Spatial organisation and behaviour of the parental chromosome sets in the nuclei of Saccharomyces cerevisiae × S. paradoxus hybrids

Peer reviewedPublisher PD

Assessing the Hierarchical Hamiltonian Splitting Integrator for Collisionless N-body Simulations

The N-body problem has become one of the hottest topics in the fields of computational dynamics and cosmology. The large dynamical range in some astrophysical problems led to the use of adaptive time steps to integrate particle trajectories, however, the search of optimal strategies is still challenging. We quantify the performance of the hierarchical time step integrator Hamiltonian Splitting (HamSp) for collisionless multistep simulations. We compare with the constant step Leap-Frog (LeapF) integrator and the adaptive one (AKDK). Additionally, we explore the impact of different time step assigning functions. There is a computational overhead in HamSp however there are two interesting advantages: choosing a convenient time-step function may compensate and even turn around the efficiency compared with AKDK. We test both reversibility and time symmetry. The symmetrized nature of the HamSp integration is able to provide time-reversible integration for medium time scales and overall deliver better energy conservation for long integration times, and the linear and angular momentum are preserved at machine precision. We address the impact of using different integrators in astrophysical systems. We found that in most situations both AKDK and HamSp are able to correctly simulate the problems. We conclude that HamSp is an attractive and competitive alternative to AKDK, with, in some cases, faster and with better energy and momentum conservation. The use of recently discussed Bridge splitting techniques with HamSp may allow to reach considerably high efficiency.Comment: 13 pages, 16 figure

Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

BACKGROUND: Several lines of evidence suggest that codon usage in the Drosophila saltans and D. willistoni lineages has shifted towards a less frequent use of GC-ending codons. Introns in these lineages show a parallel shift toward a lower GC content. These patterns have been alternatively ascribed to either a shift in mutational patterns or changes in the definition of preferred and unpreferred codons in these lineages. RESULTS AND DISCUSSION: To gain additional insight into this question, we quantified background substitutional patterns in the saltans/willistoni group using inactive copies of a novel, Q-like retrotransposable element. We demonstrate that the pattern of background substitutions in the saltans/willistoni lineage has shifted to a significant degree, primarily due to changes in mutational biases. These differences predict a lower equilibrium GC content in the genomes of the saltans/willistoni species compared with that in the D. melanogaster species group. The magnitude of the difference can readily account for changes in intronic GC content, but it appears insufficient to explain changes in codon usage within the saltans/willistoni lineage. CONCLUSION: We suggest that the observed changes in codon usage in the saltans/willistoni clade reflects either lineage-specific changes in the definitions of preferred and unpreferred codons, or a weaker selective pressure on codon bias in this lineage

The ambivalent shadow of the pre-Wilsonian rise of international law

The generation of American international lawyers who founded the American Society of International Law in 1906 and nurtured the soil for what has been retrospectively called a “moralistic legalistic approach to international relations” remains little studied. A survey of the rise of international legal literature in the U.S. from the mid-19th century to the eve of the Great War serves as a backdrop to the examination of the boosting effect on international law of the Spanish American War in 1898. An examination of the Insular Cases before the US Supreme Court is then accompanied by the analysis of a number of influential factors behind the pre-war rise of international law in the U.S. The work concludes with an examination of the rise of natural law doctrines in international law during the interwar period and the critiques addressed.by the realist founders of the field of “international relations” to the “moralistic legalistic approach to international relation

xQTL workbench: a scalable web environment for multi-level QTL analysis

Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator

The chromosomal polymorphism of Drosophila subobscura: a microevolutionary weapon to monitor global change

The Palaearctic species Drosophila subobscura recently invaded the west coast of Chile and North America. This invasion helped to corroborate the adaptive value of the rich chromosomal polymorphism of the species, as the same clinal patterns than those observed in the original Palaearctic area were reproduced in the colonized areas in a relatively short period of time. The rapid response of this polymorphism to environmental conditions makes it a good candidate to measure the effect of the global rising of temperatures on the genetic composition of populations. Indeed, the long-term variation of this polymorphism shows a general increase in the frequency of those inversions typical of low latitudes, with a corresponding decrease of those typical of populations closer to the poles. Although the mechanisms underlying these changes are not well understood, the system remains a valid tool to monitor the genetic impact of global warming on natural populations. Heredity ( 2009) 103, 364-367; doi: 10.1038/hdy.2009.86; published online 29 July 200

