Smarter maintenance through internet-based condition monitoring with indirect sensing, novelty detection, and XML

In engineering, combining a number of solutions and technologies can result in more effective systems than using only one approach on its own. In particular, it has been shown that in condition monitoring (CM), smarter maintenance systems may be obtained by integrating various sensors together. This paper extends this idea by integrating various non-homogeneous technologies horizontally. The proposed system is an internet-based condition monitoring (e-CM) prototype that can identify abnormal tension in moving belts. It is shown that by applying a classification technique, known as novelty detection, it is possible to decide the status of belt tension by processing the belt vibration signals from an optical sensor (i.e. an indirect sensing approach). A novel method for industrial network communication using XML to create a single standard format for sensor information is also used to link the sensor to the process controller via the internet using the flexible CAN bus technology; this is used together with low-cost microcontrollers with a built-in ethernet link for data acquisition and transmission. The resulting integrated approach is more efficient because: (a) it can reduce waste by minimizing process interruptions caused by direct belt inspection methods while obtaining high detection accuracy (99.67 per cent) and (b) it can provide on-line remote CM that is cost-effective, simple, standardized, and scalable across a wide area and for a relatively large number of sensors. This improvement is especially important when applied to bottleneck processes and critical components

Tomato floral induction and flower development are orchestrated by the interplay between gibberellin and two unrelated microRNA-controlled modules

