittent Olfactory Signals

Animals need to discriminate differences in spatiotemporally distributed sensory signals in terms of quality as well as quantity for generating adaptive behavior. Olfactory signals characterized by odor identity and concentration are intermittently distributed in the environment. From these intervals of stimulation, animals process odorant concentration to localize partners or food sources. Although concentration–response characteristics in olfactory neurons have traditionally been investigated using single stimulus pulses, their behavior under intermittent stimulus regimens remains largely elusive. Using the silkmoth (Bombyx mori) pheromone processing system, a simple and behaviorally well-defined model for olfaction, we investigated the neuronal representation of odorant concentration upon intermittent stimulation in the naturally occurring range. To the first stimulus in a series, the responses of antennal lobe (AL) projection neurons (PNs) showed a concentration dependence as previously shown in many olfactory systems. However, PN response amplitudes dynamically changed upon exposure to intermittent stimuli of the same odorant concentration and settled to a constant, largely concentration-independent level. As a result, PN responses emphasized odorant concentration changes rather than encoding absolute concentration in pulse trains of stimuli. Olfactory receptor neurons did not contribute to this response transformation which was due to long-lasting inhibition affecting PNs in the AL. Simulations confirmed that inhibition also provides advantages when stimuli have naturalistic properties. The primary olfactory center thus functions as an odorant concentration differentiator to efficiently detect concentration changes, thereby improving odorant source orientation over a wide concentration range.UTokyo Research掲載「匂いの濃度を効率的に表現する脳の計算メカニズムの発見」 URI: http://www.u-tokyo.ac.jp/ja/utokyo-research/research-news/a-novel-neuronal-mechanism-to-efficiently-code-odorant-concentration/UTokyo Research "A novel neuronal mechanism to efficiently code odorant concentration" URI: http://www.u-tokyo.ac.jp/en/utokyo-research/research-news/a-novel-neuronal-mechanism-to-efficiently-code-odorant-concentration

A Single Sex Pheromone Receptor Determines Chemical Response Specificity of Sexual Behavior in the Silkmoth Bombyx mori

In insects and other animals, intraspecific communication between individuals of the opposite sex is mediated in part by chemical signals called sex pheromones. In most moth species, male moths rely heavily on species-specific sex pheromones emitted by female moths to identify and orient towards an appropriate mating partner among a large number of sympatric insect species. The silkmoth, Bombyx mori, utilizes the simplest possible pheromone system, in which a single pheromone component, (E, Z)-10,12-hexadecadienol (bombykol), is sufficient to elicit full sexual behavior. We have previously shown that the sex pheromone receptor BmOR1 mediates specific detection of bombykol in the antennae of male silkmoths. However, it is unclear whether the sex pheromone receptor is the minimally sufficient determination factor that triggers initiation of orientation behavior towards a potential mate. Using transgenic silkmoths expressing the sex pheromone receptor PxOR1 of the diamondback moth Plutella xylostella in BmOR1-expressing neurons, we show that the selectivity of the sex pheromone receptor determines the chemical response specificity of sexual behavior in the silkmoth. Bombykol receptor neurons expressing PxOR1 