Operative Procedures in the Elderly in Low-Resource Settings: A Review of Médecins Sans Frontières Facilities: Reply

As the demographic transition occurs across developing countries, an increasing number of elderly individuals are affected by disasters and conflicts. This study aimed to evaluate the elderly population that underwent an operative procedure at MSF facilities

Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction

[EN] Understanding the nature of pathogen host interaction may help improve strawberry (Fragaria x anahassa) cultivars. Plant resistance to pathogenic agents usually operates through a complex network of defense mechanisms mediated by a diverse array of signaling molecules. In strawberry, resistance to a variety of pathogens has been reported to be mostly polygenic and quantitatively inherited, making it difficult to associate molecular markers with disease resistance genes. Colletotrichum acutaturn spp. is a major strawberry pathogen, and completely resistant cultivars have not been reported. Moreover, strawberry defense network components and mechanisms remain largely unknown and poorly understood. Assessment of the strawberry response to C. acutatum included a global transcript analysis, and acidic hormones SA and JA measurements were analyzed after challenge with the pathogen. Induction of transcripts corresponding to the SA and JA signaling pathways and key genes controlling major steps within these defense pathways was detected. Accordingly, SA and JA accumulated in strawberry after infection. Contrastingly, induction of several important SA, JA, and oxidative stress-responsive defense genes, including FaPR1-1, FaLOX2, FaJAR1, FaPDF1, and FaGST1, was not detected, which suggests that specific branches in these defense pathways (those leading to FaPR1-2, FaPR2-1, FaPR2-2, FaAOS, FaPR5, and FaPR10) were activated. Our results reveal that specific aspects in SA and JA dependent signaling pathways are activated in strawberry upon interaction with C. acutatum. Certain described defense-associated transcripts related to these two known signaling pathways do not increase in abundance following infection. This finding suggests new insight into a specific putative molecular strategy for defense against this pathogen.Authors are grateful to Dr. JM Lopez-Aranda (IFAPA-Centro de Churriana) for providing micropropagated strawberry plants and to Nicolas Garcia-Caparros for technical assistance. Authors also want to thank Kevin M. Folta for his insightful comments on the paper. This work was supported by Junta de Andalucia, Spain [Proyectos de Excelencia P07-AGR-02482/P12-AGR-2174, and grants to Grupo-BIO278].Amil-Ruiz, F.; Garrido-Gala, J.; Gadea Vacas, J.; Blanco-Portales, R.; Munoz-Merida, A.; Trelles, O.; De Los Santos, B.... (2016). Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction. Frontiers in Plant Science. 7(1036). https://doi.org/10.3389/fpls.2016.01036S71036Acosta, I. F., & Farmer, E. E. (2010). Jasmonates. The Arabidopsis Book, 8, e0129. doi:10.1199/tab.0129Al-Shahrour, F., Diaz-Uriarte, R., & Dopazo, J. (2004). FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics, 20(4), 578-580. doi:10.1093/bioinformatics/btg455Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410. doi:10.1016/s0022-2836(05)80360-2Amil-Ruiz, F., Blanco-Portales, R., Muñoz-Blanco, J., & Caballero, J. L. (2011). The Strawberry Plant Defense Mechanism: A Molecular Review. Plant and Cell Physiology, 52(11), 1873-1903. doi:10.1093/pcp/pcr136Amil-Ruiz, F., Garrido-Gala, J., Blanco-Portales, R., Folta, K. M., Muñoz-Blanco, J., & Caballero, J. L. (2013). Identification and