[EN] Age-regulated microRNA156 (miR156) and targets similarly control the competence to flower in diverse species. By contrast, the diterpene hormone gibberellin (GA) and the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors promote flowering in the facultative long-day Arabidopsis thaliana, but suppress it in the day-neutral tomato (Solanum lycopersicum). We combined genetic and molecular studies and described a new interplay between GA and two unrelated miRNA-associated pathways that modulates tomato transition to flowering. Tomato PROCERA/DELLA activity is required to promote flowering along with the miR156-targeted SQUAMOSA PROMOTER BINDING-LIKE (SPL/SBP) transcription factors by activating SINGLE FLOWER TRUSS (SFT) in the leaves and the MADS-Boxgene APETALA1(AP1)/MC at the shoot apex. Conversely, miR319-targeted LANCEOLATE represses floral transition by increasing GA concentrations and inactivating SFT in the leaves and AP1/MC at the shoot apex. Importantly, the combination of high GA concentrations/responses with the loss of SPL/SPB function impaired canonical meristem maturation and flower initiation in tomato. Our results reveal a cooperative regulation of tomato floral induction and flower development, integrating age cues (miR156 module) with GA responses and miR319-controlled pathways. Importantly, this study contributes to elucidate the mechanisms underlying the effects of GA in controlling flowering time in a day-neutral species.We thank Dr C. Schommer for kindly providing tcp4-soj8/+ seeds, and Carlos Rojas for Arabidopsis flowering time analyses. This work was supported by FAPESP (grant no. 15/17892-7 and fellowships nos 15/23826-7 and 13/16949-0). The authors declare no conflict of interest.Silva, G.; Silva, E.; Correa, J.; Vicente, M.; Jiang, N.; Notini, M.; Junior, A.... (2018). Tomato floral induction and flower development are orchestrated by the interplay between gibberellin and two unrelated microRNA-controlled modules. New Phytologist. 221(3):1328-1344. https://doi.org/10.1111/nph.15492S132813442213Andrés, F., & Coupland, G. (2012). The genetic basis of flowering responses to seasonal cues. Nature Reviews Genetics, 13(9), 627-639. doi:10.1038/nrg3291Bassel, G. W., Mullen, R. T., & Bewley, J. D. (2008). procerais a putative DELLA mutant in tomato (Solanum lycopersicum): effects on the seed and vegetative plant. Journal of Experimental Botany, 59(3), 585-593. doi:10.1093/jxb/erm354Ben‐Naim, O., Eshed, R., Parnis, A., Teper‐Bamnolker, P., Shalit, A., Coupland, G., … Lifschitz, E. (2006). The CCAAT binding factor can mediate interactions between CONSTANS‐like proteins and DNA. The Plant Journal, 46(3), 462-476. doi:10.1111/j.1365-313x.2006.02706.xBoss, P. K., & Thomas, M. R. (2002). Association of dwarfism and floral induction with a grape ‘green revolution’ mutation. Nature, 416(6883), 847-850. doi:10.1038/416847aBurko, Y., Shleizer-Burko, S., Yanai, O., Shwartz, I., Zelnik, I. D., Jacob-Hirsch, J., … Ori, N. (2013). A Role for APETALA1/FRUITFULL Transcription Factors in Tomato Leaf Development. The Plant Cell, 25(6), 2070-2083. doi:10.1105/tpc.113.113035Cardon, G., Höhmann, S., Klein, J., Nettesheim, K., Saedler, H., & Huijser, P. (1999). Molecular characterisation of the Arabidopsis SBP-box genes. Gene, 237(1), 91-104. doi:10.1016/s0378-1119(99)00308-xCarrera, E., Ruiz-Rivero, O., Peres, L. E. P., Atares, A., & Garcia-Martinez, J. L. (2012). Characterization of the procera Tomato Mutant Shows Novel Functions of the SlDELLA Protein in the Control of Flower Morphology, Cell Division and Expansion, and the Auxin-Signaling Pathway during Fruit-Set and Development. Plant Physiology, 160(3), 1581-1596. doi:10.1104/pp.112.204552Carvalho, R. F., Campos, M. L., Pino, L. E., Crestana, S. L., Zsögön, A., Lima, J. E., … Peres, L. E. (2011). Convergence of developmental mutants into a single tomato model system: «Micro-Tom» as an effective toolkit for plant development research. Plant Methods, 7(1), 18. doi:10.1186/1746-4811-7-18Cubas, P., Lauter, N., Doebley, J., & Coen, E. (1999). The TCP domain: a motif found in proteins regulating plant growth and development. The Plant Journal, 18(2), 215-222. doi:10.1046/j.1365-313x.1999.00444.xDavière, J.