Fourteen Months of Observations of the Possible Super-Chandrasekhar Mass Type Ia Supernova 2009dc

In this paper, we present and analyse optical photometry and spectra of the extremely luminous and slowly evolving Type Ia supernova (SN Ia) 2009dc, and offer evidence that it is a super-Chandrasekhar mass (SC) SN Ia and thus had a SC white dwarf (WD) progenitor. Optical spectra of SN 2007if, a similar object, are also shown. SN 2009dc had one of the most slowly evolving light curves ever observed for a SN Ia, with a rise time of ~23 days and Delta m_15(B) = 0.72 mag. We calculate a lower limit to the peak bolometric luminosity of ~2.4e43 erg/s, though the actual value is likely almost 40% larger. Optical spectra of SN 2009dc and SN 2007if obtained near maximum brightness exhibit strong C II features (indicative of a significant amount of unburned material), and the post-maximum spectra are dominated by iron-group elements. All of our spectra of SN 2009dc and SN 2007if also show low expansion velocities. However, we see no strong evidence in SN 2009dc for a velocity "plateau" near maximum light like the one seen in SN 2007if (Scalzo et al. 2010). The high luminosity and low expansion velocities of SN 2009dc lead us to derive a possible WD progenitor mass of more than 2 M_Sun and a Ni-56 mass of about 1.4-1.7 M_Sun. We propose that the host galaxy of SN 2009dc underwent a gravitational interaction with a neighboring galaxy in the relatively recent past. This may have led to a sudden burst of star formation which could have produced the SC WD progenitor of SN 2009dc and likely turned the neighboring galaxy into a "post-starburst galaxy." No published model seems to match the extreme values observed in SN 2009dc, but simulations do show that such massive progenitors can exist (likely as a result of the merger of two WDs) and can possibly explode as SC SNe Ia.Comment: 30 pages, 16 figures, 8 tables, re-submitted to MNRA

Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

[EN] Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8x and comparing to the high-quality reference genome "67/3" over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding.This work has been funded by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement no. 677379 (G2P-SOL project: Linking genetic resources, genomes, and phenotypes of Solanaceous crops), by the Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional/European Regional Development Fund (grant AGL2015-64755-R), and by the Spanish Ministerio de Ciencia, Innovacion y Universidades (MCIU), Agencia Estatal de Investigacion (AEI), and Fondo Europeo de Desarrollo Regional/European Regional Development Fund (grant RTI2018-09592-B-100). PG is grateful to Universitat Politecnica de Valencia and to Japan Society for the Promotion of Science for their respective postdoctoral grants [PAID-10-18 and FY2019 JSPS Postdoctoral Fellowship for Research in Japan (Standard)].Gramazio, P.; Yan, H.; Hasing, T.; Vilanova Navarro, S.; Prohens Tomás, J.; Bombarely, A. (2019). Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement. Frontiers in Plant Science. 10:1-17. https://doi.org/10.3389/fpls.2019.01220S11710Acquadro, A., Barchi, L., Gramazio, P., Portis, E., Vilanova, S., Comino, C., … Lanteri, S. (2017). Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLOS ONE, 12(7), e0180774. doi:10.1371/journal.pone.0180774Alonso-Blanco, C., Andrade, J., Becker, C., Bemm, F., Bergelson, J., Borgwardt, K. M., … Ding, W. (2016). 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell, 166(2), 481-491. doi:10.1016/j.cell.2016.05.063Aronesty, E. (2013). Comparison of Sequencing Utility Programs. The Open Bioinformatics Journal, 7(1), 1-8. doi:10.2174/1875036201307010001Barchi, L., Lanteri, S., Portis, E., Acquadro, A., Valè, G., Toppino, L., & Rotino, G. L. (2011). Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics, 12(1). doi:10.1186/1471-2164-12-304Barchi, L., Pietrella, M., Venturini, L., Minio, A., Toppino, L., Acquadro, A., … Rotino, G. L. (2019). A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Scientific Reports, 9(1). doi:10.1038/s41598-019-47985-wBarchi, L., Acquadro, A., Alonso, D., Aprea, G., Bassolino, L., Demurtas, O., … Giuliano, G. (2019). Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm. Frontiers in Plant Science, 10. doi:10.3389/fpls.2019.01005Bao, G., Zhuo, C., Qian, C., Xiao, T., Guo, Z., & Lu, S. (2015). Co-expression ofNCEDandALOimproves vitamin C level and tolerance to drought and chilling in transgenic tobacco and stylo plants. Plant Biotechnology Journal, 14(1), 206-214. doi:10.1111/pbi.12374Brozynska, M., Furtado, A., & Henry, R. J. (2015). Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnology Journal, 14(4), 1070-1085. doi:10.1111/pbi.12454Cao, J., Schneeberger, K., Ossowski, S., Günther, T., Bender, S., Fitz, J., … Weigel, D. (2011). Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics, 43(10), 956-963. doi:10.1038/ng.911Causse, M., Desplat, N., Pascual, L., Le Paslier, M.-C., Sauvage, C., Bauchet, G., … Bouchet, J.-P. (2013). Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics, 14(1), 791. doi:10.1186/1471-2164-14-791Cavanagh, C., Morell, M., Mackay, I., & Powell, W. (2008). From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Current Opinion in Plant Biology, 11(2), 215-221. doi:10.1016/j.pbi.2008.01.002Cericola, F., Portis, E., Toppino, L., Barchi, L., Acciarri, N., Ciriaci, T., … Lanteri, S. (2013). The Population Structure and Diversity of Eggplant from Asia and the Mediterranean Basin. PLoS ONE, 8(9), e73702. doi:10.1371/journal.pone.0073702Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., … Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly, 6(2), 80-92. doi:10.4161/fly.19695Conesa, A., Gotz, S., Garcia-Gomez, J. M., Terol, J., Talon, M., & Robles, M. (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18), 3674-3676. doi:10.1093/bioinformatics/bti610Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., … DePristo, M. A. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158. doi:10.1093/bioinformatics/btr330Dempewolf, H., Baute, G., Anderson, J., Kilian, B., Smith, C., & Guarino, L. (2017). Past and Future Use of Wild Relatives in Crop Breeding. Crop Science, 57(3), 1070-1082. doi:10.2135/cropsci2016.10.0885Deng, Y., Srivastava, R., & Howell, S. H. (2013). Protein kinase and ribonuclease domains of IRE1 confer stress tolerance, vegetative growth, and reproductive development in Arabidopsis. Proceedings of the National Academy of Sciences, 110(48), 19633-19638. doi:10.1073/pnas.1314749110Jadhav, S. K., Tiwari, K. L., & Gupta, S. (2012). Modified CTAB Technique for Isolation of DNA from some Medicinal Plants. Research Journal of Medicinal Plant, 6(1), 65-73. doi:10.3923/rjmp.2012.65.73Du, X., Huang, G., He, S., Yang, Z., Sun, G., Ma, X., … Li, F. (2018). Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature Genetics, 50(6), 796-802. doi:10.1038/s41588-018-0116-xFelcher, K. J., Coombs, J. J., Massa, A. N., Hansey, C. N., Hamilton, J. P., Veilleux, R. E., … Douches, D. S. (2012). Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence. PLoS ONE, 7(4), e36347. doi:10.1371/journal.pone.0036347Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012). CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28(23), 3150-3152. doi:10.1093/bioinformatics/bts565Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D. M., … Fei, Z. (2019). The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 51(6), 1044-1051. doi:10.1038/s41588-019-0410-2Gisbert, C., Prohens, J., Raigón, M. D., Stommel, J. R., & Nuez, F. (2011). Eggplant relatives as sources of variation for developing new rootstocks: Effects of grafting on eggplant yield and fruit apparent quality and composition. Scientia Horticulturae, 128(1), 14-22. doi:10.1016/j.scienta.2010.12.007Gong, Z., Lee, H., Xiong, L., Jagendorf, A., Stevenson, B., & Zhu, J.-K. (2002). RNA helicase-like protein as an early regulator of transcription factors for plant chilling and freezing tolerance. Proceedings of the National Academy of Sciences, 99(17), 11507-11512. doi:10.1073/pnas.172399299Gramazio, P., Prohens, J., Plazas, M., Andújar, I., Herraiz, F. J., Castillo, E., … Vilanova, S. (2014). Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant. BMC Plant Biology, 14(1). doi:10.1186/s12870-014-0350-zGramazio, P., Blanca, J., Ziarsolo, P., Herraiz, F. J., Plazas, M., Prohens, J., & Vilanova, S. (2016). Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. BMC Genomics, 17(1). doi:10.1186/s12864-016-2631-4Gramazio, P., Prohens, J., Plazas, M., Mangino, G., Herraiz, F. J., & Vilanova, S. (2017). Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background. Frontiers in Plant Science, 8. doi:10.3389/fpls.2017.01477Gramazio, P., Prohens, J., Borràs, D., Plazas, M., Herraiz, F. J., & Vilanova, S. (2017). Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants. Euphytica, 213(12). doi:10.1007/s10681-017-2057-3GRAMAZIO, P., PROHENS, J., PLAZAS, M., MANGINO, G., HERRAIZ, F. J., GARCÍA-FORTEA, E., & VILANOVA, S. (2018). Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 46(1), 1-13. doi:10.15835/nbha46110936Grzebelus, D., Gładysz, M., Macko-Podgórni, A., Gambin, T., Golis, B., Rakoczy, R., & Gambin, A. (2009). Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula. Gene, 448(2), 214-220. doi:10.1016/j.gene.2009.06.004Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W. J., Zhang, H., … Wang, Z. (2012). The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics, 45(1), 51-58. doi:10.1038/ng.2470Hill, T. A., Ashrafi, H., Reyes-Chin-Wo, S., Yao, J., Stoffel, K., Truco, M.-J., … Van Deynze, A. (2013). Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip. PLoS ONE, 8(2), e56200. doi:10.1371/journal.pone.0056200Hirakawa, H., Shirasawa, K., Miyatake, K., Nunome, T., Negoro, S., Ohyama, A., … Fukuoka, H. (2014). Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World. DNA Research, 21(6), 649-660. doi:10.1093/dnares/dsu027Hu, J., Manduzio, S., & Kang, H. (2019). Epitranscriptomic RNA Methylation in Plant Development and Abiotic Stress Responses. Frontiers in Plant Science, 10. doi:10.3389/fpls.2019.00500Huang, X., Wei, X., Sang, T., Zhao, Q., Feng, Q., Zhao, Y., … Han, B. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 42(11), 961-967. doi:10.1038/ng.695Hulse-Kemp, A. M., Ashrafi, H., Plieske, J., Lemm, J., Stoffel, K., Hill, T., … Van Deynze, A. (2016). A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding. Horticulture Research, 3(1). doi:10.1038/hortres.2016.36Hurtado, M., Vilanova, S., Plazas, M., Gramazio, P., Andújar, I., Herraiz, F. J., … Prohens, J. (2014). Enhancing conservation and use of local vegetable landraces: the Almagro eggplant (Solanum melongena L.) case study. Genetic Resources and Crop Evolution, 61(4), 787-795. doi:10.1007/s10722-013-0073-2Ihaka, R., & Gentleman, R. (1996). R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics, 5(3), 299-314. doi:10.1080/10618600.1996.10474713Kim, C., Guo, H., Kong, W., Chandnani, R., Shuang, L.