Validation of Reference Genes for Transcript Normalization in Strawberry (Fragaria × ananassa) Defense Responses. PLoS ONE, 8(8), e70603. doi:10.1371/journal.pone.0070603Arroyo, F. T., Moreno, J., García-Herdugo, G., Santos, B. D. los, Barrau, C., Porras, M., … Romero, F. (2005). Ultrastructure of the early stages of Colletotrichum acutatum infection of strawberry tissues. Canadian Journal of Botany, 83(5), 491-500. doi:10.1139/b05-022Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25-29. doi:10.1038/75556Aviv, D. H., Rustérucci, C., Iii, B. F. H., Dietrich, R. A., Parker, J. E., & Dangl, J. L. (2002). Runaway cell death, but not basal disease resistance, inlsd1is SA- andNIM1/NPR1-dependent. The Plant Journal, 29(3), 381-391. doi:10.1046/j.0960-7412.2001.01225.xBak, S., Beisson, F., Bishop, G., Hamberger, B., Höfer, R., Paquette, S., & Werck-Reichhart, D. (2011). Cytochromes P450. The Arabidopsis Book, 9, e0144. doi:10.1199/tab.0144Baniwal, S. K., Bharti, K., Chan, K. Y., Fauth, M., Ganguli, A., Kotak, S., … von Koskull-DÖring, P. (2004). Heat stress response in plants: a complex game with chaperones and more than twenty heat stress transcription factors. Journal of Biosciences, 29(4), 471-487. doi:10.1007/bf02712120Bhattacharjee, S. (2012). The Language of Reactive Oxygen Species Signaling in Plants. Journal of Botany, 2012, 1-22. doi:10.1155/2012/985298Birkenbihl, R. P., Diezel, C., & Somssich, I. E. (2012). Arabidopsis WRKY33 Is a Key Transcriptional Regulator of Hormonal and Metabolic Responses toward Botrytis cinerea Infection. Plant Physiology, 159(1), 266-285. doi:10.1104/pp.111.192641Caarls, L., Pieterse, C. M. J., & Van Wees, S. C. M. (2015). How salicylic acid takes transcriptional control over jasmonic acid signaling. Frontiers in Plant Science, 6. doi:10.3389/fpls.2015.00170Casado-Díaz, A., Encinas-Villarejo, S., Santos, B. de los, Schilirò, E., Yubero-Serrano, E.-M., Amil-Ruíz, F., … Caballero, J.-L. (2006). Analysis of strawberry genes differentially expressed in response to Colletotrichum infection. Physiologia Plantarum, 128(4), 633-650. doi:10.1111/j.1399-3054.2006.00798.xCharng, Y., Liu, H., Liu, N., Chi, W., Wang, C., Chang, S., & Wang, T. (2006). A Heat-Inducible Transcription Factor, HsfA2, Is Required for Extension of Acquired Thermotolerance in Arabidopsis. Plant Physiology, 143(1), 251-262. doi:10.1104/pp.106.091322Chung, S. H., Rosa, C., Scully, E. D., Peiffer, M., Tooker, J. F., Hoover, K., … Felton, G. W. (2013). Herbivore exploits orally secreted bacteria to suppress plant defenses. Proceedings of the National Academy of Sciences, 110(39), 15728-15733. doi:10.1073/pnas.1308867110Curry, K. J., Abril, M., Avant, J. B., & Smith, B. J. (2002). Strawberry Anthracnose: Histopathology of Colletotrichum acutatum and C. fragariae. Phytopathology®, 92(10), 1055-1063. doi:10.1094/phyto.2002.92.10.1055Debode, J., Van Hemelrijck, W., Baeyen, S., Creemers, P., Heungens, K., & Maes, M. (2009). Quantitative detection and monitoring ofColletotrichum acutatumin strawberry leaves using real-time PCR. Plant Pathology, 58(3), 504-514. doi:10.1111/j.1365-3059.2008.01987.xDempsey, D. A., & Klessig, D. F. (2012). SOS – too many signals for systemic acquired resistance? Trends in Plant Science, 17(9), 538-545. doi:10.1016/j.tplants.2012.05.011Dodds, P. N., & Rathjen, J. P. (2010). Plant immunity: towards an integrated view of plant–pathogen interactions. Nature Reviews Genetics, 11(8), 539-548. doi:10.1038/nrg2812Doehlemann, G., Wahl, R., Horst, R. J., Voll, L. M., Usadel, B., Poree, F., … Kämper, J. (2008). Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. The Plant Journal, 56(2), 181-195. doi:10.1111/j.1365-313x.2008.03590.xDong, X. (2004). NPR1, all things considered. Current Opinion in Plant Biology, 7(5), 547-552. doi:10.1016/j.pbi.2004.07.005Durgbanshi, A., Arbona, V., Pozo, O., Miersch, O., Sancho, J. V., & Gómez-Cadenas, A. (2005). Simultaneous Determination of Multiple Phytohormones in Plant Extracts by Liquid Chromatography−Electrospray Tandem Mass Spectrometry. Journal of Agricultural and Food Chemistry, 53(22), 8437-8442. doi:10.1021/jf050884bEl Oirdi, M., El Rahman, T. A., Rigano, L., El Hadrami, A., Rodriguez, M. C., Daayf, F., … Bouarab, K. (2011). Botrytis cinerea Manipulates the Antagonistic Effects between Immune Pathways to Promote Disease Development in Tomato. The Plant Cell, 23(6), 2405-2421. doi:10.1105/tpc.111.083394Encinas-Villarejo, S., Maldonado, A. M., Amil-Ruiz, F., de los Santos, B., Romero, F., Pliego-Alfaro, F., … Caballero, J. L. (2009). Evidence for a positive regulatory role of strawberry (Fragaria×ananassa) Fa WRKY1 and Arabidopsis At WRKY75 proteins in resistance. Journal of Experimental Botany, 60(11), 3043-3065. doi:10.1093/jxb/erp152Freeman, S., Horowitz, S., & Sharon, A. (2001). Pathogenic and Nonpathogenic Lifestyles in Colletotrichum acutatum from Strawberry and Other Plants. Phytopathology®, 91(10), 986-992. doi:10.1094/phyto.2001.91.10.986Freeman, S., Katan, T., & Shabi, E. (1998). Characterization of Colletotrichum Species Responsible for Anthracnose Diseases of Various Fruits. Plant Disease, 82(6), 596-605. doi:10.1094/pdis.1998.82.6.596Gfeller, A., Dubugnon, L., Liechti, R., & Farmer, E. E. (2010). Jasmonate Biochemical Pathway. Science Signaling, 3(109), cm3-cm3. doi:10.1126/scisignal.3109cm3Grellet-Bournonville, C. F., Martinez-Zamora, M. G., Castagnaro, A. P., & Díaz-Ricci, J. C. (2012). Temporal accumulation of salicylic acid activates the defense response against Colletotrichum in strawberry. Plant Physiology and Biochemistry, 54, 10-16. doi:10.1016/j.plaphy.2012.01.019Guidarelli, M., Carbone, F., Mourgues, F., Perrotta, G., Rosati, C., Bertolini, P., & Baraldi, E. (2011). Colletotrichum acutatum interactions with unripe and ripe strawberry fruits and differential responses at histological and transcriptional levels. Plant Pathology, 60(4), 685-697. doi:10.1111/j.1365-3059.2010.02423.xHeidrich, K., Wirthmueller, L., Tasset, C., Pouzet, C., Deslandes, L., & Parker, J. E. (2011). Arabidopsis EDS1 Connects Pathogen Effector Recognition to Cell Compartment-Specific Immune Responses. Science, 334(6061), 1401-1404. doi:10.1126/science.1211641Horowitz, S., Freeman, S., & Sharon, A. (2002). Use of Green Fluorescent Protein-Transgenic Strains to Study Pathogenic and Nonpathogenic Lifestyles in Colletotrichum acutatum. Phytopathology®, 92(7), 743-749. doi:10.1094/phyto.2002.92.7.743Ikeda, M., Mitsuda, N., & Ohme-Takagi, M. (2011). Arabidopsis HsfB1 and HsfB2b Act as Repressors of the Expression of Heat-Inducible Hsfs But Positively Regulate the Acquired Thermotolerance. Plant Physiology, 157(3), 1243-1254. doi:10.1104/pp.111.179036Ikeda, M., & Ohme-Takagi, M. (2009). A Novel Group of Transcriptional Repressors in Arabidopsis. Plant and Cell Physiology, 50(5), 970-975. doi:10.1093/pcp/pcp048Khan, A. A., & Shih, D. S. (2004). Molecular cloning, characterization, and expression analysis of two class II chitinase genes from the strawberry plant. Plant Science, 166(3), 753-762. doi:10.1016/j.plantsci.2003.11.015Krinke, O., Ruelland, E., Valentová, O., Vergnolle, C., Renou, J.