-M., Wild, M., Regnault, T., Baumberger, N., Eisler, H., Genschik, P., & Achard, P. (2014). Class I TCP-DELLA Interactions in Inflorescence Shoot Apex Determine Plant Height. Current Biology, 24(16), 1923-1928. doi:10.1016/j.cub.2014.07.012Silva, G. F. F. e, Silva, E. M., da Silva Azevedo, M., Guivin, M. A. C., Ramiro, D. A., Figueiredo, C. R., … Nogueira, F. T. S. (2014). microRNA156-targeted SPL/SBP box transcription factors regulate tomato ovary and fruit development. The Plant Journal, 78(4), 604-618. doi:10.1111/tpj.12493Gallego-Bartolome, J., Minguet, E. G., Marin, J. A., Prat, S., Blazquez, M. A., & Alabadi, D. (2010). Transcriptional Diversification and Functional Conservation between DELLA Proteins in Arabidopsis. Molecular Biology and Evolution, 27(6), 1247-1256. doi:10.1093/molbev/msq012Gallego-Giraldo, L., García-Martínez, J. L., Moritz, T., & López-Díaz, I. (2007). Flowering in Tobacco Needs Gibberellins but is not Promoted by the Levels of Active GA1 and GA4 in the Apical Shoot. Plant and Cell Physiology, 48(4), 615-625. doi:10.1093/pcp/pcm034Galvao, V. C., Horrer, D., Kuttner, F., & Schmid, M. (2012). Spatial control of flowering by DELLA proteins in Arabidopsis thaliana. Development, 139(21), 4072-4082. doi:10.1242/dev.080879García-Hurtado, N., Carrera, E., Ruiz-Rivero, O., López-Gresa, M. P., Hedden, P., Gong, F., & García-Martínez, J. L. (2012). The characterization of transgenic tomato overexpressing gibberellin 20-oxidase reveals induction of parthenocarpic fruit growth, higher yield, and alteration of the gibberellin biosynthetic pathway. Journal of Experimental Botany, 63(16), 5803-5813. doi:10.1093/jxb/ers229Gargul, J. M., Mibus, H., & Serek, M. (2013). Constitutive overexpression of Nicotiana GA 2 ox leads to compact phenotypes and delayed flowering in Kalanchoë blossfeldiana and Petunia hybrida. Plant Cell, Tissue and Organ Culture (PCTOC), 115(3), 407-418. doi:10.1007/s11240-013-0372-5Goldberg-Moeller, R., Shalom, L., Shlizerman, L., Samuels, S., Zur, N., Ophir, R., … Sadka, A. (2013). Effects of gibberellin treatment during flowering induction period on global gene expression and the transcription of flowering-control genes in Citrus buds. Plant Science, 198, 46-57. doi:10.1016/j.plantsci.2012.09.012Hauvermale, A. L., Ariizumi, T., & Steber, C. M. (2012). Gibberellin Signaling: A Theme and Variations on DELLA Repression. Plant Physiology, 160(1), 83-92. doi:10.1104/pp.112.200956Hyun, Y., Richter, R., Vincent, C., Martinez-Gallegos, R., Porri, A., & Coupland, G. (2016). Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. Developmental Cell, 37(3), 254-266. doi:10.1016/j.devcel.2016.04.001Itoh, H., Ueguchi-Tanaka, M., Sato, Y., Ashikari, M., & Matsuoka, M. (2002). The Gibberellin Signaling Pathway Is Regulated by the Appearance and Disappearance of SLENDER RICE1 in Nuclei. The Plant Cell, 14(1), 57-70. doi:10.1105/tpc.010319Jung, J.-H., Ju, Y., Seo, P. J., Lee, J.-H., & Park, C.-M. (2011). The SOC1-SPL module integrates photoperiod and gibberellic acid signals to control flowering time in Arabidopsis. The Plant Journal, 69(4), 577-588. doi:10.1111/j.1365-313x.2011.04813.xKing, R. W., & Ben-Tal, Y. (2001). A Florigenic Effect of Sucrose in Fuchsia hybrida Is Blocked by Gibberellin-Induced Assimilate Competition. Plant Physiology, 125(1), 488-496. doi:10.1104/pp.125.1.488Kubota, A., Ito, S., Shim, J. S., Johnson, R. S., Song, Y. H., Breton, G., … Imaizumi, T. (2017). TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis. PLOS Genetics, 13(6), e1006856. doi:10.1371/journal.pgen.1006856Kudla, J., & Bock, R. (2016). Lighting the Way to Protein-Protein Interactions: Recommendations on Best Practices for Bimolecular Fluorescence Complementation Analyses. The Plant Cell, 28(5), 1002-1008. doi:10.1105/tpc.16.00043Lifschitz, E., Eviatar, T., Rozman, A., Shalit, A., Goldshmidt, A., Amsellem, Z., … Eshed, Y. (2006). The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli. Proceedings of the National Academy of Sciences, 103(16), 6398-6403. doi:10.1073/pnas.0601620103Liu, J., Cheng, X., Liu, P., Li, D., Chen, T., Gu, X., & Sun, J. (2017). MicroRNA319-regulated TCPs interact with FBHs and PFT1 to activate CO transcription and control flowering time in Arabidopsis. PLOS Genetics, 13(5), e1006833. doi:10.1371/journal.pgen.1006833Livak, K. J., & Schmittgen, T. D. (2001). Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method. Methods, 25(4), 402-408. doi:10.1006/meth.2001.1262Livne, S., Lor, V. S., Nir, I., Eliaz, N., Aharoni, A., Olszewski, N. E., … Weiss, D. (2015). Uncovering DELLA-Independent Gibberellin Responses by Characterizing New Tomato procera Mutants. The Plant Cell, 27(6), 1579-1594. doi:10.1105/tpc.114.132795Lombardi-Crestana, S., da Silva Azevedo, M., e Silva, G. F. F., Pino, L. E., Appezzato-da-Glória, B., Figueira, A., … Peres, L. E. P. (2012). The Tomato (Solanum Lycopersicum cv. Micro-Tom) Natural Genetic Variation Rg1 and the DELLA Mutant Procera Control the Competence Necessary to Form Adventitious Roots and Shoots. Journal of Experimental Botany, 63(15), 