Development and diversity of Andean-derived, gene-based microsatellites for common bean (Phaseolus vulgaris L.)

<p>Abstract</p> <p>Background</p> <p>Gene-based (genic) microsatellites are a useful tool for plant genetics and simple sequence repeat loci can often be found in coding regions of the genome. While EST sequencing can be used to discover genic microsatellites, direct screening of cDNA libraries for repeat motifs can save on overall sequencing costs. The objective of this research was to screen a large cDNA library from and Andean common bean genotype for six di-nucleotide and tri-nucleotide repeat motifs through a filter hybridization approach and to develop microsatellite markers from positive clones.</p> <p>Results</p> <p>Robotics were used for high-throughput colony picking and to create a high-density filter of 18,432 double spotted cDNA clones which was followed by hybridization with repeat motif containing probes based on GA, CA, AAT, CAG, CAA and ACG repeats. A total of 1203 positive clones were identified by their addresses and sequenced from 5' ends and if required from 3' ends to confirm repeat motif and length. Out of 886 high quality sequences, 497 had complete microsatellite loci that were not truncated by the sequencing reaction and of these tri-nucleotide repeats were more common than di-nucleotide repeats. Different motifs were found in different frequencies in the 5' and 3' ends of the cDNAs. In a microsatellite development program, primers were designed for 248 SSR loci which were tested on a panel of 18 common bean genotypes to determine their potential as genetic markers finding higher average polymorphism information content for di-nucleotide repeat markers (0.3544) than for tri-nucleotide repeat markers (0.1536).</p> <p>Conclusion</p> <p>The present study provides a set of validated gene-based markers for common bean that are derived from G19833, an Andean landrace that is an important source of disease and abiotic stress tolerance which has been used for physical map development and as a mapping parent. Gene-based markers appear to be very efficient at separating divergent wild and cultivated accessions as well as Andean and Mesoamerican genepools and therefore will be useful for diversity analyses and for comparative and transcript mapping in common bean.</p

The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

<p>Abstract</p> <p>Background</p> <p>The cultivated strawberry <it>Fragaria ×ananassa </it>is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for <it>Fragaria </it>and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for <it>Fragaria </it>is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library.</p> <p>Methods</p> <p>A BAC library, consisting of 18,432 clones was constructed from <it>Fragaria vesca </it>f. <it>semperflorens </it>accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid <it>Fragaria </it>reference map (FV×FN).</p> <p>Findings</p> <p>Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid <it>Fragaria </it>FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid <it>Fragaria </it>genome, which is in accordance with the estimate of library coverage based on average insert size.</p> <p>Conclusion</p> <p>This BAC library will be used for the construction of a physical map for <it>F. vesca </it>and the superpools will permit physical anchoring of molecular markers using PCR.</p

Non-Coding Changes Cause Sex-Specific Wing Size Differences between Closely Related Species of Nasonia

The genetic basis of morphological differences among species is still poorly understood. We investigated the genetic basis of sex-specific differences in wing size between two closely related species of Nasonia by positional cloning a major male-specific locus, wing-size1 (ws1). Male wing size increases by 45% through cell size and cell number changes when the ws1 allele from N. giraulti is backcrossed into a N. vitripennis genetic background. A positional cloning approach was used to fine-scale map the ws1 locus to a 13.5 kilobase region. This region falls between prospero (a transcription factor involved in neurogenesis) and the master sex-determining gene doublesex. It contains the 5′-UTR and cis-regulatory domain of doublesex, and no coding sequence. Wing size reduction correlates with an increase in doublesex expression level that is specific to developing male wings. Our results indicate that non-coding changes are responsible for recent divergence in sex-specific morphology between two closely related species. We have not yet resolved whether wing size evolution at the ws1 locus is caused by regulatory alterations of dsx or prospero, or by another mechanism. This study demonstrates the feasibility of efficient positional cloning of quantitative trait loci (QTL) involved in a broad array of phenotypic differences among Nasonia species