-S., & Paterson, A. H. (2016). Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Science, 242, 14-22. doi:10.1016/j.plantsci.2015.04.016Kim, S., Park, M., Yeom, S.-I., Kim, Y.-M., Lee, J. M., Lee, H.-A., … Kim, K.-T. (2014). Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics, 46(3), 270-278. doi:10.1038/ng.2877Knapp, S., Vorontsova, M. S., & Prohens, J. (2013). Wild Relatives of the Eggplant (Solanum melongena L.: Solanaceae): New Understanding of Species Names in a Complex Group. PLoS ONE, 8(2), e57039. doi:10.1371/journal.pone.0057039Kouassi, B., Prohens, J., Gramazio, P., Kouassi, A. B., Vilanova, S., Galán-Ávila, A., … Plazas, M. (2016). Development of backcross generations and new interspecific hybrid combinations for introgression breeding in eggplant ( Solanum melongena ). Scientia Horticulturae, 213, 199-207. doi:10.1016/j.scienta.2016.10.039Lam, H.-M., Xu, X., Liu, X., Chen, W., Yang, G., Wong, F.-L., … Zhang, G. (2010). Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics, 42(12), 1053-1059. doi:10.1038/ng.715Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-359. doi:10.1038/nmeth.1923Levin, H. L., & Moran, J. V. (2011). Dynamic interactions between transposable elements and their hosts. Nature Reviews Genetics, 12(9), 615-627. doi:10.1038/nrg3030Lewicki, T. (1974). West African Food in the Middle Ages. doi:10.1017/cbo9780511759796Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., … Homer, N. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352Li, H. (2014). Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics, 30(20), 2843-2851. doi:10.1093/bioinformatics/btu356Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., … Huang, S. (2014). Genomic analyses provide insights into the history of tomato breeding. Nature Genetics, 46(11), 1220-1226. doi:10.1038/ng.3117Liu, J., Zheng, Z., Zhou, X., Feng, C., & Zhuang, Y. (2014). Improving the resistance of eggplant (Solanum melongena) to Verticillium wilt using wild species Solanum linnaeanum. Euphytica, 201(3), 463-469. doi:10.1007/s10681-014-1234-xMahesh, S., & Udayakumar, M. (2017). Peanut RNA Helicase AhRH47 Sustains Protein Synthesis Under Stress and Improves Stress Adaptation in Arabidopsis. Plant Molecular Biology Reporter, 36(1), 58-70. doi:10.1007/s11105-017-1056-9Meyer, R. S., Karol, K. G., Little, D. P., Nee, M. H., & Litt, A. (2012). Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication. Molecular Phylogenetics and Evolution, 63(3), 685-701. doi:10.1016/j.ympev.2012.02.006Meyer, R. S., Whitaker, B. D., Little, D. P., Wu, S.-B., Kennelly, E. J., Long, C.-L., & Litt, A. (2015). Parallel reductions in phenolic constituents resulting from the domestication of eggplant. Phytochemistry, 115, 194-206. doi:10.1016/j.phytochem.2015.02.006Michalovova, M., Vyskot, B., & Kejnovsky, E. (2013). Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization. Heredity, 111(4), 314-320. doi:10.1038/hdy.2013.51Muñoz-Falcón, J. E., Prohens, J., Vilanova, S., & Nuez, F. (2008). Characterization, diversity, and relationships of the Spanish striped (Listada) eggplants: a model for the enhancement and protection of local heirlooms. Euphytica, 164(2), 405-419. doi:10.1007/s10681-008-9688-3Muñoz-Falcón, J. E., Prohens, J., Vilanova, S., Ribas, F., Castro, A., & Nuez, F. (2008). Distinguishing a protected geographical indication vegetable (Almagro eggplant) from closely related varieties with selected morphological traits and molecular markers. Journal of the Science of Food and Agriculture, 89(2), 320-328. doi:10.1002/jsfa.3452Muñoz-Falcón, J. E., Prohens, J., Vilanova, S., & Nuez, F. (2009). Diversity in commercial varieties and landraces of black eggplants and implications for broadening the breeders’ gene pool. Annals of Applied Biology, 154(3), 453-465. doi:10.1111/j.1744-7348.2009.00314.xNaito, K., Cho, E., Yang, G., Campbell, M. A., Yano, K., Okumoto, Y., … Wessler, S. R. (2006). Dramatic amplification of a rice transposable element during recent domestication. Proceedings of the National Academy of Sciences, 103(47), 17620-17625. doi:10.1073/pnas.0605421103Nelson, M. G., Linheiro, R. S., & Bergman, C. M. (2017). McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. G3: Genes|Genomes|Genetics, 7(8), 2763-2778. doi:10.1534/g3.117.043893Nidumukkala, S., Tayi, L., Chittela, R. K., Vudem, D. R., & Khareedu, V. R. (2019). DEAD box helicases as promising molecular tools for engineering abiotic stress tolerance in plants. Critical Reviews in Biotechnology, 39(3), 395-407. doi:10.1080/07388551.2019.1566204Pascual, L., Desplat, N., Huang, B. E., Desgroux, A., Bruguier, L., Bouchet, J.