responded to its specific ligand, (Z)-11-hexadecenal (Z11-16:Ald), in a dose-dependent manner. Male moths expressing PxOR1 exhibited typical pheromone orientation behavior and copulation attempts in response to Z11-16:Ald and to females of P. xylostella. Transformation of the bombykol receptor neurons had no effect on their projections in the antennal lobe. These results indicate that activation of bombykol receptor neurons alone is sufficient to trigger full sexual behavior. Thus, a single gene defines behavioral selectivity in sex pheromone communication in the silkmoth. Our findings show that a single molecular determinant can not only function as a modulator of behavior but also as an all-or-nothing initiator of a complex species-specific behavioral sequence

Characterization of tomato Cycling Dof Factors reveals conserved and new functions in the control of flowering time and abiotic stress responses

[EN] DNA binding with One Finger (DOF) transcription factors are involved in multiple aspects of plant growth and development but their precise roles in abiotic stress tolerance are largely unknown. Here we report a group of five tomato DOF genes, homologous to Arabidopsis Cycling DOF Factors (CDFs), that function as transcriptional regulators involved in responses to drought and salt stress and flowering-time control in a gene-specific manner. SlCDF15 are nuclear proteins that display specific binding with different affinities to canonical DNA target sequences and present diverse transcriptional activation capacities in vivo. SlCDF15 genes exhibited distinct diurnal expression patterns and were differentially induced in response to osmotic, salt, heat, and low-temperature stresses. Arabidopsis plants overexpressing SlCDF1 or SlCDF3 showed increased drought and salt tolerance. In addition, the expression of various stress-responsive genes, such as COR15, RD29A, and RD10, were differentially activated in the overexpressing lines. Interestingly, overexpression in Arabidopsis of SlCDF3 but not SlCDF1 promotes late flowering through modulation of the expression of flowering control genes such as CO and FT. Overall, our data connect SlCDFs to undescribed functions related to abiotic stress tolerance and flowering time through the regulation of specific target genes and an increase in particular metabolites.This work was supported by grants from Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA; project numbers: 2009-0004-C01, 2012-0008-C01), the Spanish Ministry of Science and Innovation (project number: BIO2010-14871), and the MERIT Project (FP7 ITN2010-264474). ARC was supported by a pre-doctoral fellowship from the INIA. The authors would like to thank Mar Gonzalez and Victor Carrasco for technical assistance and Dr Pablo Gonzalez-Melendi for technical handling of the confocal microscope. We also thank Eugenio Grau for technical assistance with RT-PCR analyses.Corrales, A.; González Nebauer, S.; Carrillo, L.; Fernández Nohales, P.; Marques Signes, J.; Renau Morata, B.; Granell, A.... (2014). Characterization of tomato Cycling Dof Factors reveals conserved and new functions in the control of flowering time and abiotic stress responses. Journal of Experimental Botany. 