Herbicidal Activity of Thymbra capitata (L.) Cav. Essential Oil

[EN] The bioherbicidal potential ofThymbra capitata(L.) Cav. essential oil (EO) and its main compound carvacrol was investigated. In in vitro assays, the EO blocked the germination and seedling growth ofErigeron canadensisL.,Sonchus oleraceus(L.) L., andChenopodium albumL. at 0.125 mu L/mL, ofSetaria verticillata(L.) P.Beauv.,Avena fatuaL., andSolanum nigrumL. at 0.5 mu L/mL, ofAmaranthus retroflexusL. at 1 mu L/mL and ofPortulaca oleraceaL., andEchinochloa crus-galli(L.) P.Beauv. at 2 mu L/mL. Under greenhouse conditions,T. capitataEO was tested towards the emergent weeds from a soil seedbank in pre and post emergence, showing strong herbicidal potential in both assays at 4 mu L/mL. In addition,T. capitataEO, applied by spraying, was tested againstP. oleracea,A. fatuaandE. crus-galli. The species showed different sensibility to the EO, beingE. crus-gallithe most resistant. Experiments were performed againstA. fatuatestingT. capitataEO and carvacrol applied by spraying or by irrigation. It was verified that the EO was more active at the same doses in monocotyledons applied by irrigation and in dicotyledons applied by spraying. Carvacrol effects onArabidopsisroot morphology were also studied.This research was supported by the Universitat Politècnica de València [project number: SP20120543], by Generalitat Valenciana [project number GV/2014/039], and by the Spanish Ministry of Science, Innovation and Universities [project number: RTI2018¿094716¿B¿I00]. Thanks to Jovano Erris Nugroho and Muhamad Iqbal who collaborate to carry out in vivo experiment 4 during their internship in the Plant Health in Sustainable Cropping Systems Erasmus+ Programme. This research work has been developed as a result of a mobility stay funded by the Erasmus+-KA1 Erasmus Mundus Joint Master Degrees Programme of the European Commission under the PLANT HEALTH Project. Thanks to Xeda Italia S.r.l. for providing us Fitoil always when we need it. Thanks to Vicente Estornell Campos and the Library staff from Polytechnic University of Valencia that assisted us to get some helpful references.Verdeguer Sancho, MM.; Torres-Pagan, N.; Muñoz, M.; Jouini, A.; García-Plasencia, S.; Chinchilla, P.; Berbegal Martinez, M.... (2020). Herbicidal Activity of Thymbra capitata (L.) Cav. Essential Oil. Molecules. 25(12):1-31. https://doi.org/10.3390/molecules25122832S1312512Barros, L., Heleno, S. A., Carvalho, A. M., & Ferreira, I. C. F. R. (2010). Lamiaceae often used in Portuguese folk medicine as a source of powerful antioxidants: Vitamins and phenolics. LWT - Food Science and Technology, 43(3), 544-550. doi:10.1016/j.lwt.2009.09.024Goudjil, M. B., Zighmi, S., Hamada, D., Mahcene, Z., Bencheikh, S. E., & Ladjel, S. (2020). Biological activities of essential oils extracted from Thymus capitatus (Lamiaceae). South African Journal of Botany, 128, 274-282. doi:10.1016/j.sajb.2019.11.020Gagliano Candela, R., Maggi, F., Lazzara, G., Rosselli, S., & Bruno, M. (2019). The Essential Oil of Thymbra capitata and its Application as A Biocide on Stone and Derived Surfaces. Plants, 8(9), 300. doi:10.3390/plants8090300Tohidi, B., Rahimmalek, M., Arzani, A., & Sabzalian, M. R. (2020). Thymol, carvacrol, and antioxidant accumulation in Thymus species in response to different light spectra emitted by light-emitting diodes. Food Chemistry, 307, 125521. doi:10.1016/j.foodchem.2019.125521Vladimir-Knežević, S., Blažeković, B., Kindl, M., Vladić, J., Lower-Nedza, A., & Brantner, A. (2014). Acetylcholinesterase Inhibitory, Antioxidant and Phytochemical Properties of Selected Medicinal Plants of the Lamiaceae Family. Molecules, 19(1), 767-782. doi:10.3390/molecules19010767BRÄUCHLER, C. (2018). Delimitation and revision of the genus Thymbra (Lamiaceae). Phytotaxa, 369(1), 15. doi:10.11646/phytotaxa.369.1.2Paton, A. J., Springate, D., Suddee, S., Otieno, D., Grayer, R. J., Harley, M. M., … Savolainen, V. (2004). Phylogeny and evolution of basils and allies (Ocimeae, Labiatae) based on three plastid DNA regions. Molecular Phylogenetics and Evolution, 31(1), 277-299. doi:10.1016/j.ympev.2003.08.002Pastore, J. F. B., Harley, R. M., Forest, F., Paton, A., & van den Berg, C. (2011). Phylogeny of the subtribe Hyptidinae (Lamiaceae tribe Ocimeae) as inferred from nuclear and plastid DNA. TAXON, 60(5), 1317-1329. doi:10.1002/tax.605008Salmaki, Y., Zarre, S., Ryding, O., Lindqvist, C., Bräuchler, C., Heubl, G., … Bendiksby, M. (2013). Molecular phylogeny of tribe Stachydeae (Lamiaceae subfamily Lamioideae). Molecular Phylogenetics and Evolution, 69(3), 535-551. doi:10.1016/j.ympev.2013.07.024Salmaki, Y., Kattari, S., Heubl, G., & Bräuchler, C. (2016). Phylogeny of non-monophyletic Teucrium (Lamiaceae: Ajugoideae): Implications