5689-5703. doi:10.1093/jxb/ers221Lozano, R., Gimenez, E., Cara, B., Capel, J., & Angosto, T. (2009). Genetic analysis of reproductive development in tomato. The International Journal of Developmental Biology, 53(8-9-10), 1635-1648. doi:10.1387/ijdb.072440rlMartin, K., Kopperud, K., Chakrabarty, R., Banerjee, R., Brooks, R., & Goodin, M. M. (2009). Transient expression inNicotiana benthamianafluorescent marker lines provides enhanced definition of protein localization, movement and interactionsin planta. The Plant Journal, 59(1), 150-162. doi:10.1111/j.1365-313x.2009.03850.xMartínez-Bello, L., Moritz, T., & López-Díaz, I. (2015). Silencing C19-GA 2-oxidases induces parthenocarpic development and inhibits lateral branching in tomato plants. Journal of Experimental Botany, 66(19), 5897-5910. doi:10.1093/jxb/erv300Meissner, R., Chague, V., Zhu, Q., Emmanuel, E., Elkind, Y., & Levy, A. A. (2000). A high throughput system for transposon tagging and promoter trapping in tomato. The Plant Journal, 22(3), 265-274. doi:10.1046/j.1365-313x.2000.00735.xMolinero-Rosales, N., Jamilena, M., Zurita, S., Gomez, P., Capel, J., & Lozano, R. (1999). FALSIFLORA, the tomato orthologue of FLORICAULA and LEAFY, controls flowering time and floral meristem identity. The Plant Journal, 20(6), 685-693. doi:10.1046/j.1365-313x.1999.00641.xMorea, E. G. O., da Silva, E. M., e Silva, G. F. F., Valente, G. T., Barrera Rojas, C. H., Vincentz, M., & Nogueira, F. T. S. (2016). Functional and evolutionary analyses of the miR156 and miR529 families in land plants. BMC Plant Biology, 16(1). doi:10.1186/s12870-016-0716-5Mounet, F., Moing, A., Garcia, V., Petit, J., Maucourt, M., Deborde, C., … Lemaire-Chamley, M. (2009). Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development. Plant Physiology, 149(3), 1505-1528. doi:10.1104/pp.108.133967Nir, I., Shohat, H., Panizel, I., Olszewski, N., Aharoni, A., & Weiss, D. (2017). The Tomato DELLA Protein PROCERA Acts in Guard Cells to Promote Stomatal Closure. The Plant Cell, 29(12), 3186-3197. doi:10.1105/tpc.17.00542Ohad, N., Shichrur, K., & Yalovsky, S. (2007). The Analysis of Protein-Protein Interactions in Plants by Bimolecular Fluorescence Complementation. Plant Physiology, 145(4), 1090-1099. doi:10.1104/pp.107.107284Ori, N., Cohen, A. R., Etzioni, A., Brand, A., Yanai, O., Shleizer, S., … Eshed, Y. (2007). Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nature Genetics, 39(6), 787-791. doi:10.1038/ng2036Pal, S., Zhao, J., Khan, A., Yadav, N. S., Batushansky, A., Barak, S., … Rachmilevitch, S. (2016). Paclobutrazol induces tolerance in tomato to deficit irrigation through diversified effects on plant morphology, physiology and metabolism. Scientific Reports, 6(1). doi:10.1038/srep39321Palatnik, J. F., Wollmann, H., Schommer, C., Schwab, R., Boisbouvier, J., Rodriguez, R., … Weigel, D. (2007). Sequence and Expression Differences Underlie Functional Specialization of Arabidopsis MicroRNAs miR159 and miR319. Developmental Cell, 13(1), 115-125. doi:10.1016/j.devcel.2007.04.012Parapunova, V., Busscher, M., Busscher-Lange, J., Lammers, M., Karlova, R., Bovy, A. G., … de Maagd, R. A. (2014). Identification, cloning and characterization of the tomato TCP transcription factor family. BMC Plant Biology, 14(1), 157. doi:10.1186/1471-2229-14-157Park, S. J., Jiang, K., Schatz, M. C., & Lippman, Z. B. (2011). Rate of meristem maturation determines inflorescence architecture in tomato. Proceedings of the National Academy of Sciences, 109(2), 639-644. doi:10.1073/pnas.1114963109Pharis, R. P., & King, R. W. (1985). Gibberellins and Reproductive Development in Seed Plants. Annual Review of Plant Physiology, 36(1), 517-568. doi:10.1146/annurev.pp.36.060185.002505Porri, A., Torti, S., Romera-Branchat, M., & Coupland, G. (2012). Spatially distinct regulatory roles for gibberellins in the promotion of flowering of Arabidopsis under long photoperiods. Development, 139(12), 2198-2209. doi:10.1242/dev.077164Preston, J. C., & Hileman, L. C. (2013). Functional Evolution in the Plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family. Frontiers in Plant Science, 4. doi:10.3389/fpls.2013.00080Reinecke, D. M., Wickramarathna, A. D., Ozga, J. A., Kurepin, L. V., Jin, A. L., Good, A. G., & Pharis, R. P. (2013). Gibberellin 3-oxidase Gene Expression Patterns Influence Gibberellin Biosynthesis, Growth, and Development in Pea. PLANT PHYSIOLOGY, 163(2), 929-945. doi:10.1104/pp.113.225987Rubio-Somoza, I., & Weigel, D. (2011). MicroRNA networks and developmental plasticity in plants. Trends in Plant Science, 16(5), 258-264. doi:10.1016/j.tplants.2011.03.001Rubio-Somoza, I., Zhou, C.