The survival of dynamical fossils in dwarf spheroidal galaxies in conventional and modified dynamics

The survival of unbound density substructure against orbital mixing imposes strong constraints on the slope of the underlying gravitational potential and provides a new test on modified gravities. Here we investigate whether the interpretation that the stellar clump in Ursa Minor (UMi) dwarf spheroidal galaxy is a `dynamical fossil' is consistent with Modified Newtonian dynamics (MOND). For UMi mass models inferred by fitting the velocity dispersion profile, the stellar clump around the second peak of UMi is erased very rapidly, within 1.25 Gyr (6.5 orbits), even with the inclusion of self-gravity. We find that the clump can hardly survive for more than 2 Gyr even under more generous conditions. Alternative scenarios which could lead to a kinematically cold clump are discussed but, so far, none of them were found to be fully satisfactory. Our conclusion is that the cold clump in UMi poses a challenge for both LambdaCDM and MOND.Comment: 14 pages, 13 figures, accepted for publication in MNRA

Exploring the effects of pressure on the radial accretion of dark matter by a Schwarzschild supermassive black hole

Based on the numerical solution of the time-dependent relativistic Euler equations onto a fixed Schwarzschild background space-time, we estimate the accretion rate of radial flow toward the horizon of a test perfect fluid obeying an ideal gas equation of state. We explore the accretion rate in terms of the initial density of the fluid for various values of the inflow velocity in order to investigate whether or not sufficiently arbitrary initial conditions allow a steady state accretion process depending on the values of the pressure. We extrapolate our results to the case where the fluid corresponds to dark matter and the black hole is a supermassive black hole seed. Then we estimate the equation of state parameters that provide a steady state accretion process. We found that when the pressure of the dark matter is zero, the black hole's mass grows up to values that are orders of magnitude above $10^{9}M_{\odot}$ during a lapse of 10Gyr, whereas in the case of the accretion of the ideal gas dark matter with non zero pressure the accreted mass can be of the order of $\sim 1M_{\odot}/10Gyr$ for black holes of $10^{6}M_{\odot}$. This would imply that if dark matter near a supermassive black hole acquires an equation of state with non trivial pressure, the contribution of accreted dark matter to the supermassive black hole growth could be small, even though only radial accretion is considered.Comment: 9 pages, 24 eps figures, 2 tables. Accepted for publication in MNRA

Collisional dark matter density profiles around supermassive black holes

We solve the spherically symmetric time dependent relativistic Euler equations on a Schwarzschild background space-time for a perfect fluid, where the perfect fluid models the dark matter and the space-time background is that of a non-rotating supermassive black hole. We consider the fluid obeys an ideal gas equation of state as a simple model of dark matter with pressure. Assuming out of equilibrium initial conditions we search for late-time attractor type of solutions, which we found to show a constant accretion rate for the non-zero pressure case, that is, the pressure itself suffices to produce stationary accretion regimes. We then analyze the resulting density profile of such late-time solutions with the function $A/r^{\kappa}$. For different values of the adiabatic index we find different slopes of the density profile, and we study such profile in two regions: a region one near the black hole, located from the horizon up to 50$M$ and a region two from $\sim 800M$ up to $\sim 1500M$, which for a black hole of $10^{9}M_{\odot}$ corresponds to $\sim 0.1$pc. The profile depends on the adiabatic index or equivalently on the pressure of the fluid and our findings are as follows: in the near region the density profile shows values of $\kappa <1.5$ and in the limit of the pressure-less case $\kappa \rightarrow 1.5$; on the other hand, in region two, the value of $\kappa<0.3$ in all the cases we studied. If these results are to be applied to the dark matter problem, the conclusion is that, in the limit of pressure-less gas the density profile is cuspy only near the black hole and approaches a non-cuspy profile at bigger scales within 1pc. These results show on the one hand that pressure suffices to provide flat density profiles of dark matter and on the other hand show that the presence of a central black hole does not distort the density profile of dark matter at scales of 0.1pc.Comment: 7 pages, 8 eps figures, accepted for publication in MNRA