for character evolution and taxonomy. Taxon, 65(4), 805-822. doi:10.12705/654.8LI, B., & OLMSTEAD, R. G. (2017). Two new subfamilies in Lamiaceae. Phytotaxa, 313(2), 222. doi:10.11646/phytotaxa.313.2.9Bräuchler, C., Meimberg, H., & Heubl, G. (2010). Molecular phylogeny of Menthinae (Lamiaceae, Nepetoideae, Mentheae) – Taxonomy, biogeography and conflicts. Molecular Phylogenetics and Evolution, 55(2), 501-523. doi:10.1016/j.ympev.2010.01.016World Checklist of Lamiaceae. Facilitated by the Royal Botanic Gardens, Kewhttp://wcsp.science.kew.orgHarley, R. M., Atkins, S., Budantsev, A. L., Cantino, P. D., Conn, B. J., Grayer, R., … Upson, T. (2004). Labiatae. Flowering Plants · Dicotyledons, 167-275. doi:10.1007/978-3-642-18617-2_11Miceli, A., Negro, C., & Tommasi, L. (2006). Essential oil variability in Thymbra capitata (L.) Cav. growing wild in Southern Apulia (Italy). Biochemical Systematics and Ecology, 34(6), 528-535. doi:10.1016/j.bse.2005.12.010Delgado-Adámez, J., Garrido, M., Bote, M. E., Fuentes-Pérez, M. C., Espino, J., & Martín-Vertedor, D. (2017). Chemical composition and bioactivity of essential oils from flower and fruit of Thymbra capitata and Thymus species. Journal of Food Science and Technology, 54(7), 1857-1865. doi:10.1007/s13197-017-2617-5Alves, T. M. de A., Silva, A. F., Brandão, M., Grandi, T. S. M., Smânia, E. de F. A., Smânia Júnior, A., & Zani, C. L. (2000). Biological screening of Brazilian medicinal plants. Memórias do Instituto Oswaldo Cruz, 95(3), 367-373. doi:10.1590/s0074-02762000000300012BOUNATIROU, S., SMITI, S., MIGUEL, M., FALEIRO, L., REJEB, M., NEFFATI, M., … PEDRO, L. (2007). Chemical composition, antioxidant and antibacterial activities of the essential oils isolated from Tunisian Thymus capitatus Hoff. et Link. Food Chemistry, 105(1), 146-155. doi:10.1016/j.foodchem.2007.03.059Nejad Ebrahimi, S., Hadian, J., Mirjalili, M. H., Sonboli, A., & Yousefzadi, M. (2008). Essential oil composition and antibacterial activity of Thymus caramanicus at different phenological stages. Food Chemistry, 110(4), 927-931. doi:10.1016/j.foodchem.2008.02.083Casiglia, S., Bruno, M., Scandolera, E., Senatore, F., & Senatore, F. (2019). Influence of harvesting time on composition of the essential oil of Thymus capitatus (L.) Hoffmanns. & Link. growing wild in northern Sicily and its activity on microorganisms affecting historical art crafts. Arabian Journal of Chemistry, 12(8), 2704-2712. doi:10.1016/j.arabjc.2015.05.017Grayer, R. J., & Harborne, J. B. (1994). A survey of antifungal compounds from higher plants, 1982–1993. Phytochemistry, 37(1), 19-42. doi:10.1016/0031-9422(94)85005-4Kalemba, D., & Kunicka, A. (2003). Antibacterial and Antifungal Properties of Essential Oils. Current Medicinal Chemistry, 10(10), 813-829. doi:10.2174/0929867033457719Ricci, D., Fraternale, D., Giamperi, L., Bucchini, A., Epifano, F., Burini, G., & Curini, M. (2005). Chemical composition, antimicrobial and antioxidant activity of the essential oil of Teucrium marum (Lamiaceae). Journal of Ethnopharmacology, 98(1-2), 195-200. doi:10.1016/j.jep.2005.01.022Al-Mustafa, A. H., & Al-Thuniba, O. Y. (2008). Antioxidant Activity of Some Jordanian Medicinal Plants Used Traditionally for Treatment of Diabetes. Pakistan Journal of Biological Sciences, 11(3), 351-358. doi:10.3923/pjbs.2008.351.358Dhifi, W., Bellili, S., Jazi, S., Bahloul, N., & Mnif, W. (2016). Essential Oils’ Chemical Characterization and Investigation of Some Biological Activities: A Critical Review. Medicines, 3(4), 25. doi:10.3390/medicines3040025Ruberto, G., Biondi, D., & Piattelli, M. (1992). The Essential Oil of SicilianThymus capitatus(L.) Hoffmanns, et Link. Journal of Essential Oil Research, 4(4), 417-418. doi:10.1080/10412905.1992.9698094Saija, A., Speciale, A., Trombetta, D., Leto, C., Tuttolomondo, T., La Bella, S., … Ruberto, G. (2016). Phytochemical, Ecological and Antioxidant Evaluation of Wild Sicilian Thyme: Thymbra capitata (L.) Cav . Chemistry & Biodiversity, 13(12), 1641-1655. doi:10.1002/cbdv.201600072Arras, G., & Grella, G. E. (1992). Wild thyme,Thymus capitatus, essential oil seasonal changes and antimycotic activity. Journal of Horticultural Science, 67(2), 197-202. doi:10.1080/00221589.1992.11516237Tommasi, L., Negro, C., Cerfeda, A., Nutricati, E., Zuccarello, V., De Bellis, L., & Miceli, A. (2007). Influence of Environmental Factors on Essential Oil Variability inThymbra capitata(L.) Cav. Growing Wild in Southern Puglia (Italy). Journal of Essential Oil Research, 19(6), 572-580. doi:10.1080/10412905.2007.9699335Salas, J. B., Téllez, T. R., Alonso, M. J. P., Pardo, F. M. V., de los Ángeles Cases Capdevila, M., & Rodríguez, C. G. (2010). Chemical composition and antioxidant activity of the essential oil ofThymbra capitata(L.) Cav. in