-P., Taconnat, L., … Zachowski, A. (2007). Phosphatidylinositol 4-Kinase Activation Is an Early Response to Salicylic Acid in Arabidopsis Suspension Cells. Plant Physiology, 144(3), 1347-1359. doi:10.1104/pp.107.100842Kubigsteltig, I., Laudert, D., & Weiler, E. W. (1999). Structure and regulation of the Arabidopsis thaliana allene oxide synthase gene. Planta, 208(4), 463-471. doi:10.1007/s004250050583Leandro, L. F. S., Gleason, M. L., Nutter, F. W., Wegulo, S. N., & Dixon, P. M. (2001). Germination and Sporulation of Colletotrichum acutatum on Symptomless Strawberry Leaves. Phytopathology®, 91(7), 659-664. doi:10.1094/phyto.2001.91.7.659Leon-Reyes, A., Van der Does, D., De Lange, E. S., Delker, C., Wasternack, C., Van Wees, S. C. M., … Pieterse, C. M. J. (2010). Salicylate-mediated suppression of jasmonate-responsive gene expression in Arabidopsis is targeted downstream of the jasmonate biosynthesis pathway. Planta, 232(6), 1423-1432. doi:10.1007/s00425-010-1265-zLi, J., Brader, G., Kariola, T., & Tapio Palva, E. (2006). WRKY70 modulates the selection of signaling pathways in plant defense. The Plant Journal, 46(3), 477-491. doi:10.1111/j.1365-313x.2006.02712.xLi, J., Brader, G., & Palva, E. T. (2004). The WRKY70 Transcription Factor: A Node of Convergence for Jasmonate-Mediated and Salicylate-Mediated Signals in Plant Defense. The Plant Cell, 16(2), 319-331. doi:10.1105/tpc.016980Liu, P.-P., von Dahl, C. C., Park, S.-W., & Klessig, D. F. (2011). Interconnection between Methyl Salicylate and Lipid-Based Long-Distance Signaling during the Development of Systemic Acquired Resistance in Arabidopsis and Tobacco. Plant Physiology, 155(4), 1762-1768. doi:10.1104/pp.110.171694Lodha, T. D., & Basak, J. (2011). Plant–Pathogen Interactions: What Microarray Tells About It? Molecular Biotechnology, 50(1), 87-97. doi:10.1007/s12033-011-9418-2López-Ráez, J. A., Verhage, A., Fernández, I., García, J. M., Azcón-Aguilar, C., Flors, V., & Pozo, M. J. (2010). Hormonal and transcriptional profiles highlight common and differential host responses to arbuscular mycorrhizal fungi and the regulation of the oxylipin pathway. Journal of Experimental Botany, 61(10), 2589-2601. doi:10.1093/jxb/erq089Maas, J. L. (Ed.). (1998). Compendium of Strawberry Diseases, Second Edition. doi:10.1094/9780890546178Makowski, R. M. D., & Mortensen, K. (1998). Latent infections and penetration of the bioherbicide agent Colletotrichum gloeosporioides f. sp. malvae in non-target field crops under controlled environmental conditions. Mycological Research, 102(12), 1545-1552. doi:10.1017/s0953756298006960Maleck, K., Levine, A., Eulgem, T., Morgan, A., Schmid, J., Lawton, K. A., … Dietrich, R. A. (2000). The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nature Genetics, 26(4), 403-410. doi:10.1038/82521Marcel, S., Sawers, R., Oakeley, E., Angliker, H., & Paszkowski, U. (2010). Tissue-Adapted Invasion Strategies of the Rice Blast Fungus Magnaporthe oryzae. The Plant Cell, 22(9), 3177-3187. doi:10.1105/tpc.110.078048Ndamukong, I., Abdallat, A. A., Thurow, C., Fode, B., Zander, M., Weigel, R., & Gatz, C. (2007). SA-inducible Arabidopsis glutaredoxin interacts with TGA factors and suppresses JA-responsive PDF1.2 transcription. The Plant Journal, 50(1), 128-139. doi:10.1111/j.1365-313x.2007.03039.xPajerowska-Mukhtar, K. M., Wang, W., Tada, Y., Oka, N., Tucker, C. L., Fonseca, J. P., & Dong, X. (2012). The HSF-like Transcription Factor TBF1 Is a Major Molecular Switch for Plant Growth-to-Defense Transition. Current Biology, 22(2), 103-112. doi:10.1016/j.cub.2011.12.015Pe�a-Cort�s, H., Barrios, P., Dorta, F., Polanco, V., S�nchez, C., S�nchez, E., & Ram�rez, I. (2004). Involvement of Jasmonic Acid and Derivatives in Plant Response to Pathogen and Insects and in