-P., … Causse, M. (2014). Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnology Journal, 13(4), 565-577. doi:10.1111/pbi.12282Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., … Rokhsar, D. S. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229), 551-556. doi:10.1038/nature07723Plazas, M., Vilanova, S., Gramazio, P., Rodríguez-Burruezo, A., Fita, A., Herraiz, F. J., … Prohens, J. (2016). Interspecific Hybridization between Eggplant and Wild Relatives from Different Genepools. Journal of the American Society for Horticultural Science, 141(1), 34-44. doi:10.21273/jashs.141.1.34(2011). Genome sequence and analysis of the tuber crop potato. Nature, 475(7355), 189-195. doi:10.1038/nature10158Prohens, J., Gramazio, P., Plazas, M., Dempewolf, H., Kilian, B., Díez, M. J., … Vilanova, S. (2017). Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. Euphytica, 213(7). doi:10.1007/s10681-017-1938-9Prohens, J., Whitaker, B. D., Plazas, M., Vilanova, S., Hurtado, M., Blasco, M., … Stommel, J. R. (2013). Genetic diversity in morphological characters and phenolic acids content resulting from an interspecific cross between eggplant,Solanum melongena, and its wild ancestor (S. incanum). Annals of Applied Biology, 162(2), 242-257. doi:10.1111/aab.12017Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., … Huang, S. (2013). A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nature Genetics, 45(12), 1510-1515. doi:10.1038/ng.2801Quinlan, A. R., & Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842. doi:10.1093/bioinformatics/btq033Ranil, R. H. G., Niran, H. M. L., Plazas, M., Fonseka, R. M., Fonseka, H. H., Vilanova, S., … Prohens, J. (2015). Improving seed germination of the eggplant rootstock Solanum torvum by testing multiple factors using an orthogonal array design. Scientia Horticulturae, 193, 174-181. doi:10.1016/j.scienta.2015.07.030Salas, P., Prohens, J., & Seguí-Simarro, J. M. (2011). Evaluation of androgenic competence through anther culture in common eggplant and related species. Euphytica, 182(2), 261-274. doi:10.1007/s10681-011-0490-2Salikhov, K., Sacomoto, G., & Kucherov, G. (2014). Using cascading Bloom filters to improve the memory usage for de Brujin graphs. Algorithms for Molecular Biology, 9(1), 2. doi:10.1186/1748-7188-9-2Särkinen, T., Bohs, L., Olmstead, R. G., & Knapp, S. (2013). A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evolutionary Biology, 13(1), 214. doi:10.1186/1471-2148-13-214Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., … Graves, T. A. (2009). The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science, 326(5956), 1112-1115. doi:10.1126/science.1178534Shi, L., Wu, Y., & Sheen, J. (2018). TOR signaling in plants: conservation and innovation. Development, 145(13), dev160887. doi:10.1242/dev.160887Shivakumara, T. N., Sreevathsa, R., Dash, P. K., Sheshshayee, M. S., Papolu, P. K., Rao, U., … UdayaKumar, M. (2017). Overexpression of Pea DNA Helicase 45 (PDH45) imparts tolerance to multiple abiotic stresses in chili (Capsicum annuum L.). Scientific Reports, 7(1). doi:10.1038/s41598-017-02589-0Sim, S.-C., Durstewitz, G., Plieske, J., Wieseke, R., Ganal, M. W., Van Deynze, A., … Francis, D. M. (2012). Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato. PLoS ONE, 7(7), e40563. doi:10.1371/journal.pone.0040563Sim, S.-C., Van Deynze, A., Stoffel, K., Douches, D. S., Zarka, D., Ganal, M. W., … Francis, D. M. (2012). High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding. PLoS ONE, 7(9), e45520. doi:10.1371/journal.pone.0045520Stommel, J. R., & Whitaker, B. D. (2003). Phenolic Acid Content and Composition of Eggplant Fruit in a Germplasm Core Subset. Journal of the American Society for Horticultural Science, 128(5), 704-710. doi:10.21273/jas