Analysis of fouling resistances under dynamic membrane filtration

The mechanisms of fouling in the ultrafiltration of polyethylene glycol (PEG) are analysed using the complete blocking and the intermediate blocking Hermia's models adapted to crossflow filtration. The parameters of these models were theoretically estimated. The predicted results were compared with experimental data. Ultrafiltration experiments were performed with Carbosep M2 monotubular ceramic (Orelis, S.A. (France)). The fouling ultrafiltration experiments were carried out at a constant temperature and feed concentration and different feed flow rates and transmembrane pressures. The precision in the predictions is very high. The results showed that the phenomenon controlling fouling was intermediate blocking for high fouling conditions. © 2011 Elsevier B.V.The authors of this work wish to gratefully acknowledge the financial support of the Spanish Ministry of Science and Technology (MCYT) through its project no. CTQ2005-03398.Vincent Vela, MC.; Cuartas Uribe, BE.; Alvarez Blanco, S.; Lora García, J. (2011). Analysis of fouling resistances under dynamic membrane filtration. Chemical Engineering and Processing: Process Intensification. 50(4):404-408. https://doi.org/10.1016/j.cep.2011.02.010S40440850

Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis

[EN] Ovule development is essential for plant survival, as it allows correct embryo and seed development upon fertilization. The female gametophyte is formed in the central area of the nucellus during ovule development, in a complex developmental programme that involves key regulatory genes and the plant hormones auxins and brassinosteroids. Here we provide novel evidence of the role of gibberellins (GAs) in the control of megagametogenesis and embryo sac development, via the GA-dependent degradation of RGA-LIKE1 (RGL1) in the ovule primordia. YPet-rgl1.17 plants, which express a dominant version of RGL1, showed reduced fertility, mainly due to altered embryo sac formation that varied from partial to total ablation. YPet-rgl1.17 ovules followed normal development of the megaspore mother cell, meiosis, and formation of the functional megaspore, but YPet-rgl1.17 plants had impaired mitotic divisions of the functional megaspore. This phenotype is RGL1-specific, as it is not observed in any other dominant mutants of the DELLA proteins. Expression analysis of YPet-rgl1.17 coupled to in situ localization of bioactive GAs in ovule primordia led us to propose a mechanism of GA-mediated RGL1 degradation that allows proper embryo sac development. Taken together, our data unravel a novel specific role of GAs in the control of female gametophyte development.We wish to thank the IBMCP microscopy facility, and Ms J. Yun for technical assistance. We also thank Jennifer Nemhauser (University of Washington, USA) for the HACR sensor. Cambridge proofreading (https://proofreading.org/order/) provided proofreading and editing of this manuscript. This work was supported by grants from the Spanish Ministry for Science and Innovation-FEDER [BIO2017-83138R] to MAP-A and National Science Foundation [MCB-0923727] to JMA. MAP-A received a fellowship of the `Salvador de Madariaga' program from Spanish Ministry of Science and Innovation. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Gomez, MD.; Barro-Trastoy, D.; Fuster Almunia, C.; Tornero Feliciano, P.; Alonso, JM.; Perez Amador, MA. (2020). Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis. Journal of Experimental Botany. 71(22):7059-7072. https://doi.org/10.1093/jxb/eraa395S705970727122Bai, M.-Y., Shang, J.-X., Oh, E., Fan, M., Bai, Y., Zentella, R., … Wang, Z.-Y. (2012). Brassinosteroid, gibberellin and phytochrome impinge on a common transcription module in Arabidopsis. Nature Cell Biology, 14(8), 810-817. doi:10.1038/ncb2546Battaglia, R., Brambilla, V., & Colombo, L. (2008). Morphological analysis of female gametophyte development in thebel1 stk shp1 shp2mutant. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, 142(3), 643-649. doi:10.1080/11263500802411098Beeckman, T., De Rycke, R., Viane, R., & Inzé, D. (2000). Histological Study of Seed Coat Development in Arabidopsis thaliana. Journal of Plant Research, 113(2), 139-148. doi:10.1007/pl00013924Bencivenga, S., Simonini, S., Benková, E., & Colombo, L. (2012). The Transcription Factors BEL1 and SPL Are Required for Cytokinin and Auxin Signaling During Ovule Development in Arabidopsis. The Plant Cell, 24(7), 2886-2897. doi:10.1105/tpc.112.100164Brumos, J., Zhao, C., Gong, Y., Soriano, D., Patel, A. P., Perez-Amador, M. A., … Alonso, J. M. (2019). An Improved Recombineering Toolset for Plants. The Plant Cell, 32(1), 100-122. doi:10.1105/tpc.19.00431Clough, 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.xCoen, O., Lu, J., Xu, W., De Vos, D., Péchoux, C., Domergue, F., … Magnani, E. (2019). Deposition of a cutin apoplastic barrier separating seed maternal and zygotic tissues. BMC Plant Biology, 19(1). doi:10.1186/s12870-019-1877-9Cucinotta, M., Di Marzo, M., Guazzotti, A., de Folter, S., Kater, M. M., & Colombo, L. (2020). Gynoecium size and ovule number are interconnected traits that impact seed yield. Journal of Experimental Botany, 71(9), 2479-2489. doi:10.1093/jxb/eraa050Davière, J.-M., & Achard, P. (2013). Gibberellin signaling in plants. Development, 140(6), 1147-1151. doi:10.1242/dev.087650Davière, J.-M., & Achard, P. (2016). A Pivotal Role of DELLAs in Regulating Multiple Hormone Signals. Molecular Plant, 9(1), 10-20. doi:10.1016/j.molp.2015.09.011Dill, A., Jung, H.-S., & Sun, T. -p. (2001). The DELLA motif is essential for gibberellin-induced degradation of RGA. Proceedings of the National Academy of Sciences, 98(24), 14162-14167. doi:10.1073/pnas.251534098Ferreira, L. G., de Alencar Dusi, D. M., Irsigler, A. S. T., Gomes, A. C. M. M., Mendes, M. A., Colombo, L., & de Campos Carneiro, V. T. (2017). GID1 expression is associated with ovule development of sexual and apomictic plants. Plant Cell Reports, 37(2), 293-306. doi:10.1007/s00299-017-2230-0Fleck, B., & Harberd, N. P. (2002). Evidence that theArabidopsisnuclear gibberellin signalling protein GAI is not destabilised by gibberellin. The Plant Journal, 32(6), 935-947. doi:10.1046/j.1365-313x.2002.01478.xGallego-Bartolome, J., Minguet, E. G., Grau-Enguix, F., Abbas, M., Locascio, A., Thomas, S. G., … Blazquez, M. A. (2012). Molecular mechanism for the interaction between gibberellin and brassinosteroid signaling pathways in Arabidopsis. Proceedings of the National Academy of Sciences, 109(33), 13446-13451. doi:10.1073/pnas.1119992109Gallego-Bartolome, J., Minguet, E. G., Marin, J. A., Prat, S., Blazquez, M. A., & Alabadi, D. (2010). Transcriptional Diversification and Functional Conservation between DELLA Proteins in Arabidopsis. Molecular Biology and Evolution, 27(6), 1247-1256. doi:10.1093/molbev/msq012Gomez, M. D., Barro-Trastoy, D., Escoms, E., Saura-Sánchez, M., Sánchez, I., Briones-Moreno, A., … Perez-Amador, M. A. (2018). Gibberellins negatively modulate ovule number in plants. Development. doi:10.1242/dev.163865G�mez, M. D., Beltr�n, J.-P., & Ca�as, L. A. (2004). The pea END1 promoter drives anther-specific gene expression in different plant species. Planta, 219(6), 967-981. doi:10.1007/s00425-004-1300-zGómez, M. D., Fuster-Almunia, C., Ocaña-Cuesta, J., Alonso, J. M., & Pérez-Amador, M. A. (2019). RGL2 controls flower development, ovule number and fertility in Arabidopsis. Plant Science, 281, 82-92. doi:10.1016/j.plantsci.2019.01.014Gomez, M. D., Ventimilla, D., Sacristan, R., & Perez-Amador, M. A. (2016). Gibberellins Regulate Ovule Integument Development by Interfering with the Transcription Factor ATS. Plant Physiology, 172(4), 2403-2415. doi:10.1104/pp.16.01231Hedden, P., & Sponsel, V. (2015). A Century of Gibberellin Research. Journal of Plant Growth Regulation, 34(4), 740-760. doi:10.1007/s00344-015-9546-1Khakhar, A., Leydon, A. R., Lemmex, A. C., Klavins, E., & Nemhauser, J. L. (2018). Synthetic hormone-responsive transcription factors can monitor and re-program plant development. eLife, 7. doi:10.7554/elife.34702Koorneef, M., Elgersma, A., Hanhart, C. J., Loenen-Martinet, E. P., Rijn, L., & Zeevaart, J. A. D. (1985). A gibberellin insensitive mutant of Arabidopsis thaliana. Physiologia Plantarum, 65(1), 33-39. doi:10.1111/j.1399-3054.1985.tb02355.xKurihara, D., Mizuta, Y., Sato, Y., & Higashiyama, T. (2015). ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging. Development. doi:10.1242/dev.127613Lee, S. (2002). Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition. Genes & Development, 16(5), 646-658. doi:10.1101/gad.969002Li, Q.-F., Wang, C., Jiang, L., Li, S., Sun, S. S. M., & He, J.-X. (2012). An Interaction Between BZR1 and DELLAs Mediates Direct Signaling Crosstalk Between Brassinosteroids and Gibberellins in Arabidopsis. Science Signaling, 5(244). doi:10.1126/scisignal.2002908Lieber, D., Lora, J., Schrempp, S., Lenhard, M., & Laux, T. (2011). Arabidopsis WIH1 and WIH2 Genes Act in the Transition from Somatic to Reproductive Cell Fate. Current Biology, 21(12), 1009-1017. doi:10.1016/j.cub.2011.05.015Lora, J., Herrero, M., Tucker, M. R., & Hormaza, J. I. (2016). The transition from somatic to germline identity shows conserved and specialized features during angiosperm evolution. New Phytologist, 216(2), 495-509. doi:10.1111/nph.14330Murashige, 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.xPeng, J., Carol, P., Richards, D. E., King, K. E., Cowling, R. J., Murphy, G. P., & Harberd, N. P. (1997). The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses . Genes & Development, 11(23), 3194-3205. doi:10.1101/gad.11.23.3194Pinto, S. C., Mendes, M. A., Coimbra, S., & Tucker, M. R. (2019). Revisiting the Female Germline and Its Expanding Toolbox. Trends in Plant Science, 24(5), 455-467. doi:10.1016/j.tplants.2019.02.003Schneitz, K., Hulskamp, M., & Pruitt, R. E. (1995). Wild-type ovule development in Arabidopsis thaliana: a light microscope study of cleared whole-mount tissue. The Plant Journal, 7(5), 731-749. doi:10.1046/j.1365-313x.1995.07050731.xErbasol Serbes, I., Palovaara, J., & Groß-Hardt, R. (2019). Development and function of the flowering plant female gametophyte. Plant Development and Evolution, 401-434. doi:10.1016/bs.ctdb.2018.11.016Sun, T. (2011). The Molecular Mechanism and Evolution of the GA–GID1–DELLA Signaling Module in Plants. Current Biology, 21(9), R338-R345. doi:10.1016/j.cub.2011.02.036Tucker, M. R., Okada, T., Hu, Y., Scholefield, A., Taylor, J. M., & Koltunow, A. M. G. (2012). Somatic small RNA pathways promote the mitotic events of megagametogenesis during female reproductive development in Arabidopsis. Development, 139(8), 1399-1404. doi:10.1242/dev.075390Ursache, R., Andersen, T. G., Marhavý, P., & Geldner, N. (2018). A protocol for combining fluorescent proteins with histological stains for diverse cell wall components. The Plant Journal, 93(2), 399-412. doi:10.1111/tpj.13784Villanueva, J. M., Broadhvest, J., Hauser, B. A., Meister, R. J., Schneitz, K., & Gasser, C. S. (1999). INNER NO OUTER regulates abaxial- adaxial patterning in Arabidopsis ovules. Genes & Development, 13(23), 3160-3169. doi:10.1101/gad.13.23.3160Wen, C.-K., & Chang, C. (2002). Arabidopsis RGL1 Encodes a Negative Regulator of Gibberellin Responses. The Plant Cell, 14(1), 87-100. doi:10.1105/tpc.010325Wu, J., Mohamed, D., Dowhanik, S., Petrella, R., Gregis, V., Li, J., … Gazzarrini, S. (2020). Spatiotemporal Restriction of FUSCA3 Expression by Class I BPCs Promotes Ovule Development and Coordinates Embryo and Endosperm Growth. The Plant Cell, 32(6), 1886-1904. doi:10.1105/tpc.19.00764Yang, W.-C., Shi, D.-Q., & Chen, Y.-H. (2010). Female Gametophyte Development in Flowering Plants. Annual Review of Plant Biology, 61(1), 89-108. doi:10.1146/annurev-arplant-042809-112203Yang, W.-C., Ye, D., Xu, J., & Sundaresan, V. (1999). The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein. Genes & Development, 13(16), 2108-2117. doi:10.1101/gad.13.16.2108Zhao, L., He, J., Cai, H., Lin, H., Li, Y., Liu, R., … Qin, Y. (2014). Comparative expression profiling reveals gene functions in female meiosis and gametophyte development in Arabidopsis. The Plant Journal, 80(4), 615-628. doi:10.1111/tpj.12657Zhou, R., Benavente, L. M., Stepanova, A. N., & Alonso, J. M. (2011). A recombineering-based gene tagging system for Arabidopsis. The Plant Journal, 66(4), 712-723. doi:10.1111/j.1365-313x.2011.04524.