Fruit Ripening. Journal of Plant Growth Regulation, 23(3), 246-260. doi:10.1007/s00344-004-0035-1Pernas, M., Ryan, E., & Dolan, L. (2010). SCHIZORIZA Controls Tissue System Complexity in Plants. Current Biology, 20(9), 818-823. doi:10.1016/j.cub.2010.02.062Pieterse, C. M. J., Leon-Reyes, A., Van der Ent, S., & Van Wees, S. C. M. (2009). Networking by small-molecule hormones in plant immunity. Nature Chemical Biology, 5(5), 308-316. doi:10.1038/nchembio.164Rahman, T. A. E., Oirdi, M. E., Gonzalez-Lamothe, R., & Bouarab, K. (2012). Necrotrophic Pathogens Use the Salicylic Acid Signaling Pathway to Promote Disease Development in Tomato. Molecular Plant-Microbe Interactions®, 25(12), 1584-1593. doi:10.1094/mpmi-07-12-0187-rRen, C.-M., Zhu, Q., Gao, B.-D., Ke, S.-Y., Yu, W.-C., Xie, D.-X., & Peng, W. (2008). Transcription Factor WRKY70 Displays Important but No Indispensable Roles in Jasmonate and Salicylic Acid Signaling. Journal of Integrative Plant Biology, 50(5), 630-637. doi:10.1111/j.1744-7909.2008.00653.xRietz, S., Stamm, A., Malonek, S., Wagner, S., Becker, D., Medina-Escobar, N., … Parker, J. E. (2011). Different roles of Enhanced Disease Susceptibility1 (EDS1) bound to and dissociated from Phytoalexin Deficient4 (PAD4) in Arabidopsis immunity. New Phytologist, 191(1), 107-119. doi:10.1111/j.1469-8137.2011.03675.xRobert-Seilaniantz, A., Grant, M., & Jones, J. D. G. (2011). Hormone Crosstalk in Plant Disease and Defense: More Than Just JASMONATE-SALICYLATE Antagonism. Annual Review of Phytopathology, 49(1), 317-343. doi:10.1146/annurev-phyto-073009-114447Cristina, M., Petersen, M., & Mundy, J. (2010). Mitogen-Activated Protein Kinase Signaling in Plants. Annual Review of Plant Biology, 61(1), 621-649. doi:10.1146/annurev-arplant-042809-112252Rouhier, N. (2006). Genome-wide analysis of plant glutaredoxin systems. Journal of Experimental Botany, 57(8), 1685-1696. doi:10.1093/jxb/erl001Ruepp, A. (2004). The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research, 32(18), 5539-5545. doi:10.1093/nar/gkh894Rusterucci, C. (2001). The Disease Resistance Signaling Components EDS1 and PAD4 Are Essential Regulators of the Cell Death Pathway Controlled by LSD1 in Arabidopsis. THE PLANT CELL ONLINE, 13(10), 2211-2224. doi:10.1105/tpc.13.10.2211Sarowar, S., Zhao, Y., Soria-Guerra, R. E., Ali, S., Zheng, D., Wang, D., & Korban, S. S. (2011). Expression profiles of differentially regulated genes during the early stages of apple flower infection with Erwinia amylovora. Journal of Experimental Botany, 62(14), 4851-4861. doi:10.1093/jxb/err147Sasaki, Y. (2001). Monitoring of Methyl Jasmonate-responsive Genes in Arabidopsis by cDNA Macroarray: Self-activation of Jasmonic Acid Biosynthesis and Crosstalk with Other Phytohormone Signaling Pathways. DNA Research, 8(4), 153-161. doi:10.1093/dnares/8.4.153Schenk, P. M., Kazan, K., Manners, J. M., Anderson, J. P., Simpson, R. S., Wilson, I. W., … Maclean, D. J. (2003). Systemic Gene Expression in Arabidopsis during an Incompatible Interaction with Alternaria brassicicola. Plant Physiology, 132(2), 999-1010. doi:10.1104/pp.103.021683Simpson, D. W. (1991). Resistance toBotrytis cinereain pistillate genotypes of the cultivated strawberryFragaria ananassa. Journal of Horticultural Science, 66(6), 719-723. doi:10.1080/00221589.1991.11516203Shulaev, V., Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., … Mane, S. P. (2010). The genome of woodland strawberry (Fragaria vesca). Nature Genetics, 43(2), 109-116. doi:10.1038/ng.740Song, W. C., Funk, C. D., & Brash, A. R. (1993). Molecular cloning of an allene oxide synthase: a cytochrome P450 specialized for