Spain. Acta Botanica Gallica, 157(1), 55-63. doi:10.1080/12538078.2010.10516189Rodrigues, L. S., Monteiro, P., Maldoa-Martins, M., Monteiro, A., Povoa, O., & Teixeira, G. (2006). BIODIVERSITY STUDIES ON PORTUGUESE THYMBRA CAPITATA. Acta Horticulturae, (723), 127-132. doi:10.17660/actahortic.2006.723.13El Hadj Ali, I. B., Guetat, A., & Boussaid, M. (2012). Variation of Volatiles in Tunisian Populations of Thymbra capitata (L.) Cav. (Lamiaceae). Chemistry & Biodiversity, 9(7), 1272-1285. doi:10.1002/cbdv.201100344Katz, D. A., Sneh, B., & Friedman, J. (1987). The allelopathic potential ofCoridothymus capitatus L. (Labiatae). Preliminary studies on the roles of the shrub in the inhibition of annuals germination and/or to promote allelopathically active actinomycetes. Plant and Soil, 98(1), 53-66. doi:10.1007/bf02381727Dudai, N., Poljakoff-Mayber, A., Mayer, A. M., Putievsky, E., & Lerner, H. R. (1999). Journal of Chemical Ecology, 25(5), 1079-1089. doi:10.1023/a:1020881825669Saoud, I., Hamrouni, L., Gargouri, S., Amri, I., Hanana, M., Fezzani, T., … Jamoussi, B. (2013). Chemical composition, weed killer and antifungal activities of Tunisian thyme (Thymus capitatusHoff. et Link.) essential oils. Acta Alimentaria, 42(3), 417-427. doi:10.1556/aalim.42.2013.3.15Chaimovitsh, D., Shachter, A., Abu-Abied, M., Rubin, B., Sadot, E., & Dudai, N. (2016). Herbicidal Activity of Monoterpenes Is Associated with Disruption of Microtubule Functionality and Membrane Integrity. Weed Science, 65(1), 19-30. doi:10.1614/ws-d-16-00044.1Verdeguer, M., Castañeda, L. G., Torres-Pagan, N., Llorens-Molina, J. A., & Carrubba, A. (2020). Control of Erigeron bonariensis with Thymbra capitata, Mentha piperita, Eucalyptus camaldulensis, and Santolina chamaecyparissus Essential Oils. Molecules, 25(3), 562. doi:10.3390/molecules25030562Cordeau, S., Triolet, M., Wayman, S., Steinberg, C., & Guillemin, J.-P. (2016). Bioherbicides: Dead in the water? A review of the existing products for integrated weed management. Crop Protection, 87, 44-49. doi:10.1016/j.cropro.2016.04.016Mahmood, I., Imadi, S. R., Shazadi, K., Gul, A., & Hakeem, K. R. (2016). Effects of Pesticides on Environment. Plant, Soil and Microbes, 253-269. doi:10.1007/978-3-319-27455-3_13Harker, K. N., & O’Donovan, J. T. (2013). Recent Weed Control, Weed Management, and Integrated Weed Management. Weed Technology, 27(1), 1-11. doi:10.1614/wt-d-12-00109.1Olson, S. (2015). An Analysis of the Biopesticide Market Now and Where it is Going. Outlooks on Pest Management, 26(5), 203-206. doi:10.1564/v26_oct_04Santamarina, M., Ibáñez, M., Marqués, M., Roselló, J., Giménez, S., & Blázquez, M. (2017). Bioactivity of essential oils in phytopathogenic and post-harvest fungi control. Natural Product Research, 31(22), 2675-2679. doi:10.1080/14786419.2017.1286479Tuttolomondo, T., Dugo, G., Leto, C., Cicero, N., Tropea, A., Virga, G., … La Bella, S. (2015). Agronomical and chemical characterisation ofThymbra capitata(L.) Cav. biotypes from Sicily, Italy. Natural Product Research, 29(14), 1289-1299. doi:10.1080/14786419.2014.997726Miguel, M. G., Gago, C., Antunes, M. D., Megías, C., Cortés-Giraldo, I., Vioque, J., … Figueiredo, A. C. (2015). Antioxidant and Antiproliferative Activities of the Essential Oils fromThymbra capitataandThymusSpecies Grown in Portugal. Evidence-Based Complementary and Alternative Medicine, 2015, 1-8. doi:10.1155/2015/851721Karousou, R., Koureas, D. N., & Kokkini, S. (2005). Essential oil composition is related to the natural habitats: Coridothymus capitatus and Satureja thymbra in NATURA 2000 sites of Crete. Phytochemistry, 66(22), 2668-2673. doi:10.1016/j.phytochem.2005.09.020Vasilakoglou, I., Dhima, K., Paschalidis, K., & Ritzoulis, C. (2013). Herbicidal potential onLolium rigidumof nineteen major essential oil components and their synergy. Journal of Essential Oil Research, 25(1), 1-10. doi:10.1080/10412905.2012.751054Hazrati, H., Saharkhiz, M. J., Niakousari, M., & Moein, M. (2017). Natural herbicide activity of Satureja hortensis L. essential oil nanoemulsion on the seed germination and morphophysiological features of two important weed species. Ecotoxicology and Environmental Safety, 142, 423-430. doi:10.1016/j.ecoenv.2017.04.041Pinheiro, P. F., Costa, A. V., Alves, T. de A., Galter, I. N., Pinheiro, C. A., Pereira, A. F., … Fontes, M. M. P. (2015). Phytotoxicity and Cytotoxicity of Essential Oil from Leaves of Plectranthus amboinicus, Carvacrol, and Thymol in Plant Bioassays. Journal of Agricultural and Food Chemistry, 63(41), 8981-8990. doi:10.1021/acs.jafc.5b03049Tworkoski, T. (2002). Herbicide effects of essential oils. Weed Science, 50(4), 425-431. doi:10.1614/0043-1745(2002)050[0425:heoeo]2.0.co;2Benvenuti, S., Cioni, P. L., Flamini, G., & Pardossi, A. (2017). Weeds