LIVER BIOCHEMISTRY PROFILE IN WHITE-TAILED DEER (ODOCOILEUS VIRGINIANUS) REARED IN CAPTIVITY

El presente estudio se llevó a cabo con 23 venados cola blanca (Odocoileus virginianus), de ambos sexos, y criados en cautiverio en la provincia de Lima, con el objetivo de determinar el perfil bioquímico sanguíneo hepático a través de los valores séricos de Bilirrubina Total y Directa, Proteínas Totales, Albúmina, Alanino Amino Transferasa (ALT), Aspartato Amino Transferasa (AST), Fosfatasa Alcalina (FA), y Gamma Glutamil Transferasa (GGT). Los animales (7 machos y 16 hembras), pertenecientes a tres zoológicos o zoocriaderos, fueron anestesiados con clorhidrato de ketamina o con la combinación de clorhidrato de ketamina y clorhidrato de xilacina. Se extrajo 7 ml de sangre por punción de la vena safena en tubos estériles sin anticoagulante, y los sueros fueron analizados con kits comerciales. Los valores encontrados (media ± DE) fueron para Bilirrubina Total: 0.6 ± 0.3 mg/dl; Bilirrubina Directa: 0.08 ± 0.06 mg/dl; Proteínas Totales: 6.6 ± 0.7 g/dl; Albúmina: 3.6 ± 0.5 g/dl; ALT: 26.0 ± 9.7 UI/l; AST: 87.6 ± 22.9 UI/l; FA: 73.9 ± 33.8 UI/l; y GGT: 42.5 ± 12.6 UI/l. No hubo diferencia estadística entre sexos con excepción de BT y albúmina (p<0.05).This study was carried out with 23 adult white-tailed deer (Odocoileus virginianus)of both sexes, kept in captivity in the province of Lima to establish reference liverbiochemistry profilevalues (Total and direct bilirubin, total protein, albumin, alanineamino transferase (ALT), aspartate amino transferase (AST), alkaline phosphatase (AF),and gamma glutamyl transferase (GGT). The animals (7 males and 16 females) were from three local zoos and were anesthesyzed with ketamine hydrochloride or with acombination of ketamine hydrochloride and xylazine hydrochloride. Blood samples (7ml) were collected from the saphenous vein in sterile tubes and serum was analyzedusing commercial kits. The values (mean ± SD) were Total Bilirubin: 0.6 ± 0.3 mg/dl;Direct Bilirubin: 0.08 ± 0.06 mg/dl; Total Protein: 6.6 ± 0.7 g/dl; Albumin: 3.6 ± 0.5 g/dl;ALT: 26.0 ± 9.7 UI/l; AST: 87.6 ± 22.9 UI/l; AF: 73.9 ± 33.8 UI/l, and GGT: 42.5 ± 12.6 UI/l.There were no statistical differences due to sex except for total bilirubin and albumin(p<0.05

An ensemble indicator-based density estimator for evolutionary multi-objective optimization

International audienceEnsemble learning is one of the most employed methods in machine learning. Its main ground is the construction of stronger mechanisms based on the combination of elementary ones. In this paper, we employ AdaBoost, which is one of the most well-known ensemble methods, to generate an ensemble indicator-based density estimator for multi-objective optimization. It combines the search properties of five density estimators, based on the hypervolume, R2, IGD+, ε+, and ∆p quality indicators. Through the multi-objective evolutionary search process, the proposed ensemble mechanism adapts itself using a learning process that takes the preferences of the underlying quality indicators into account. The proposed method gives rise to the ensemble indicator-based multi-objective evolutionary algorithm (EIB-MOEA) that shows a robust performance on different multi-objective optimization problems when compared with respect to several existing indicator-based multi-objective evolutionary algorithms