the metabolism of fatty acid hydroperoxides. Proceedings of the National Academy of Sciences, 90(18), 8519-8523. doi:10.1073/pnas.90.18.8519Spoel, S. H., & Dong, X. (2012). How do plants achieve immunity? Defence without specialized immune cells. Nature Reviews Immunology, 12(2), 89-100. doi:10.1038/nri3141Spoel, S. H., Johnson, J. S., & Dong, X. (2007). Regulation of tradeoffs between plant defenses against pathogens with different lifestyles. Proceedings of the National Academy of Sciences, 104(47), 18842-18847. doi:10.1073/pnas.0708139104Staswick, P. E., & Tiryaki, I. (2004). The Oxylipin Signal Jasmonic Acid Is Activated by an Enzyme That Conjugates It to Isoleucine in Arabidopsis. The Plant Cell, 16(8), 2117-2127. doi:10.1105/tpc.104.023549Ten Hove, C. A., Willemsen, V., de Vries, W. J., van Dijken, A., Scheres, B., & Heidstra, R. (2010). SCHIZORIZA Encodes a Nuclear Factor Regulating Asymmetry of Stem Cell Divisions in the Arabidopsis Root. Current Biology, 20(5), 452-457. doi:10.1016/j.cub.2010.01.018Turner, J. G., Ellis, C., & Devoto, A. (2002). The Jasmonate Signal Pathway. The Plant Cell, 14(suppl 1), S153-S164. doi:10.1105/tpc.000679Tusher, V. G., Tibshirani, R., & Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences, 98(9), 5116-5121. doi:10.1073/pnas.091062498Uknes, S., Mauch-Mani, B., Moyer, M., Potter, S., Williams, S., Dincher, S., … Ryals, J. (1992). Acquired resistance in Arabidopsis. The Plant Cell, 4(6), 645-656. doi:10.1105/tpc.4.6.645Vargas, W. A., Martín, J. M. S., Rech, G. E., Rivera, L. P., Benito, E. P., Díaz-Mínguez, J. M., … Sukno, S. A. (2012). Plant Defense Mechanisms Are Activated during Biotrophic and Necrotrophic Development of Colletotricum graminicola in Maize. Plant Physiology, 158(3), 1342-1358. doi:10.1104/pp.111.190397Venugopal, S. C., Jeong, R.-D., Mandal, M. K., Zhu, S., Chandra-Shekara, A. C., Xia, Y., … Kachroo, P. (2009). Enhanced Disease Susceptibility 1 and Salicylic Acid Act Redundantly to Regulate Resistance Gene-Mediated Signaling. PLoS Genetics, 5(7), e1000545. doi:10.1371/journal.pgen.1000545Vlot, A. C., Liu, P.-P., Cameron, R. K., Park, S.-W., Yang, Y., Kumar, D., … Klessig, D. F. (2008). Identification of likely orthologs of tobacco salicylic acid-binding protein 2 and their role in systemic acquired resistance inArabidopsis thaliana. The Plant Journal, 56(3), 445-456. doi:10.1111/j.1365-313x.2008.03618.xWang, D., Amornsiripanitch, N., & Dong, X. (2006). A Genomic Approach to Identify Regulatory Nodes in the Transcriptional Network of Systemic Acquired Resistance in Plants. PLoS Pathogens, 2(11), e123. doi:10.1371/journal.ppat.0020123Wang, D. (2005). Induction of Protein Secretory Pathway Is Required for Systemic Acquired Resistance. Science, 308(5724), 1036-1040. doi:10.1126/science.1108791Wang, G.-F., Seabolt, S., Hamdoun, S., Ng, G., Park, J., & Lu, H. (2011). Multiple Roles of WIN3 in Regulating Disease Resistance, Cell Death, and Flowering Time in Arabidopsis. Plant Physiology, 156(3), 1508-1519. doi:10.1104/pp.111.176776Wiermer, M., Feys, B. J., & Parker, J. E. (2005). Plant immunity: the EDS1 regulatory node. Current Opinion in Plant Biology, 8(4), 383-389. doi:10.1016/j.pbi.2005.05.010Windram, O., Madhou, P., McHattie, S., Hill, C., Hickman, R., Cooke, E., … Denby, K. J. (2012). Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis. Th

Principles of meiotic chromosome assembly revealed in S. cerevisiae

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we use Saccharomyces cerevisiae to explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent in S. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process