Developmental role of the tomato Mediator complex subunit MED18 in pollen ontogeny

[EN] Pollen development is a crucial step in higher plants, which not only makes possible plant fertilization and seed formation, but also determines fruit quality and yield in crop species. Here, we reported a tomato T-DNA mutant, pollen deficient1 (pod1), characterized by an abnormal anther development and the lack of viable pollen formation, which led to the production of parthenocarpic fruits. Genomic analyses and the characterization of silencing lines proved that pod1 mutant phenotype relies on the tomato SlMED18 gene encoding the subunit 18 of Mediator multi-protein complex involved in RNA polymerase II transcription machinery. The loss of SlMED18 function delayed tapetum degeneration, which resulted in deficient microspore development and scarce production of viable pollen. A detailed histological characterization of anther development proved that changes during microgametogenesis and a significant delay in tapetum degeneration are associated with a high proportion of degenerated cells and, hence, should be responsible for the low production of functional pollen grains. Expression of pollen marker genes indicated that SlMED18 is essential for the proper transcription of a subset of genes specifically required to pollen formation and fruit development, revealing a key role of SlMED18 in male gametogenesis of tomato. Additionally, SlMED18 is able to rescue developmental abnormalities of the Arabidopsis med18 mutant, indicating that most biological functions have been conserved in both species. Significance Statement Pollination is a key development process in the life cycle of flowering plants. Genetic and molecular characterization of a tomato mutant have led to the identification of POD1 gene encoding the Mediator complex subunit MED18 whose function is required for tapetum tissue degeneration, a crucial step for pollen development. Furthermore, we show that MED18 fulfils an essential role in tomato, ensuring proper gene regulation during pollen ontogeny.This research was supported by the Spanish Ministry of Economy and Competitiveness (grants AGL2015-64991-C3-1-R, AGL2015-64991-C3-2-R, AGL2015-64991-C3-3-R, BIO2013-43098-R, BFU2016-77243-P and BIO2016-77559-R) and Junta de Andalucia (grant P12-AGR-1482).Pérez Martín, F.; Juan Yuste-Lisbona, F.; Pineda, B.; García Sogo, B.; Del Olmo, I.; Alché, JDD.; Egea, I.... (2018). Developmental role of the tomato Mediator complex subunit MED18 in pollen ontogeny. The Plant Journal. 96(2):300-315. https://doi.org/10.1111/tpj.14031S300315962Allen, B. L., & Taatjes, D. J. (2015). The Mediator complex: a central integrator of transcription. Nature Reviews Molecular Cell Biology, 16(3), 155-166. doi:10.1038/nrm3951Atarés, A., Moyano, E., Morales, B., Schleicher, P., García-Abellán, J. O., Antón, T., … Pineda, B. (2011). An insertional mutagenesis programme with an enhancer trap for the identification and tagging of genes involved in abiotic stress tolerance in the tomato wild-related species Solanum pennellii. Plant Cell Reports, 30(10), 1865-1879. doi:10.1007/s00299-011-1094-yBaulcombe, D. C. (1996). Mechanisms of Pathogen-Derived Resistance to Viruses in Transgenic Plants. The Plant Cell, 1833-1844. doi:10.1105/tpc.8.10.1833Bourbon, H.-M. (2008). Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Research, 36(12), 3993-4008. doi:10.1093/nar/gkn349Buendía-Monreal, M., & Gillmor, C. S. (2016). Mediator: A key regulator of plant development. Developmental Biology, 419(1), 7-18. doi:10.1016/j.ydbio.2016.06.009Canales, C., Bhatt, A. M., Scott, R., & Dickinson, H. (2002). EXS, a Putative LRR Receptor Kinase, Regulates Male Germline Cell Number and Tapetal Identity and Promotes Seed Development in Arabidopsis. Current Biology, 12(20), 1718-1727. doi:10.1016/s0960-9822(02)01151-xCarbonell-Bejerano, P., Urbez, C., Carbonell, J., Granell, A., & Perez-Amador, M. A. (2010). A Fertilization-Independent Developmental Program Triggers Partial Fruit Development and Senescence Processes in Pistils of Arabidopsis. Plant Physiology, 154(1), 163-172. doi:10.1104/pp.110.160044Chadick, J. Z., & Asturias, F. J. (2005). Structure of eukaryotic Mediator complexes. Trends in Biochemical Sciences, 30(5), 264-271. doi:10.1016/j.tibs.2005.03.001Chuang, C.