Gastrointestinal helminths in sheepdogs in farmers communities of Puno, Peru

Se determinó la frecuencia de helmintiasis gastrointestinal en perros pastores de los distritos de Ajoyani y Macusani, provincia de Carabaya, y de los distritos de Ocuvíri, Palca, Lampa y Santa Lucía, provincia de Lampa, Puno, Perú. Se colectaron muestras de heces de 352 perros cruzados, mayormente adultos, y aparentemente sanos, entre enero a marzo de 2008. La evaluación coproparasitológica hizo por el método de Flotación con solución azucarada o de Sheather y por Sedimentación Espontánea. Las muestras colectadas fueron preservadas tanto en formol al 10% como en bicromato al 2.5%. El 20.5 ± 4.2% de los perros se encontró con algún tipo de helminto gastrointestinal. La frecuencia de animales con huevos de Taenia fue de 14.5 ± 3.7%, Trichuris vulpis de 2.6 ± 1.7%, y Capillaria sp de 0.9 ± 1%, en tanto que fue de 1.4 ± 1.2% para Toxocara canis, Toxascaris leonina y Ancylostoma sp. Asimismo, la frecuencia de Sarcocystis sp. fue de 9.1 ± 3%, Entamoeba coli de 16.5 ± 3.9% e Isospora sp. de 11.9 ± 3.4%. La edad, sexo y zona agroclimática no constituyeron factores de riesgo para el parasitismo de los canes. El monoparasitismo se presentó en el 90.9% de los perros que presentaron infecciones parasitarias. El análisis de las muestras preservadas con formol al 10% y Bicromato al 2.5% dieron resultados bastante similares y, por lo tanto, moderadamente concordantes y mutuamente reemplazables al ser evaluadas mediante la prueba de Kappa y Mc Nemar.The frequency of gastrointestinal helminths in sheepdogs of Ajoyani and Macusani districts in the province of Carabaya, and in the districts of Ocuvíri, Palca, Lampa, and Santa Lucía in the province of Lampa, Puno, Peru was determined. Stool samples were collected from 352 crossbreed dogs, mostly adults and apparently healthy, during January to March 2008. The coproparasitological evaluation was done by the methods of flotation with sugar solution or Sheather’s, and by the spontaneous sedimentation technique. Samples were preserved in both 10% formaldehyde and 2.5% bichromate. The resulted showed 20.5 ± 4.2% of dogs were infected with gastrointestinal helminthes. The frequency of dogs with eggs of Taenia was 14.5 ± 3.7%, Trichuris vulpis was 2.6 ± 1.7%, Capillaria sp was 0.9 ± 1%, while for Toxocara canis, Toxascaris leonina, and Ancylostoma sp was 1.4 ± 1.2% each. Besides, the frecuency of Sarcocystis sp was 9.1 ± 3%, Entamoeba coli was 16.5 ± 3.9%, and Isospora sp was 11.9 ± 3.4%. Age, sex, and agro-climatic zone were not considered risk factors for gastrointestinal parasitism. Monoparasitism occurred in 90.9% of dogs with parasite infections. Analysis of samples preserved with 10% formaldehyde or 2.5% bichromate showed similar results and therefore both substances were considered moderately consistent and mutually replaceable according to the Kappa and Mc Nemar tests

Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus

A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events

Association of Angiotensin II Type 2 Receptor Gene A1818T Polymorphism with Progression of Immunoglobulin A Nephropathy in Korean Patients

