Transcriptomic analysis of a near-isogenic line of melon with high fruit flesh firmness during ripening

This is the peer reviewed version of the following article: Zarid, M., García-Carpintero, V., Esteras, C., Esteva, J., Bueso, M.C., Cañizares, J., Picó, M.B., Monforte, A.J. and Fernández-Trujillo, J.P. (2021), Transcriptomic analysis of a near-isogenic line of melon with high fruit flesh firmness during ripening. J Sci Food Agric, 101: 754-777, which has been published in final form at https://doi.org/10.1002/jsfa.10688. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.[EN] BACKGROUND A near-isogenic line (NIL) of melon (SC10-2) with introgression in linkage group X was studied from harvest (at firm-ripe stage of maturity) until day 18 of postharvest storage at 20.5 degrees C together with its parental control ('Piel de Sapo', PS). RESULTS SC10-2 showed higher flesh firmness and whole fruit hardness but lower juiciness than its parental. SC10-2 showed a decrease in respiration rate accompanied by a decrease in ethylene production during ripening, both of which fell to a greater extent than in PS. The introgression affected 11 volatile organic compounds (VOCs), the levels of which during ripening were generally higher in SC10-2 than in PS. Transcriptomic analysis from RNA-Seq revealed differentially expressed genes (DEGs) associated with the effects studied. For example, 909 DEGs were exclusive to the introgression, and only 23 DEGs were exclusive to postharvest ripening time. Major functions of the DEGs associated with introgression or ripening time were identified by cluster analysis. About 37 genes directly and/or indirectly affected the delay in ripening of SC10-2 compared with PS in general and, more particularly, the physiological and quality traits measured and, probably, the differential non-climacteric response. Of the former genes, we studied in more detail at least five that mapped in the introgression in linkage group (LG) X, and 32 outside it. CONCLUSION There is an apparent control of textural changes, VOCs and fruit ripening by an expression quantitative trait locus located in LG X together with a direct control on them due to genes presented in the introgression (CmTrpD,CmNADH1,CmTCP15,CmGDSL esterase/lipase, andCmHK4-like) and CmNAC18.This work was funded by grants 11784/PI/09 (Seneca Foundation, Region of Murcia) and Ministry of Economy and Innovation (AGL2010-20858). M Zarid acknowledges an UE-Erasmus predoctoral fellowship, a program coordinated by the University of Murcia in the framework of CMN. Thanks are due to Semillas Fitó SA (Barcelona, Spain), for providing seeds of PS melons and IRTACRAG for the seeds of SC10-2. We acknowledge the assistance of P Varó and his team in CIFEA-Torre Pacheco for crop management, to N Dos-Santos, M Medina, M García-Gutiérrez, A Hakmaoui, E Cuadros, I Canales and AA Escudero (UPCT) for sampling and technical assistance, to SAIT-UPCT for GC-MS analysis, to AG Sifres (COMAV) for RNA extraction, and to CNAG (Barcelona) for professional assistance in RNA-Seq. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.Zarid, M.; García-Carpintero, V.; Esteras Gómez, C.; Esteva, J.; Bueso, MC.; Cañizares Sales, J.; Picó Sirvent, MB.... (2021). Transcriptomic analysis of a near-isogenic line of melon with high fruit flesh firmness during ripening. Journal of the Science of Food and Agriculture. 