65(4):995-1012. https://doi.org/10.1093/jxb/ert451S9951012654AbuQamar, S., Luo, H., Laluk, K., Mickelbart, M. V., & Mengiste, T. (2009). Crosstalk between biotic and abiotic stress responses in tomato is mediated by theAIM1transcription factor. The Plant Journal, 58(2), 347-360. doi:10.1111/j.1365-313x.2008.03783.xAlonso, R., Oñate-Sánchez, L., Weltmeier, F., Ehlert, A., Diaz, I., Dietrich, K., … Dröge-Laser, W. (2009). A Pivotal Role of the Basic Leucine Zipper Transcription Factor bZIP53 in the Regulation of Arabidopsis Seed Maturation Gene Expression Based on Heterodimerization and Protein Complex Formation. The Plant Cell, 21(6), 1747-1761. doi:10.1105/tpc.108.062968Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402. doi:10.1093/nar/25.17.3389An, H. (2004). CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. Development, 131(15), 3615-3626. doi:10.1242/dev.01231Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., … Stockinger, H. (2012). ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research, 40(W1), W597-W603. doi:10.1093/nar/gks400Atherton, J. G., & Harris, G. P. (1986). Flowering. The Tomato Crop, 167-200. doi:10.1007/978-94-009-3137-4_4Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., … Noble, W. S. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research, 37(Web Server), W202-W208. doi:10.1093/nar/gkp335Ben-Naim, O., Eshed, R., Parnis, A., Teper-Bamnolker, P., Shalit, A., Coupland, G., … Lifschitz, E. (2006). The CCAAT binding factor can mediate interactions between CONSTANS-like proteins and DNA. The Plant Journal, 46(3), 462-476. doi:10.1111/j.1365-313x.2006.02706.xBEUVE, N., RISPAIL, N., LAINE, P., CLIQUET, J.-B., OURRY, A., & LE DEUNFF, E. (2004). Putative role of gamma -aminobutyric acid (GABA) as a long-distance signal in up-regulation of nitrate uptake in Brassica napus L. Plant, Cell and Environment, 27(8), 1035-1046. doi:10.1111/j.1365-3040.2004.01208.xBlumwald, E. (2000). Sodium transport and salt tolerance in plants. Current Opinion in Cell Biology, 12(4), 431-434. doi:10.1016/s0955-0674(00)00112-5Bombarely, A., Menda, N., Tecle, I. Y., Buels, R. M., Strickler, S., Fischer-York, T., … Mueller, L. A. (2010). The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Research, 39(Database), D1149-D1155. doi:10.1093/nar/gkq866Bressan, R., Bohnert, H., & Zhu, J.-K. (2009). Abiotic Stress Tolerance: From Gene Discovery in Model Organisms to Crop Improvement. Molecular Plant, 2(1), 1-2. doi:10.1093/mp/ssn097Calvert, A. (1959). Effect of the Early Environment on the Development of Flowering in Tomato II. Light and Temperature Interactions. Journal of Horticultural Science, 34(3), 154-162. doi:10.1080/00221589.1959.11513954Carmel-Goren, L., Liu, Y. S., Lifschitz, E., & Zamir, D. (2003). TheSELF-PRUNINGgene family in tomato. Plant Molecular Biology, 52(6), 1215-1222. doi:10.1023/b:plan.0000004333.96451.11Chaves, M. M., Flexas, J., & Pinheiro, C. (2008). Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Annals of Botany, 103(4), 551-560. doi:10.1093/aob/mcn125Claussen, W. (2005). Proline as a measure of stress in tomato plants. Plant Science, 168(1), 241-248. doi:10.1016/j.plantsci.2004.07.039Clough, S. J., & Bent, A. F. (1998). Floral dip: a simplified method forAgrobacterium-mediated transformation ofArabidopsis thaliana. The Plant Journal, 16(6), 735-743. doi:10.1046/j.1365-313x.1998.00343.xCuartero, J., & Fernández-Muñoz, R. (1998). Tomato and salinity. Scientia Horticulturae, 78(1-4), 83-125. doi:10.1016/s0304-4238(98)00191-5Czechowski, T., Stitt, M., Altmann, T., Udvardi, M. K., & Scheible, W.-R. (2005). Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis. Plant Physiology, 139(1), 5-17. doi:10.1104/pp.105.063743Diaz, I., Vicente-Carbajosa, J., Abraham, Z., Martinez, M., Isabel-La Moneda, I., & Carbonero, P. (2002). The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development. The Plant Journal, 29(4), 453-464. doi:10.1046/j.0960-7412.2001.01230.xDieleman, J. A., & Heuvelink, E. (1992). Factors affecting the number of leaves preceding the first inflorescence in the tomato. Journal of Horticultural Science, 67(1), 1-10. doi:10.1080/00221589.1992.11516214Farrant, J. M., & Moore, J. P. (2011). Programming desiccation-tolerance: from plants to seeds to resurrection plants. Current Opinion in Plant Biology, 14(3), 340-345. doi:10.1016/j.pbi.2011.03.018Fiehn, O., Kopka, J., Trethewey, R. N., & Willmitzer, L. (2000). Identification of Uncommon Plant Metabolites Based on Calculation of Elemental Compositions Using Gas Chromatography and Quadrupole Mass Spectrometry. Analytical Chemistry, 72(15), 3573-3580. doi:10.1021/ac991142iFornara, F., Panigrahi, K. C. S., Gissot, L., Sauerbrunn, N., Rühl, M., Jarillo, J. A., & Coupland, G. (2009). Arabidopsis DOF Transcription Factors Act Redundantly to Reduce CONSTANS Expression and Are Essential for a Photoperiodic Flowering Response. Developmental Cell, 17(1), 75-86. doi:10.1016/j.devcel.2009.06.015Gaquerel, E., Heiling, S., Schoettner, M., Zurek, G., & Baldwin, I. T. (2010). Development and Validation of a Liquid Chromatography−Electrospray Ionization−Time-of-Flight Mass Spectrometry Method for Induced Changes inNicotiana attenuataLeaves during Simulated Herbivory. Journal of Agricultural and Food Chemistry, 58(17), 9418-9427. doi:10.1021/jf1017737Gardiner, J., Sherr, I., & Scarpella, E. (2010). Expression of DOF genes identifies early stages of vascular development in Arabidopsis leaves. The International Journal of Developmental Biology, 54(8-9), 1389-1396. doi:10.1387/ijdb.093006jgGong, P., Zhang, J., Li, H., Yang, C., Zhang, C., Zhang, X., … Ye, Z. (2010). Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato. Journal of Experimental Botany, 61(13), 3563-3575. doi:10.1093/jxb/erq167Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., … Rokhsar, D. S. (2011). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40(D1), D1178-D1186. doi:10.1093/nar/gkr944Gualberti, G., Papi, M., Bellucci, L., Ricci, I., Bouchez, D., Camilleri, C., … Vittorioso, P. (2002). Mutations in the Dof Zinc Finger Genes DAG2 and DAG1 Influence with Opposite Effects the Germination of Arabidopsis Seeds. The Plant Cell, 14(6), 1253-1263. doi:10.1105/tpc.010491Guindon, S., & Gascuel, O. (2003). A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology, 52(5), 696-704. doi:10.1080/10635150390235520Gullberg, J., Jonsson, P., Nordström, A., Sjöström, M., & Moritz, T. (2004). Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Analytical Biochemistry, 331(2), 283-295. doi:10.1016/j.ab.2004.04.037Guo, Y., Qin, G., Gu, H., & Qu, L.-J. (2009). Dof5.6/HCA2, a Dof Transcription Factor Gene, Regulates Interfascicular Cambium Formation and Vascular Tissue Development in Arabidopsis. The Plant Cell, 21(11), 3518-3534. doi:10.1105/tpc.108.064139Haupt-Herting, S., Klug, K., & Fock, H. P. (2001). A New Approach to Measure Gross CO2 Fluxes in Leaves. Gross CO2 Assimilation, Photorespiration, and Mitochondrial Respiration in the Light in Tomato under Drought Stress. Plant Physiology, 126(1), 388-396. doi:10.1104/pp.126.1.388Hernando-Amado, S., González-Calle, V., Carbonero, P., & Barrero-Sicilia, C. (2012). The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling. BMC Plant Biology, 12(1), 202. doi:10.1186/1471-2229-12-202Hoekstra, F. A., Golovina, E. A., & Buitink, J. (2001). Mechanisms of plant desiccation tolerance. Trends in Plant Science, 6(9), 431-438. doi:10.1016/s1360-1385(01)02052-0Hoffman, N. E., Ko, K., Milkowski, D., & Pichersky, E. (1991). Isolation and characterization of