-M., Confraria, A., Martinho, C., von Born, P., Baena-Gonzalez, E., … Weigel, D. (2014). Temporal Control of Leaf Complexity by miRNA-Regulated Licensing of Protein Complexes. Current Biology, 24(22), 2714-2719. doi:10.1016/j.cub.2014.09.058Salinas, M., Xing, S., Höhmann, S., Berndtgen, R., & Huijser, P. (2011). Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. Planta, 235(6), 1171-1184. doi:10.1007/s00425-011-1565-ySarvepalli, K., & Nath, U. (2011). Hyper-activation of the TCP4 transcription factor in Arabidopsis thaliana accelerates multiple aspects of plant maturation. The Plant Journal, 67(4), 595-607. doi:10.1111/j.1365-313x.2011.04616.xSerrano-Mislata, A., Bencivenga, S., Bush, M., Schiessl, K., Boden, S., & Sablowski, R. (2017). DELLA genes restrict inflorescence meristem function independently of plant height. Nature Plants, 3(9), 749-754. doi:10.1038/s41477-017-0003-yShikata, M., & Ezura, H. (2016). Micro-Tom Tomato as an Alternative Plant Model System: Mutant Collection and Efficient Transformation. Methods in Molecular Biology, 47-55. doi:10.1007/978-1-4939-3115-6_5Stettler, R. F. (1964). DOSAGE EFFECTS OF THE LANCEOLATE GENE IN TOMATO. American Journal of Botany, 51(3), 253-264. doi:10.1002/j.1537-2197.1964.tb06628.xVarkonyi-Gasic, E., Wu, R., Wood, M., Walton, E. F., & Hellens, R. P. (2007). Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods, 3(1), 12. doi:10.1186/1746-4811-3-12Vendemiatti, E., Zsögön, A., Silva, G. F. F. e, de Jesus, F. A., Cutri, L., Figueiredo, C. R. F., … Peres, L. E. P. (2017). Loss of type-IV glandular trichomes is a heterochronic trait in tomato and can be reverted by promoting juvenility. Plant Science, 259, 35-47. doi:10.1016/j.plantsci.2017.03.006Vicente, M. H., Zsögön, A., de Sá, A. F. L., Ribeiro, R. V., & Peres, L. E. P. (2015). Semi-determinate growth habit adjusts the vegetative-to-reproductive balance and increases productivity and water-use efficiency in tomato ( Solanum lycopersicum ). Journal of Plant Physiology, 177, 11-19. doi:10.1016/j.jplph.2015.01.003Wang, J.-W., Czech, B., & Weigel, D. (2009). miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana. Cell, 138(4), 738-749. doi:10.1016/j.cell.2009.06.014Wilkie, J. D., Sedgley, M., & Olesen, T. (2008). Regulation of floral initiation in horticultural trees. Journal of Experimental Botany, 59(12), 3215-3228. doi:10.1093/jxb/ern188Yamaguchi, A., Wu, M.-F., Yang, L., Wu, G., Poethig, R. S., & Wagner, D. (2009). The MicroRNA-Regulated SBP-Box Transcription Factor SPL3 Is a Direct Upstream Activator of LEAFY, FRUITFULL, and APETALA1. Developmental Cell, 17(2), 268-278. doi:10.1016/j.devcel.2009.06.007Yamaguchi, N., Winter, C. M., Wu, M.-F., Kanno, Y., Yamaguchi, A., Seo, M., & Wagner, D. (2014). Gibberellin Acts Positively Then Negatively to Control Onset of Flower Formation in Arabidopsis. Science, 344(6184), 638-641. doi:10.1126/science.1250498Yamaguchi, S. (2008). Gibberellin Metabolism and its Regulation. Annual Review of Plant Biology, 59(1), 225-251. doi:10.1146/annurev.arplant.59.032607.092804Yamamoto, A., Nakamura, T., Adu-Gyamfi, J. J., & Saigusa, M. (2002). RELATIONSHIP BETWEEN CHLOROPHYLL CONTENT IN LEAVES OF SORGHUM AND PIGEONPEA DETERMINED BY EXTRACTION METHOD AND BY CHLOROPHYLL METER (SPAD-502). Journal of Plant Nutrition, 25(10), 2295-2301. doi:10.1081/pln-120014076Yanai, O., Shani, E., Russ, D., & Ori, N. (2011). Gibberellin partly mediates LANCEOLATE activity in tomato. The Plant Journal, 68(4), 571-582. doi:10.1111/j.1365-313x.2011.04716.xYu, S., Galvão, V. C., Zhang, Y.-C., Horrer, D., Zhang, T.-Q., Hao, Y.-H., … Wang, J.-W. (2012). Gibberellin Regulates the Arabidopsis Floral Transition through miR156-Targeted SQUAMOSA PROMOTER BINDING–LIKE Transcription Factors. The Plant Cell, 24(8), 3320-3332. doi:10.1105/tpc.112.101014Yuste-Lisbona, F. J., Quinet, M., Fernández-Lozano, A., Pineda, B., Moreno, V., Angosto, T., & Lozano, R. (2016). Characterization of vegetative inflorescence (mc-vin) mutant provides new insight into the role of MACROCALYX in regulating inflorescence development of tomato. Scientific Reports, 6(1). doi:10.1038/srep18796Zhang, S., Zhang, D., Fan, S., Du, L., Shen, Y., Xing, L., … Han, M. (2016). Effect of exogenous GA 3 and its inhibitor paclobutrazol on floral formation, endogenous hormones, and flowering-associated genes in ‘Fuji’ apple ( Malus domestica Borkh.). Plant Physiology and Biochemistry, 107, 178-186. doi:10.1016/j.plaphy.2016.06.005Zhang, X., Zou, Z., Zhang, J., Zhang, Y., Han, Q., Hu, T., … Ye, Z. (2010). Over-expression of sly-miR156a in tomato results in multiple vegetative and reproductive trait alterations and partial phenocopy of the sft mutant. FEBS Letters, 585(2), 435-439. doi:10.1016/j.febslet.2010.12.03