for weed control: Asteraceae essential oils as natural herbicides. Weed Research, 57(5), 342-353. doi:10.1111/wre.12266N. MALPASSI, R. (2006). Herbicide effects on cuticle ultrastructure in Eleusine indica and Portulaca oleracea. BIOCELL, 30(1), 51-56. doi:10.32604/biocell.2006.30.051Schreiber, L. (1995). A mechanistic approach towards surfactant/wax interactions: Effects of octaethyleneglycolmonododecylether on sorption and diffusion of organic chemicals in reconstituted cuticular wax of barley leaves. Pesticide Science, 45(1), 1-11. doi:10.1002/ps.2780450102Hull, H. M., Morton, H. L., & Wharrie, J. R. (1975). Environmental influences on cuticle development and resultant foliar penetration. The Botanical Review, 41(4), 421-452. doi:10.1007/bf02860832Kern, A. J., Jackson, L. L., & Dyer, W. E. (1997). Fatty acid and wax biosynthesis in susceptible and triallate-resistantAvena fatuaL. Pesticide Science, 51(1), 21-26. doi:10.1002/(sici)1096-9063(199709)51:13.0.co;2-9SANYAL, D., BHOWMIK, P. C., & REDDY, K. N. (2008). Effects of surfactants on primisulfuron activity in barnyardgrass (Echinochloa crus-galli [L.] Beauv.) and green foxtail (Setaria viridis [L.] Beauv.). Weed Biology and Management, 8(1), 46-53. doi:10.1111/j.1445-6664.2007.00273.xPrinciples of Soil and Plant Water Relations. (2014). doi:10.1016/c2013-0-12871-1Kim, H. K., Park, J., & Hwang, I. (2014). Investigating water transport through the xylem network in vascular plants. Journal of Experimental Botany, 65(7), 1895-1904. doi:10.1093/jxb/eru075Norris, R. F. (1974). PENETRATION OF 2,4-D IN RELATION TO CUTICLE THICKNESS. American Journal of Botany, 61(1), 74-79. doi:10.1002/j.1537-2197.1974.tb06029.xSchönherr, J., & Riederer, M. (1989). Foliar Penetration and Accumulation of Organic Chemicals in Plant Cuticles. Reviews of Environmental Contamination and Toxicology, 1-70. doi:10.1007/978-1-4613-8850-0_1GOURET, E., ROHR, R., & CHAMEL, A. (1993). Ultrastructure and chemical composition of some isolated plant cuticles in relation to their permeability to the herbicide, diuron. New Phytologist, 124(3), 423-431. doi:10.1111/j.1469-8137.1993.tb03832.xRiederer, M., & Schönherr, J. (1985). Accumulation and transport of (2,4-dichlorophenoxy)acetic acid in plant cuticles. Ecotoxicology and Environmental Safety, 9(2), 196-208. doi:10.1016/0147-6513(85)90022-3Melo, C. R., Picanço, M. C., Santos, A. A., Santos, I. B., Pimentel, M. F., Santos, A. C. C., … Bacci, L. (2018). Toxicity of essential oils of Lippia gracilis chemotypes and their major compounds on Diaphania hyalinata and non-target species. Crop Protection, 104, 47-51. doi:10.1016/j.cropro.2017.10.013Araniti, F., Graña, E., Krasuska, U., Bogatek, R., Reigosa, M. J., Abenavoli, M. R., & Sánchez-Moreiras, A. M. (2016). Loss of Gravitropism in Farnesene-Treated Arabidopsis Is Due to Microtubule Malformations Related to Hormonal and ROS Unbalance. PLOS ONE, 11(8), e0160202. doi:10.1371/journal.pone.0160202Smyth, D. R. (2016). Helical growth in plant organs: mechanisms and significance. Development, 143(18), 3272-3282. doi:10.1242/dev.134064Graña, E., Costas-Gil, A., Longueira, S., Celeiro, M., Teijeira, M., Reigosa, M. J., & Sánchez-Moreiras, A. M. (2017). Auxin-like effects of the natural coumarin scopoletin on Arabidopsis cell structure and morphology. Journal of Plant Physiology, 218, 45-55. doi:10.1016/j.jplph.2017.07.007Verbelen, J.-P., Le, J., Vissenberg, K., De Cnodder, T., Vandenbussche, F., Sugimoto, K., & Van Der Straeten, D. (2008). Microtubules And The Control Of Cell Elongation In Arabidopsis Roots. NATO Science for Peace and Security Series C: Environmental Security, 73-90. doi:10.1007/978-1-4020-8843-8_4Blume, Y. B., Krasylenko, Y. A., & Yemets, A. I. (2012). Effects of phytohormones on the cytoskeleton of the plant cell. Russian Journal of Plant Physiology, 59(4), 515-529. doi:10.1134/s1021443712040036López-González, D., Costas-Gil, A., Reigosa, M. J., Araniti, F., & Sánchez-Moreiras, A. M. (2020). A natural indole alkaloid, norharmane, affects PIN expression patterns and compromises root growth in Arabidopsis thaliana. Plant Physiology and Biochemistry, 151, 378-390. doi:10.1016/j.plaphy.2020.03.047The International Herbicide-Resistant Weed Databasewww.weedscience.orgAngelini, L. G., Carpanese, G., Cioni, P. L., Morelli, I., Macchia, M., & Flamini, G. (2003). Essential Oils from Mediterranean Lamiaceae as Weed Germination Inhibitors. Journal of Agricultural and Food Chemistry, 51(21), 6158-6164. doi:10.1021/jf0210728DÍAZ-TIELAS, C., GRAÑA, E., SOTELO, T., REIGOSA, M. J., & SÁNCHEZ-MOREIRAS, A. M. (2012). The natural compound trans-chalcone induces programmed cell death in Arabidopsis thaliana roots. Plant, Cell & Environment, 35(8), 1500-1517. doi:10.1111/j.1365-3040.2012.02506.

Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth

Science and innovation are not a luxury but a prerequisite for social and economic development (Annan, 2003)

A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas

Helicobacter pylori is a common component of the human stomach microbiota, possibly dating back to the speciation of Homo sapiens. A history of pathogen evolution in allopatry has led to the development of genetically distinct H. pylori subpopulations, associated with different human populations, and more recent admixture among H. pylori subpopulations can provide information about human migrations. However, little is known about the degree to which some H. pylori genes are conserved in the face of admixture, potentially indicating host adaptation, or how virulence genes spread among different populations. We analyzed H. pylori genomes from 14 countries in the Americas, strains from the Iberian Peninsula, and public genomes from Europe, Africa, and Asia, to investigate how admixture varies across different regions and gene families. Whole-genome analyses of 723 H. pylori strains from around the world showed evidence of frequent admixture in the American strains with a complex mosaic of contributions from H. pylori populations originating in the Americas as well as other continents. Despite the complex admixture, distinctive genomic fingerprints were identified for each region, revealing novel American H. pylori subpopulations. A pan-genome Fst analysis showed that variation in virulence genes had the strongest fixation in America, compared with non-American populations, and that much of the variation constituted non-synonymous substitutions in functional domains. Network analyses suggest that these virulence genes have followed unique evolutionary paths in the American populations, spreading into different genetic backgrounds, potentially contributing to the high risk of gastric cancer in the region.Fil: Muñoz Ramirez, Zilia Y.. INSTITUTO POLITÉCNICO NACIONAL (IPN);Fil: Pascoe, Ben. University of Bath; Reino UnidoFil: Mendez Tenorio, Alfonso. INSTITUTO POLITÉCNICO NACIONAL (IPN);Fil: Mourkas, Evangelos. University of Bath; Reino UnidoFil: Sandoval Motta, Santiago. Consejo Nacional de Ciencia y Tecnología; MéxicoFil: Perez Perez, Guillermo. New York University Langone Medical Center; Estados UnidosFil: Morgan, Douglas R.. University of Alabama at Birmingahm; Estados UnidosFil: Dominguez, Ricardo Leonel. Western Honduras Gastric Cancer Prevention Initiative Hospital de Occidente Santa Rosa de Copan; HondurasFil: Ortiz Princz, Diana. No especifíca;Fil: Cavazza, Maria Eugenia. No especifíca;Fil: Rocha, Gifone. Universidade Federal de Minas Gerais; BrasilFil: Queiroz, Dulcienne. Universidade Federal de Minas Gerais; BrasilFil: Catalano, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Zerbetto de Palma, Gerardo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; ArgentinaFil: Goldman, Cinthia Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Venegas, Alejandro. Universidad Diego Portales; ChileFil: Alarcon, Teresa. Universidad Autónoma de Madrid; EspañaFil: Oleastro, Monica. Universidade Nova de Lisboa; PortugalFil: Vale, Filipa F.. Universidade Nova de Lisboa; PortugalFil: Goodman, Karen J.. University of Alberta; CanadáFil: Torres, Roberto C.. Instituto Mexicano del Seguro Social; MéxicoFil: Berthenet, Elvire. Swansea University Medical School; Reino UnidoFil: Hitchings, Matthew D.. Swansea University Medical School; Reino UnidoFil: Blaser, Martin J.. Rutgers University; Estados UnidosFil: Sheppard, Samuel K.. University of Bath; Reino UnidoFil: Thorell, Kaisa. University of Gothenburg; SueciaFil: Torres, Javier. Instituto Mexicano del Seguro Social; Méxic

Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross

Drought is a major constraint to common bean (Phaseolus vulgaris L.) production, especially in developing countries where irrigation for the crop is infrequent. The Mesoamerican genepool is the most widely grown subdivision of common beans that include small red, small cream and black seeded varieties. The objective of this study was to develop a reliable genetic map for a Mesoamerican × Mesoamerican drought tolerant × susceptible cross and to use this map to analyze the inheritance of yield traits under drought and fully irrigated conditions over 3 years of experiments. The source of drought tolerance used in the cross was the cream-seeded advanced line BAT477 crossed with the small red variety DOR364 and the population was made up of recombinant inbred lines in the F5 generation. Quantitative trait loci were detected by composite interval mapping for the traits of overall seed yield, yield per day, 100 seed weight, days to flowering and days to maturity for each field environment consisting of two treatments (irrigated and rainfed) and lattice design experiments with three repetitions for a total of six environments. The genetic map based on amplified fragment length polymorphism and random amplified polymorphic DNA markers was anchored with 60 simple sequence repeat (SSR) markers and had a total map length of 1,087.5 cM across 11 linkage groups covering the whole common bean genome with saturation of one marker every 5.9 cM. Gaps for the genetic map existed on linkage groups b03, b09 and b11 but overall there were only nine gaps larger than 15 cM. All traits were inherited quantitatively, with the greatest number for seed weight followed by yield per day, yield per se, days to flowering and days to maturity. The relevance of these results for breeding common beans is discussed in particular in the light of crop improvement for drought tolerance in the Mesoamerican genepool

The interplay between functioning problems and symptoms in first episode of psychosis: an approach from network analysis

The relationship between psychotic symptoms and global measures of functioning has been widely studied. No previous study has assessed so far the interplay between specific clinical symptoms and particular areas of functioning in first-episode psychosis (FEP) using network analysis methods. A total of 191 patients with FEP (age 24.45 ± 6.28 years, 64.9% male) participating in an observational and longitudinal study (AGES-CM) comprised the study sample. Functioning problems were assessed with the WHO Disability Assessment Schedule (WHODAS), whereas the Positive and Negative Syndrome Scale (PANSS) was used to assess symptom severity. Network analysis were conducted with the aim of analysing the patterns of relationships between the different dimensions of functioning and PANSS symptoms and factors at baseline. According to our results, the most important nodes were “conceptual disorganization”, “emotional withdrawal”, “lack of spontaneity and flow of conversation”, “delusions”, “unusual thought content”, “dealing with strangers” and “poor rapport”. Our findings suggest that these symptoms and functioning dimensions should be prioritized in the clinical assessment and management of patients with FEP. These areas may also become targets of future early intervention strategies, so as to improve quality of life in this populationThis work was supported by the Madrid Regional Government (R&D activities in Biomedicine (grant number S2017/BMD-3740 - AGES-CM 2-CM)) and Structural Funds of the European Union. Ana Izquierdo’s work is supported by the PFIS predoctoral program (FI17/00138) from the Instituto de Salud Carlos III (Spain) and co-funded by the European Union (ERDF/ESF, "A way to make Europe”/ “Investing in your future”) and The Biomedical Research Foundation of La Princesa University Hospital. Angela Ib´a˜nez thanks the support of CIBERSAM and of the Spanish Ministry of Science, Innovation and Universities. Instituto de Salud Carlos III (PI16/00834 and PI19/01295) co-financed by ERDF Funds from the European Commission. Covadonga M. Díaz-Caneja holds a Juan Rod´es Grant from Instituto de Salud Carlos III (JR19/00024). Celso Arango was supported by the Spanish Ministry of Science and Innovation. Instituto de Salud Carlos III (SAM16PE07CP1, PI16/02012, PI19/ 024), co-financed by ERDF Funds from the European Commission, “A way of making Europe”, CIBERSAM. Madrid Regional Government (B2017/BMD-3740 AGES-CM-2), European Union Structural Funds. European Union Seventh Framework Program under grant agreements FP7-4-HEALTH-2009-2.2.1-2-241909 (Project EU-GEI), FP7- HEALTH- 2013-2.2.1-2-603196 (Project PSYSCAN) and FP7- HEALTH-2013- 2.2.1-2-602478 (Project METSY); and European Union H2020 Program under the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement No 115916, Project PRISM, and grant agreement No 777394, Project AIMS-2-TRIALS), Fundaci´on Familia Alonso, Fundaci´on Alicia Koplowitz and Fundaci´on Mutua Madrile˜n