tomato cDNA and genomic clones encoding the ubiquitin gene ubi3. Plant Molecular Biology, 17(6), 1189-1201. doi:10.1007/bf00028735Huang, Z., Zhang, Z., Zhang, X., Zhang, H., Huang, D., & Huang, R. (2004). Tomato TERF1 modulates ethylene response and enhances osmotic stress tolerance by activating expression of downstream genes. FEBS Letters, 573(1-3), 110-116. doi:10.1016/j.febslet.2004.07.064HUSSEY, G. (1963). Growth and Development in the Young Tomato: I. THE EFFECT OF TEMPERATURE AND LIGHT INTENSITY ON GROWTH OF THE SHOOT APEX AND LEAF PRIMORDIA. Journal of Experimental Botany, 14(2), 316-325. doi:10.1093/jxb/14.2.316Imaizumi, T. (2005). FKF1 F-Box Protein Mediates Cyclic Degradation of a Repressor of CONSTANS in Arabidopsis. Science, 309(5732), 293-297. doi:10.1126/science.1110586IWAMOTO, M., HIGO, K., & TAKANO, M. (2009). Circadian clock- and phytochrome-regulated Dof-like gene,Rdd1, is associated with grain size in rice. Plant, Cell & Environment, 32(5), 592-603. doi:10.1111/j.1365-3040.2009.01954.xJang, S., Marchal, V., Panigrahi, K. C. S., Wenkel, S., Soppe, W., Deng, X.-W., … Coupland, G. (2008). Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response. The EMBO Journal, 27(8), 1277-1288. doi:10.1038/emboj.2008.68Jones, M. L. (2013). Mineral nutrient remobilization during corolla senescence in ethylene-sensitive and -insensitive flowers. AoB Plants, 5(0), plt023-plt023. doi:10.1093/aobpla/plt023Karimi, M., Depicker, A., & Hilson, P. (2007). Recombinational Cloning with Plant Gateway Vectors. Plant Physiology, 145(4), 1144-1154. doi:10.1104/pp.107.106989Kerepesi, I., & Galiba, G. (2000). Osmotic and Salt Stress-Induced Alteration in Soluble Carbohydrate Content in Wheat Seedlings. Crop Science, 40(2), 482. doi:10.2135/cropsci2000.402482xKinet, J. M. (1977). Effect of light conditions on the development of the inflorescence in tomato. Scientia Horticulturae, 6(1), 15-26. doi:10.1016/0304-4238(77)90074-7Kirby, J., & Kavanagh, T. A. (2002). NAN fusions: a synthetic sialidase reporter gene as a sensitive and versatile partner for GUS. The Plant Journal, 32(3), 391-400. doi:10.1046/j.1365-313x.2002.01422.xKloosterman, B., Abelenda, J. A., Gomez, M. del M. C., Oortwijn, M., de Boer, J. M., Kowitwanich, K., … Bachem, C. W. B. (2013). Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature, 495(7440), 246-250. doi:10.1038/nature11912Konishi, M., & Yanagisawa, S. (2007). Sequential activation of two Dof transcription factor gene promoters during vascular development in Arabidopsis thaliana. Plant Physiology and Biochemistry, 45(8), 623-629. doi:10.1016/j.plaphy.2007.05.001Krohn, N. M., Yanagisawa, S., & Grasser, K. D. (2002). Specificity of the Stimulatory Interaction between Chromosomal HMGB Proteins and the Transcription Factor Dof2 and Its Negative Regulation by Protein Kinase CK2-mediated Phosphorylation. Journal of Biological Chemistry, 277(36), 32438-32444. doi:10.1074/jbc.m203814200Kurai, T., Wakayama, M., Abiko, T., Yanagisawa, S., Aoki, N., & Ohsugi, R. (2011). Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions. Plant Biotechnology Journal, 9(8), 826-837. doi:10.1111/j.1467-7652.2011.00592.xKushwaha, H., Gupta, S., Singh, V. K., Rastogi, S., & Yadav, D. (2010). Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis. Molecular Biology Reports, 38(8), 5037-5053. doi:10.1007/s11033-010-0650-9Lakhssassi, N., Doblas, V. G., Rosado, A., del Valle, A. E., Posé, D., Jimenez, A. J., … Botella, M. A. (2012). The Arabidopsis TETRATRICOPEPTIDE THIOREDOXIN-LIKE Gene Family Is Required for Osmotic Stress Tolerance and Male Sporogenesis. Plant Physiology, 158(3), 1252-1266. doi:10.1104/pp.111.188920Lee, H. E., Shin, D., Park, S. R., Han, S.