We determined the relationship between the progression of immunoglobulin A nephropathy (IgAN) and the A1818T polymorphism in intron 2 of Angiotensin II type 2 receptor (AT2R) gene, which might play protective roles in the pathogenesis of IgAN. Patients with biopsy-proven IgAN were recruited from the registry of the Progressive REnal disease and Medical Informatics and gEnomics Research (PREMIER) which was sponsored by the Korean Society of Nephrology. A1818T polymorphism of AT2R gene was analyzed with PCR-RFLP method and the association with the progression of IgAN, which was defined as over 50% increase in baseline serum creatinine level, was analyzed with survival analysis. Among the 480 patients followed for more than 10 months, the group without T allele had significantly higher rates of progression of IgAN than the group with T allele (11.4% vs. 3.9%, p=0.024), although there were no significant differences in the baseline variables such as initial serum creatinine level, the degree of proteinuria, and blood pressure. In the Cox's proportional hazard model, the hazard ratio of disease progression in the patients with T allele was 0.221 (95% confidence interval for Exp(B): 0.052-0.940, p=0.041) compared to that of without T allele. In conclusion, A1818T polymorphism of AT2R gene was associated with the progression of IgAN

Numerical study of effect of elastomeric stress absorbers on stress reduction in bone-dental implant interface

Objective This paper focused on optimal stress distribution in the mandibular bone surrounding a dental implant and is devoted to the development of a modified Osteoplant® implant type in order to minimize stress concentration in the bone-implant interface. Material and Methods This study investigated 0.4 mm thick layers of two elastomeric stress barriers incorporated into the dental implant using 3-D finite element analysis. Results Overall, this proposed implant provoked lower load transfer in bone-implant interface due to the effect of the elastomers as stress absorbers. The stress level in the bone was reduced between 28% and 42% for three load cases: 75 N, 60 N and 27 N in corono-apical, linguo-buccal and disto-mesial direction, respectively. Conclusion The proposed model provided an acceptable solution for load transfer reduction to the mandible. This investigation also permitted to choose how to incorporate two elastomers into the Osteoplant® implant system

Effects of Angiopoietin-2-Blocking Antibody on Endothelial Cell–Cell Junctions and Lung Metastasis

Background: Angiopoietin-2 (Ang2), a ligand for endothelial TEK (Tie2) tyrosine kinase receptor, is induced in hypoxic endothelial cells of tumors, where it promotes tumor angiogenesis and growth. However, the effects of Ang2 on tumor lymphangiogenesis and metastasis are poorly characterized. Methods: We addressed the effect of Ang2 on tumor progression and metastasis using systemic Ang2 overexpression in mice carrying tumor xenografts, endothelium-specific overexpression of Ang2 in VEC-tTA/Tet-OS-Ang2 transgenic mice implanted with isogenic tumors, and administration of Ang2-blocking antibodies to tumor-bearing immunodeficient mice. Fisher's exact test was used for analysis of metastasis occurrence, and repeated measures one-way analysis of variance was used for the analysis of primary tumor growth curves. Unpaired t test was used for all other analyses. All statistical tests were two-sided. Results: Adenoviral expression of Ang2 increased lymph node and lung metastasis in tumor xenografts. The metastatic burden in the lungs was increased in transgenic mice in which Ang2 expression was induced specifically in the vascular endothelium (tumor burden per grid, VEC-tTA/Tet-OS-Ang2 mice [n = 5] vs control mice [n = 4]: 45.23 vs 12.26 mm[superscript 2], difference = 32.67 mm[superscript 2], 95% confidence interval = 31.87 to 34.07, P < .001). Ang2-blocking antibodies reduced lymph node and lung metastasis, as well as tumor lymphangiogenesis, and decreased tumor cell homing to the lungs after intravenous injection. In the lung metastases, Ang2 overexpression decreased endothelial integrity, whereas the Ang2-blocking antibodies improved endothelial cell–cell junctions and basement membrane contacts of metastasis-associated lung capillaries. At the cellular level, the Ang2-blocking antibodies induced the internalization of Ang2-Tie2 receptor complexes from endothelial cell–cell junctions in endothelial–tumor cell cocultures. Conclusion: Our results indicate that blocking Ang2 inhibits metastatic dissemination in part by enhancing the integrity of endothelial cell–cell junctions