-F., & Meyerowitz, E. M. (2000). Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 97(9), 4985-4990. doi:10.1073/pnas.060034297Clough, 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.xColeman, A. W., & Goff, L. J. (1985). Applications of Fluorochromes to Pollen Biology. I. Mithramycin and 4′,6-Diamidino-2-Phenylindole (Dapi) as Vital Stains and for Quantitation of Nuclear Dna. Stain Technology, 60(3), 145-154. doi:10.3109/10520298509113905Conaway, R. C., Sato, S., Tomomori-Sato, C., Yao, T., & Conaway, J. W. (2005). The mammalian Mediator complex and its role in transcriptional regulation. Trends in Biochemical Sciences, 30(5), 250-255. doi:10.1016/j.tibs.2005.03.002Cottrell, H. J. (1948). Tetrazolium Salt as a Seed Germination Indicator. Annals of Applied Biology, 35(1), 123-131. doi:10.1111/j.1744-7348.1948.tb07355.xCrane, M. B. (1915). Heredity of types of inflorescence and fruits in tomato. Journal of Genetics, 5(1), 1-11. doi:10.1007/bf02982149Davoine, C., Abreu, I. N., Khajeh, K., Blomberg, J., Kidd, B. N., Kazan, K., … Björklund, S. (2017). Functional metabolomics as a tool to analyze Mediator function and structure in plants. PLOS ONE, 12(6), e0179640. doi:10.1371/journal.pone.0179640Ellul, P., Garcia-Sogo, B., Pineda, B., Ríos, G., Roig, L., & Moreno, V. (2003). The ploidy level of transgenic plants in Agrobacterium-mediated transformation of tomato cotyledons (Lycopersicon esculentum L.Mill.) is genotype and procedure dependent. Theoretical and Applied Genetics, 106(2), 231-238. doi:10.1007/s00122-002-0928-yFallath, T., Kidd, B. N., Stiller, J., Davoine, C., Björklund, S., Manners, J. M., … Schenk, P. M. (2017). MEDIATOR18 and MEDIATOR20 confer susceptibility to Fusarium oxysporum in Arabidopsis thaliana. PLOS ONE, 12(4), e0176022. doi:10.1371/journal.pone.0176022Feng, B., Lu, D., Ma, X., Peng, Y., Sun, Y., Ning, G., & Ma, H. (2012). Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development. The Plant Journal, 72(4), 612-624. doi:10.1111/j.1365-313x.2012.05104.xGillaspy, G., Ben-David, H., & Gruissem, W. (1993). Fruits: A Developmental Perspective. The Plant Cell, 1439-1451. doi:10.1105/tpc.5.10.1439Gleave, A. P. (1992). A versatile binary vector system with a T-DNA organisational structure conducive to efficient integration of cloned DNA into the plant genome. Plant Molecular Biology, 20(6), 1203-1207. doi:10.1007/bf00028910Gómez, J. F., Talle, B., & Wilson, Z. A. (2015). Anther and pollen development: A conserved developmental pathway. Journal of Integrative Plant Biology, 57(11), 876-891. doi:10.1111/jipb.12425Gorman, S. W., McCormick, S., & Rick, C. (1997). Male Sterility in Tomato. Critical Reviews in Plant Sciences, 16(1), 31-53. doi:10.1080/07352689709701945Helliwell, C. (2003). Constructs and methods for high-throughput gene silencing in plants. Methods, 30(4), 289-295. doi:10.1016/s1046-2023(03)00036-7Honys, D., & Twell, D. (2004). Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biology, 5(11). doi:10.1186/gb-2004-5-11-r85Jeong, H.-J., Kang, J.-H., Zhao, M., Kwon, J.-K., Choi, H.-S., Bae, J. H., … Kang, B.-C. (2014). Tomato Male sterile 1035 is essential for pollen development and meiosis in anthers. Journal of Experimental Botany, 65(22), 6693-6709. doi:10.1093/jxb/eru389Jimenez-Lopez, J. C., Zienkiewicz, A., Zienkiewicz, K., Alché, J. D., & Rodríguez-García, M. I. (2015). Biogenesis of protein bodies during legumin accumulation in developing olive (Olea europaea L.) seed. Protoplasma, 253(2), 517-530. doi:10.1007/s00709-015-0830-5Kornberg, R. D. (2005). Mediator and the mechanism of transcriptional activation. Trends in Biochemical Sciences, 30(5), 235-239. doi:10.1016/j.tibs.2005.03.011Lai, Z., Schluttenhofer, C. M., Bhide, K., Shreve, J., Thimmapuram, J., Lee, S. Y., … Mengiste, T. (2014). MED18 interaction with distinct transcription factors regulates multiple plant functions. Nature Communications, 5(1). doi:10.1038/ncomms4064Larivière, L., Geiger, S., Hoeppner, S., Röther, S., Sträßer, K., & Cramer, P. (2006). Structure and TBP binding of the Mediator head subcomplex Med8–Med18–Med20. Nature Structural & Molecular Biology, 13(10), 895-901. doi:10.1038/nsmb1143Lee, S. K., Chen, X., Huang, L., & Stargell, L. A. (2013). The head module of Mediator directs activation of preloaded RNAPII in vivo. Nucleic Acids Research, 41(22), 10124-10134. doi:10.1093/nar/gkt796Li, D.