-E., Jeong, M.-J., Kwon, T.-R., … Byun, M.-O. (2007). Ethylene responsive element binding protein 1 (StEREBP1) from Solanum tuberosum increases tolerance to abiotic stress in transgenic potato plants. Biochemical and Biophysical Research Communications, 353(4), 863-868. doi:10.1016/j.bbrc.2006.12.095Lijavetzky, D., Carbonero, P., & Vicente-Carbajosa, J. (2003). BMC Evolutionary Biology, 3(1), 17. doi:10.1186/1471-2148-3-17Livak, K. J., & Schmittgen, T. D. (2001). Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method. Methods, 25(4), 402-408. doi:10.1006/meth.2001.1262Mackay, J. P., & Crossley, M. (1998). Zinc fingers are sticking together. Trends in Biochemical Sciences, 23(1), 1-4. doi:10.1016/s0968-0004(97)01168-7Mena, M., Vicente-Carbajosa, J., Schmidt, R. J., & Carbonero, P. (1998). An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm. The Plant Journal, 16(1), 53-62. doi:10.1046/j.1365-313x.1998.00275.xMizoguchi, T., Wright, L., Fujiwara, S., Cremer, F., Lee, K., Onouchi, H., … Coupland, G. (2005). Distinct Roles of GIGANTEA in Promoting Flowering and Regulating Circadian Rhythms in Arabidopsis. The Plant Cell, 17(8), 2255-2270. doi:10.1105/tpc.105.033464Moreno-Risueno, M. Á., Martínez, M., Vicente-Carbajosa, J., & Carbonero, P. (2006). The family of DOF transcription factors: from green unicellular algae to vascular plants. Molecular Genetics and Genomics, 277(4), 379-390. doi:10.1007/s00438-006-0186-9Moreno-Risueno, M. Á., Díaz, I., Carrillo, L., Fuentes, R., & Carbonero, P. (2007). The HvDOF19 transcription factor mediates the abscisic acid-dependent repression of hydrolase genes in germinating barley aleurone. The Plant Journal, 51(3), 352-365. doi:10.1111/j.1365-313x.2007.03146.xMurashige, T., & Skoog, F. (1962). A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures. Physiologia Plantarum, 15(3), 473-497. doi:10.1111/j.1399-3054.1962.tb08052.xNakagawa, T., Kurose, T., Hino, T., Tanaka, K., Kawamukai, M., Niwa, Y., … Kimura, T. (2007). Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. Journal of Bioscience and Bioengineering, 104(1), 34-41. doi:10.1263/jbb.104.34Oñate-Sánchez, L., & Vicente-Carbajosa, J. (2008). DNA-free RNA isolation protocols for Arabidopsis thaliana, including seeds and siliques. BMC Research Notes, 1(1), 93. doi:10.1186/1756-0500-1-93ORELLANA, S., YAÑEZ, M., ESPINOZA, A., VERDUGO, I., GONZÁLEZ, E., RUIZ-LARA, S., & CASARETTO, J. A. (2010). The transcription factor SlAREB1 confers drought, salt stress tolerance and regulates biotic and abiotic stress-related genes in tomato. Plant, Cell & Environment, 33(12), 2191-2208. doi:10.1111/j.1365-3040.2010.02220.xPapi, M., Sabatini, S., Altamura, M. M., Hennig, L., Schäfer, E., Costantino, P., & Vittorioso, P. (2002). Inactivation of the Phloem-Specific Dof Zinc Finger GeneDAG1 Affects Response to Light and Integrity of the Testa of Arabidopsis Seeds. Plant Physiology, 128(2), 411-417. doi:10.1104/pp.010488Pinheiro, C., & Chaves, M. M. (2010). Photosynthesis and drought: can we make metabolic connections from available data? Journal of Experimental Botany, 62(3), 869-882. doi:10.1093/jxb/erq340Pnueli, L. (2001). Tomato SP-Interacting Proteins Define a Conserved Signaling System That Regulates Shoot Architecture and Flowering. THE PLANT CELL ONLINE, 13(12), 2687-2702. doi:10.1105/tpc.13.12.2687Rajasekaran, L. R., Aspinall, D., & Paleg, L. G. (2000). Physiological mechanism of tolerance of Lycopersicon spp. exposed to salt stress. Canadian Journal