Genetic, environmental and stochastic factors in monozygotic twin discordance with a focus on epigenetic differences

PMCID: PMC3566971This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

De novo domestication of wild tomato using genome editing

Breeding of crops over millennia for yield and productivity1 has led to reduced genetic diversity. As a result, beneficial traits of wild species, such as disease resistance and stress tolerance, have been lost2. We devised a CRISPR–Cas9 genome engineering strategy to combine agronomically desirable traits with useful traits present in wild lines. We report that editing of six loci that are important for yield and productivity in present-day tomato crop lines enabled de novo domestication of wild Solanum pimpinellifolium. Engineered S. pimpinellifolium morphology was altered, together with the size, number and nutritional value of the fruits. Compared with the wild parent, our engineered lines have a threefold increase in fruit size and a tenfold increase in fruit number. Notably, fruit lycopene accumulation is improved by 500% compared with the widely cultivated S. lycopersicum. Our results pave the way for molecular breeding programs to exploit the genetic diversity present in wild plants

Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci

<p>Abstract</p> <p>Background</p> <p>Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within <it>Lepus</it>, therefore it is possible that introgressive hybridization events also occur among Chinese <it>Lepus </it>species and contribute to the current taxonomic confusion.</p> <p>Results</p> <p>Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese <it>Lepus </it>species. Remarkably, the mtDNA of <it>L. mandshuricus </it>was completely replaced by mtDNA from <it>L. timidus </it>and <it>L. sinensis</it>. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species.</p> <p>Conclusion</p> <p>This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.</p