Implementation of virtual learning environments as a motivating strategy for the development of reading skills

El presente artículo presenta los resultados derivados del estudio Implementación de Ambientes virtuales de Aprendizaje como estrategia motivadora para el desarrollo de competencias lectoras. Además de analizar el uso de ambientes virtuales de aprendizaje como estrategia motivadora para el desarrollo de competencias lectoras, se proponen alternativas pertinentes para dinamizar los espacios de enseñanza-aprendizaje. La problemática general en las aulas de clases en torno al proceso de aprendizaje y en específico de las competencias lectoras de los estudiantes, promueve la búsqueda de caminos para el aprovechamiento y la estructuración de oportunidades para que el colectivo de docentes fortalezcna e innoven en sus prácticas pedagógicas y así generar mayor interés y motivación en ellos. La población objeto de estudio estuvo conformada por estudiantes de 9 grado de la Institución Educativa Néstor Andrés Rangel Alfaro. El estudio tuvo como propósito fomentar los ambientes virtuales de aprendizaje como una estrategia motivadora que fortalece el del desarrollo de las competencias lectorasThis article presents the results derived from the study Implementation of virtual learning environments as a motivating strategy for the development of reading skills; In addition to establishing how the use of virtual learning environments as a motivating strategy for the development of reading skills, it is relevant to boost the teaching-learning spaces. The general problems in the classroom around the learning process and specifically the reading skills of students, promotes the structuring of opportunities for teachers to strengthen and innovate in their pedagogical practices and thus generate greater interest and motivation in them. The population studied was made up of 9th grade students from the Néstor Andrés Rangel Alfaro Educational Institution. The purpose of the study was to promote virtual learning environments as a motivating strategy that strengthens the development of reading skills

RICORS2040 : The need for collaborative research in chronic kidney disease

Chronic kidney disease (CKD) is a silent and poorly known killer. The current concept of CKD is relatively young and uptake by the public, physicians and health authorities is not widespread. Physicians still confuse CKD with chronic kidney insufficiency or failure. For the wider public and health authorities, CKD evokes kidney replacement therapy (KRT). In Spain, the prevalence of KRT is 0.13%. Thus health authorities may consider CKD a non-issue: very few persons eventually need KRT and, for those in whom kidneys fail, the problem is 'solved' by dialysis or kidney transplantation. However, KRT is the tip of the iceberg in the burden of CKD. The main burden of CKD is accelerated ageing and premature death. The cut-off points for kidney function and kidney damage indexes that define CKD also mark an increased risk for all-cause premature death. CKD is the most prevalent risk factor for lethal coronavirus disease 2019 (COVID-19) and the factor that most increases the risk of death in COVID-19, after old age. Men and women undergoing KRT still have an annual mortality that is 10- to 100-fold higher than similar-age peers, and life expectancy is shortened by ~40 years for young persons on dialysis and by 15 years for young persons with a functioning kidney graft. CKD is expected to become the fifth greatest global cause of death by 2040 and the second greatest cause of death in Spain before the end of the century, a time when one in four Spaniards will have CKD. However, by 2022, CKD will become the only top-15 global predicted cause of death that is not supported by a dedicated well-funded Centres for Biomedical Research (CIBER) network structure in Spain. Realizing the underestimation of the CKD burden of disease by health authorities, the Decade of the Kidney initiative for 2020-2030 was launched by the American Association of Kidney Patients and the European Kidney Health Alliance. Leading Spanish kidney researchers grouped in the kidney collaborative research network Red de Investigación Renal have now applied for the Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS) call for collaborative research in Spain with the support of the Spanish Society of Nephrology, Federación Nacional de Asociaciones para la Lucha Contra las Enfermedades del Riñón and ONT: RICORS2040 aims to prevent the dire predictions for the global 2040 burden of CKD from becoming true