of Plant Science, 80(1), 151-159. doi:10.4141/p99-003Rizhsky, L., Liang, H., Shuman, J., Shulaev, V., Davletova, S., & Mittler, R. (2004). When Defense Pathways Collide. The Response of Arabidopsis to a Combination of Drought and Heat Stress. Plant Physiology, 134(4), 1683-1696. doi:10.1104/pp.103.033431Rueda-López, M., Crespillo, R., Cánovas, F. M., & Ávila, C. (2008). Differential regulation of two glutamine synthetase genes by a single Dof transcription factor. The Plant Journal, 56(1), 73-85. doi:10.1111/j.1365-313x.2008.03573.xSawa, M., Nusinow, D. A., Kay, S. A., & Imaizumi, T. (2007). FKF1 and GIGANTEA Complex Formation Is Required for Day-Length Measurement in Arabidopsis. Science, 318(5848), 261-265. doi:10.1126/science.1146994Seki, M., Umezawa, T., Urano, K., & Shinozaki, K. (2007). Regulatory metabolic networks in drought stress responses. Current Opinion in Plant Biology, 10(3), 296-302. doi:10.1016/j.pbi.2007.04.014Shannon, M. C., & Grieve, C. M. (1998). Tolerance of vegetable crops to salinity. Scientia Horticulturae, 78(1-4), 5-38. doi:10.1016/s0304-4238(98)00189-7Shaw, L. M., McIntyre, C. L., Gresshoff, P. M., & Xue, G.-P. (2009). Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation. Functional & Integrative Genomics, 9(4), 485-498. doi:10.1007/s10142-009-0130-2Shelp, B. J., Bown, A. W., & Faure, D. (2006). Extracellular γ-Aminobutyrate Mediates Communication between Plants and Other Organisms. Plant Physiology, 142(4), 1350-1352. doi:10.1104/pp.106.088955Shelp, B. (1999). Metabolism and functions of gamma-aminobutyric acid. Trends in Plant Science, 4(11), 446-452. doi:10.1016/s1360-1385(99)01486-7Skirycz, A., Jozefczuk, S., Stobiecki, M., Muth, D., Zanor, M. I., Witt, I., & Mueller-Roeber, B. (2007). Transcription factor AtDOF4;2 affects phenylpropanoid metabolism in Arabidopsis thaliana. New Phytologist, 175(3), 425-438. doi:10.1111/j.1469-8137.2007.02129.xSkirycz, A., Reichelt, M., Burow, M., Birkemeyer, C., Rolcik, J., Kopka, J., … Witt, I. (2006). DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. The Plant Journal, 47(1), 10-24. doi:10.1111/j.1365-313x.2006.02767.xSuárez-López, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F., & Coupland, G. (2001). CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature, 410(6832), 1116-1120. doi:10.1038/35074138Sun, S.-J., Guo, S.-Q., Yang, X., Bao, Y.-M., Tang, H.-J., Sun, H., … Zhang, H.-S. (2010). Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. Journal of Experimental Botany, 61(10), 2807-2818. doi:10.1093/jxb/erq120Takada, S., & Goto, K. (2003). TERMINAL FLOWER2, an Arabidopsis Homolog of HETEROCHROMATIN PROTEIN1, Counteracts the Activation of FLOWERING LOCUS T by CONSTANS in the Vascular Tissues of Leaves to Regulate Flowering Time. The Plant Cell, 15(12), 2856-2865. doi:10.1105/tpc.016345Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28(10), 2731-2739. doi:10.1093/molbev/msr121Thompson, J. (1997). The CLUSTAL_X windows

Conserved genes and pathways in primary human fibroblast strains undergoing replicative and radiation induced senescence

Additional file 3: Figure S3. Regulation of genes of Arrhythmogenic right ventricular cardiomyopathy pathway during senescence induction in HFF strains Genes of the “Arrhythmogenic right ventricular cardiomyopathy” pathway which are significantly up- (green) and down- (red) regulated (log2 fold change >1) during irradiation induced senescence (120 h after 20 Gy irradiation) in HFF strains. Orange color signifies genes which are commonly up-regulated during both, irradiation induced and replicative senescence