Conflicts Between Parents and Health Professionals About a Child's Medical Treatment: Using Clinical Ethics Records to Find Gaps in the Bioethics Literature

Clinical ethics records offer bioethics researchers a rich source of cases that clinicians have identified as ethically complex. In this paper, we suggest that clinical ethics records can be used to point to types of cases that lack attention in the current bioethics literature, identifying new areas in need of more detailed bioethical work. We conducted an analysis of the clinical ethics records of one paediatric hospital in Australia, focusing specifically on conflicts between parents and health professionals about a child's medical treatment. We identified, analysed, and compared cases of this type from the clinical ethics records with cases of this type discussed in bioethics journals. While the cases from journals tended to describe situations involving imminent risk to the child's life, a significant proportion of the clinical ethics records cases involved different stakes for the child involved. These included distress, poorer functional outcome, poorer psychosocial outcome, or increased risk of surgical complications. Our analysis suggests that one type of case that warrants more detailed ethics research is parental refusal of recommended treatment, where the refusal does not endanger the child's life but rather some other aspect of the child's well-being

Drawing the line on In Vitro Gametogenesis

In vitro gametogenesis (IVG) might offer numerous research and clinical benefits. Some potential clinical applications of IVG, such as allowing opposite‐sex couples experiencing infertility to have genetically related children, have attracted support. Others, such as enabling same‐sex reproduction and solo reproduction, have attracted significantly more criticism. In this paper, we examine how different ethical principles might help us to draw lines and distinguish between ethically desirable and undesirable uses of IVG. We discuss the alleged distinction between therapeutic and non‐therapeutic uses of assisted reproduction in the context of IVG, and show how it is both problematic to apply in practice and theoretically dubious. We then discuss how the ethical principles of reproductive justice and beneficence apply to IVG for opposite‐sex reproduction, same‐sex reproduction, and solo reproduction. We suggest that these principles generate strong reasons for the use of IVG for opposite‐sex and same‐sex reproduction, but not for solo reproduction

Drawing the line on in vitro gametogenesis

In vitro gametogenesis (IVG) might offer numerous research and clinical benefits. Some potential clinical applications of IVG, such as allowing opposite-sex couples experiencing infertility to have genetically related children, have attracted support. Others, such as enabling same-sex reproduction and solo reproduction, have attracted significantly more criticism. In this paper, we examine how different ethical principles might help us to draw lines and distinguish between ethically desirable and undesirable uses of IVG. We discuss the alleged distinction between therapeutic and non-therapeutic uses of assisted reproduction in the context of IVG, and show how it is both problematic to apply in practice and theoretically dubious. We then discuss how the ethical principles of reproductive justice and beneficence apply to IVG for opposite-sex reproduction, same-sex reproduction, and solo reproduction. We suggest that these principles generate strong reasons for the use of IVG for opposite-sex and same-sex reproduction, but not for solo reproduction

Clinicians’ views and experiences with offering and returning results from exome sequencing to parents of infants with hearing loss

Exome sequencing (ES) is an effective method for identifying the genetic cause of hearing loss in infants diagnosed through newborn hearing screening programs. ES has the potential to be integrated into routine clinical care, yet little is known about the experiences of clinicians offering this test to families. To address this gap, clinicians involved in a clinical study using ES to identify the cause of infants’ hearing loss were interviewed to explore their experiences with offering and returning results to parents. Interview transcripts were analysed using inductive content analysis. Twelve clinicians participated: seven genetic counsellors, four clinical geneticists, and one paediatrician. Most clinicians were supportive of offering ES to infants with hearing loss, primarily because results may inform the child’s clinical management. However, some expressed concerns, questioning the utility of this information, particularly for isolated hearing loss. Clinicians had differing views regarding the optimal time to offer ES to families; while some felt that families can manage everything at once, others recommended delaying testing until parents have come to terms with their child’s diagnosis. These findings show the complexity involved in determining how ES should be offered to families following the diagnosis of a child with hearing loss, particularly with regards to when testing is suggested