-D., Xue, J.-S., Zhu, J., & Yang, Z.-N. (2017). Gene Regulatory Network for Tapetum Development in Arabidopsis thaliana. Frontiers in Plant Science, 8. doi:10.3389/fpls.2017.01559Liu, X., Huang, J., Parameswaran, S., Ito, T., Seubert, B., Auer, M., … Zhao, D. (2009). The SPOROCYTELESS/NOZZLE Gene Is Involved in Controlling Stamen Identity in Arabidopsis. Plant Physiology, 151(3), 1401-1411. doi:10.1104/pp.109.145896Lora, J., Hormaza, J. I., Herrero, M., & Gasser, C. S. (2011). Seedless fruits and the disruption of a conserved genetic pathway in angiosperm ovule development. Proceedings of the National Academy of Sciences, 108(13), 5461-5465. doi:10.1073/pnas.1014514108Lozano, R., Angosto, T., Gómez, P., Payán, C., Capel, J., Huijser, P., … Martı́nez-Zapater, J. M. (1998). Tomato Flower Abnormalities Induced by Low Temperatures Are Associated with Changes of Expression of MADS-Box Genes. Plant Physiology, 117(1), 91-100. doi:10.1104/pp.117.1.91Ma, H. (2005). MOLECULAR GENETIC ANALYSES OF MICROSPOROGENESIS AND MICROGAMETOGENESIS IN FLOWERING PLANTS. Annual Review of Plant Biology, 56(1), 393-434. doi:10.1146/annurev.arplant.55.031903.141717McNeil, K. J., & Smith, A. G. (2009). A glycine-rich protein that facilitates exine formation during tomato pollen development. Planta, 231(4), 793-808. doi:10.1007/s00425-009-1089-xMercier, R. (2003). The meiotic protein SWI1 is required for axial element formation and recombination initiation in Arabidopsis. Development, 130(>14), 3309-3318. doi:10.1242/dev.00550Mukundan, B., & Ansari, A. (2011). Novel Role for Mediator Complex Subunit Srb5/Med18 in Termination of Transcription. Journal of Biological Chemistry, 286(43), 37053-37057. doi:10.1074/jbc.c111.295915Muschietti, J., Dircks, L., Vancanneyt, G., & McCormick, S. (1994). LAT52 protein is essential for tomato pollen development: pollen expressing antisense LAT52 RNA hydrates and germinates abnormally and cannot achieve fertilization. The Plant Journal, 6(3), 321-338. doi:10.1046/j.1365-313x.1994.06030321.xOzga, J. A., & Reinecke, D. M. (2003). Hormonal Interactions in Fruit Development. Journal of Plant Growth Regulation, 22(1), 73-81. doi:10.1007/s00344-003-0024-9Pacini, E. (2010). Relationships between Tapetum, Loculus, and Pollen during Development. International Journal of Plant Sciences, 171(1), 1-11. doi:10.1086/647923Pérez-Martín, F., Yuste-Lisbona, F. J., Pineda, B., Angarita-Díaz, M. P., García-Sogo, B., Antón, T., … Lozano, R. (2017). A collection of enhancer trap insertional mutants for functional genomics in tomato. Plant Biotechnology Journal, 15(11), 1439-1452. doi:10.1111/pbi.12728Pina, C., Pinto, F., Feijó, J. A., & Becker, J. D. (2005). Gene Family Analysis of the Arabidopsis Pollen Transcriptome Reveals Biological Implications for Cell Growth, Division Control, and Gene Expression Regulation. Plant Physiology, 138(2), 744-756. doi:10.1104/pp.104.057935Polowick, P. L., & Sawhney, V. K. (1993). An ultrastructural study of pollen development in tomato (Lycopersicon esculentum). I. Tetrad to early binucleate microspore stage. Canadian Journal of Botany, 71(8), 1039-1047. doi:10.1139/b93-120Polowick, P. L., & Sawhney, V. K. (1993). An ultrastructural study of pollen development in tomato (Lycopersicon esculentum). II. Pollen maturation. Canadian Journal of Botany, 71(8), 1048-1055. doi:10.1139/b93-121Rutley, N., & Twell, D. (2015). A decade of pollen transcriptomics. Plant Reproduction, 28(2), 73-89. doi:10.1007/s00497-015-0261-7Samanta, S., & Thakur, J. K. (2015). Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants. Frontiers in Plant Science, 6. doi:10.3389/fpls.2015.00757Schiefthaler, U., Balasubramanian, S., Sieber, P., Chevalier, D., Wisman, E., & Schneitz, K. (1999). Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 96(20), 11664-11669. doi:10.1073/pnas.96.20.11664Scott, R. J. (2004). Stamen Structure and Function. THE PLANT CELL ONLINE, 16(suppl_1), S46-S60. doi:10.1105/tpc.017012Smirnova, A., Leide, J., & Riederer, M. (2012). Deficiency in a Very-Long-Chain Fatty Acid β-Ketoacyl-Coenzyme A Synthase of Tomato Impairs Microgametogenesis and Causes Floral Organ Fusion. Plant Physiology, 161(1), 196-209. doi:10.1104/pp.112.206656Sorensen, A.-M., Kröber, S., Unte, U. S., Huijser, P., Dekker, K., & Saedler, H. (2003). TheArabidopsis ABORTED MICROSPORES(AMS) gene encodes a MYC class transcription factor. The Plant Journal, 33(2), 413-423. doi:10.1046/j.1365-313x.2003.01644.xWang, Y., Hu, Z., Zhang, J., Yu, X., Guo, J.-E., Liang, H., … Chen, G. (2018). Silencing SlMED18, tomato Mediator subunit 18 gene, restricts internode elongation and leaf expansion. Scientific Reports, 8(1). doi:10.1038/s41598-018-21679-1Wesley, S. V., Helliwell, C. A., Smith, N. A., Wang, M., Rouse, D. T., Liu, Q., … Waterhouse, P. M. (2001). Construct design for efficient, effective and high-throughput gene silencing in plants. The Plant Journal, 27(6), 581-590. doi:10.1046/j.1365-313x.2001.01105.xWilson, Z. A., & Zhang, D.-B. (2009). From Arabidopsis to rice: pathways in pollen development. Journal of Experimental Botany, 60(5), 1479-1492. doi:10.1093/jxb/erp095Wilson, Z. A., Morroll, S. M., Dawson, J., Swarup, R., & Tighe, P. J. (2001). The Arabidopsis MALE STERILITY1 (MS1) gene is a transcriptional regulator of male gametogenesis, with homology to the PHD-finger family of transcription factors. The Plant Journal, 28(1), 27-39. doi:10.1046/j.1365-313x.2001.01125.xWiner, J., Jung, C. K. S., Shackel, I., & Williams, P. M. (1999). Development and Validation of Real-Time Quantitative Reverse Transcriptase–Polymerase Chain Reaction for Monitoring Gene Expression in Cardiac Myocytesin Vitro. Analytical Biochemistry, 270(1), 41-49. doi:10.1006/abio.1999.4085Yang, W.-C., Ye, D., Xu, J., & Sundaresan, V. (1999). The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein. Genes & Development, 13(16), 2108-2117. doi:10.1101/gad.13.16.2108Yang, C.-Y., Spielman, M., Coles, J. P., Li, Y., Ghelani, S., Bourdon, V., … Dickinson, H. G. (2003). TETRASPORE encodes a kinesin required for male meiotic cytokinesis in Arabidopsis. The Plant Journal, 34(2), 229-240. doi:10.1046/j.1365-313x.2003.01713.xYang, C., Vizcay-Barrena, G., Conner, K., & Wilson, Z. A. (2007). MALE STERILITY1 Is Required for Tapetal Development and Pollen Wall Biosynthesis. The Plant Cell, 19(11), 3530-3548. doi:10.1105/tpc.107.054981Yuan, W., Li, X., Chang, Y., Wen, R., Chen, G., Zhang, Q., & Wu, C. (2009). Mutation of the rice genePAIR3results in lack of bivalent formation in meiosis. The Plant Journal, 59(2), 303-315. doi:10.1111/j.1365-313x.2009.03870.xYuste-Lisbona, F. J., Quinet, M., Fernández-Lozano, A., Pineda, B., Moreno, V., Angosto, T., & Lozano, R. (2016). Characterization of vegetative inflorescence (mc-vin) mutant provides new insight into the role of MACROCALYX in regulating inflorescence development of tomato. Scientific Reports, 6(1). doi:10.1038/srep18796Zhao, D.-Z. (2002). The EXCESS MICROSPOROCYTES1 gene encodes a putative leucine-rich repeat receptor protein kinase that controls somatic and reproductive cell fates in the Arabidopsis anther. Genes & Development, 16(15), 2021-2031. doi:10.1101/gad.997902Zheng, Z., Guan, H., Leal, F., Grey, P. H., & Oppenheimer, D. G. (2013). Mediator Subunit18 Controls Flowering Time and Floral Organ Identity in Arabidopsis. PLoS ONE, 8(1), e53924. doi:10.1371/journal.pone.0053924Zhou, S., Wang, Y., Li, W., Zhao, Z., Ren, Y., Wang, Y., … Wan, J. (2011). Pollen Semi-Sterility1 Encodes a Kinesin-1–Like Protein Important for Male Meiosis, Anther Dehiscence, and Fertility in Rice. The Plant Cell, 23(1), 111-129. doi:10.1105/tpc.109.07369

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

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