101(2):754-777. https://doi.org/10.1002/jsfa.10688S7547771012Ríos, P., Argyris, J., Vegas, J., Leida, C., Kenigswald, M., Tzuri, G., … Garcia-Mas, J. (2017). ETHQV6.3 is involved in melon climacteric fruit ripening and is encoded by a NAC domain transcription factor. The Plant Journal, 91(4), 671-683. doi:10.1111/tpj.13596Ezura, H., & Owino, W. O. (2008). Melon, an alternative model plant for elucidating fruit ripening. Plant Science, 175(1-2), 121-129. doi:10.1016/j.plantsci.2008.02.004Guo, X., Xu, J., Cui, X., Chen, H., & Qi, H. (2017). iTRAQ-based Protein Profiling and Fruit Quality Changes at Different Development Stages of Oriental Melon. BMC Plant Biology, 17(1). doi:10.1186/s12870-017-0977-7Chaparro-Torres, L. A., Bueso, M. C., & Fernández-Trujillo, J. P. (2015). Aroma volatiles obtained at harvest by HS-SPME/GC-MS and INDEX/MS-E-nose fingerprint discriminate climacteric behaviour in melon fruit. Journal of the Science of Food and Agriculture, 96(7), 2352-2365. doi:10.1002/jsfa.7350Pech, J. C., Bouzayen, M., & Latché, A. (2008). Climacteric fruit ripening: Ethylene-dependent and independent regulation of ripening pathways in melon fruit. Plant Science, 175(1-2), 114-120. doi:10.1016/j.plantsci.2008.01.003Dahmani-Mardas, F., Troadec, C., Boualem, A., Lévêque, S., Alsadon, A. A., Aldoss, A. A., … Bendahmane, A. (2010). Engineering Melon Plants with Improved Fruit Shelf Life Using the TILLING Approach. PLoS ONE, 5(12), e15776. doi:10.1371/journal.pone.0015776González, M., Xu, M., Esteras, C., Roig, C., Monforte, A. J., Troadec, C., … Picó, B. (2011). Towards a TILLING platform for functional genomics in Piel de Sapo melons. BMC Research Notes, 4(1). doi:10.1186/1756-0500-4-289Yano, R., Nonaka, S., & Ezura, H. (2017). Melonet-DB, a Grand RNA-Seq Gene Expression Atlas in Melon (Cucumis melo L.). Plant and Cell Physiology, 59(1), e4-e4. doi:10.1093/pcp/pcx193Perpiñá, G., Esteras, C., Gibon, Y., Monforte, A. J., & Picó, B. (2016). A new genomic library of melon introgression lines in a cantaloupe genetic background for dissecting desirable agronomical traits. BMC Plant Biology, 16(1). doi:10.1186/s12870-016-0842-0Pereira, L., Ruggieri, V., Pérez, S., Alexiou, K. G., Fernández, M., Jahrmann, T., … Garcia-Mas, J. (2018). QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map. BMC Plant Biology, 18(1). doi:10.1186/s12870-018-1537-5Eduardo, I., Arús, P., & Monforte, A. J. (2005). Development of a genomic library of near isogenic lines (NILs) in melon (Cucumis melo L.) from the exotic accession PI161375. Theoretical and Applied Genetics, 112(1), 139-148. doi:10.1007/s00122-005-0116-yMoreno, E., Obando, J. M., Dos-Santos, N., Fernández-Trujillo, J. P., Monforte, A. J., & Garcia-Mas, J. (2007). Candidate genes and QTLs for fruit ripening and softening in melon. Theoretical and Applied Genetics, 116(4), 589-602. doi:10.1007/s00122-007-0694-yGalpaz, N., Gonda, I., Shem‐Tov, D., Barad, O., Tzuri, G., Lev, S., … Katzir, N. (2018). Deciphering genetic factors that determine melon fruit‐quality traits using RNA ‐Seq‐based high‐resolution QTL and eQTL mapping. The Plant Journal, 94(1), 169-191. doi:10.1111/tpj.13838Saladié, M., Cañizares, J., Phillips, M. A., Rodriguez-Concepcion, M., Larrigaudière, C., Gibon, Y., … Garcia-Mas, J. (2015). Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties. BMC Genomics, 16(1). doi:10.1186/s12864-015-1649-3Zhang, H., Wang, H., Yi, H., Zhai, W., Wang, G., & Fu, Q. (2016). Transcriptome profiling of Cucumis melo fruit development and ripening. Horticulture Research, 3(1). doi:10.1038/hortres.2016.14Eduardo, I., Arús, P., Monforte, A. J., Obando, J., Fernández-Trujillo, J. P., Martínez, J. A., … van der Knaap, E. (2007). Estimating the Genetic Architecture of Fruit Quality Traits in Melon Using a Genomic Library of Near Isogenic Lines. Journal of the American Society for Horticultural Science, 132(1), 80-89. doi:10.21273/jashs.132.1.80Nimmakayala, P., Tomason, Y. R., Abburi, V. L., Alvarado, A., Saminathan, T., Vajja, V. G., … Reddy, U. K. (2016). Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map. Frontiers in Plant Science, 7. doi:10.3389/fpls.2016.01437Fernández-Trujillo, J. P., Fernández-Talavera, M., Ruiz-León, M., Roca, M. J., & Dos-Santos, N. (2012). AROMA VOLATILES DURING WHOLE MELON RIPENING IN A CLIMACTERIC NEAR-ISOGENIC LINE AND ITS INBRED NON-CLIMACTERIC PARENTS. Acta Horticulturae, (934), 951-957. doi:10.17660/actahortic.2012.934.127Obando-Ulloa, J. M., Moreno, E., García-Mas, J., Nicolai, B., Lammertyn, J., Monforte, A. J., & Fernández-Trujillo, J. P. (2008). Climacteric or non-climacteric behavior in melon fruit. Postharvest Biology and Technology, 49(1), 27-37. doi:10.1016/j.postharvbio.2007.11.004Obando-Ulloa, J. M., Nicolai, B., Lammertyn, J., Bueso, M. C., Monforte, A. J., & Fernández-Trujillo, J. P. (2009). Aroma volatiles associated with the senescence of climacteric or non-climacteric melon fruit. Postharvest Biology and Technology, 52(2), 146-155. doi:10.1016/j.postharvbio.2008.11.007Gonda, I., Bar, E., Portnoy, V., Lev, S., Burger, J., Schaffer, A. A., … Lewinsohn, E. (2010). Branched-chain and aromatic amino acid catabolism into aroma volatiles in Cucumis melo L. fruit. Journal of Experimental Botany, 61(4), 1111-1123. doi:10.1093/jxb/erp390Dos-Santos, N., Bueso, M. C., & Fernández-Trujillo, J. P. (2013). Aroma volatiles as biomarkers of textural differences at harvest in non-climacteric near-isogenic lines of melon. Food Research International, 54(2), 1801-1812. doi:10.1016/j.foodres.2013.09.031Obando, J., Fernández-Trujillo, J. P., Martínez, J. A., Alarcón, A. L., Eduardo, I., Arús, P., & Monforte, A. J. (2008). Identification of Melon Fruit Quality Quantitative Trait Loci Using Near-isogenic Lines. Journal of the American Society for Horticultural Science, 133(1), 139-151. doi:10.21273/jashs.133.1.139Gomes, M. H., Fundo, J., Obando-Ulloa, J. M., Fernández-Trujillo, J. P., & Almeida, D. P. F. (2010). GENETIC BACKGROUND OF QUALITY AND CELL WALL CHANGES IN FRESH-CUT MELONS. Acta Horticulturae, (877), 1011-1018. doi:10.17660/actahortic.2010.877.136Dos-Santos, N., Jiménez-Araujo, A., Rodríguez-Arcos, R., & Fernández-Trujillo, J. P. (2011). Cell Wall Polysaccharides of Near-Isogenic Lines of Melon (Cucumis melo L.) and Their Inbred Parentals Which Show Differential Flesh Firmness or Physiological Behavior. Journal of Agricultural and Food Chemistry, 59(14), 7773-7784. doi:10.1021/jf201155aFernández-Trujillo, J. P., Obando-Ulloa, J. M., Martínez, J. A., Moreno, E., García-Mas, J., & Monforte, A. J. (2008). Climacteric and non-climacteric behavior in melon fruit. Postharvest Biology and Technology, 50(2-3), 125-134. doi:10.1016/j.postharvbio.2008.04.007Fernández-Trujillo, J., Zarid, M., & Bueso, M. (2018). Methodology to Remove Strong Outliers of Non-Climacteric Melon Fruit Aroma at Harvest Obtained by HS-SPME GC-MS Analysis. Separations, 5(2), 30. doi:10.3390/separations5020030AndrewsS FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics (2010). Available:http://www.bioinformatics.babraham.ac.uk/projects/fastqc.Kim, D., Langmead, B., & Salzberg, S. L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12(4), 357-360. doi:10.1038/nmeth.3317Pertea, M., Pertea, G. M., Antonescu, C. M., Chang, T.-C., Mendell, J. T., & Salzberg, S. L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33(3), 290-295. doi:10.1038/nbt.3122FuJ FrazeeAC Collado‐TorresL JaffeAEandLeekJT Ballgown: flexible isoform‐level differential expression analysis. R package version 2.12.0(2018).Howe, E. A., Sinha, R., Schlauch, D., & Quackenbush, J. (2011). RNA-Seq analysis in MeV. Bioinformatics, 27(22), 3209-3210. doi:10.1093/bioinformatics/btr490MEV Multi experiment viewer. TM4 MeV stand‐alone client(2018).http://mev.tm4.org/#/welcome. Available:https://sourceforge.net/projects/mev-tm4/[5 October 2018].Conesa, 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/bti610Paul, V., Pandey, R., & Srivastava, G. C. (2011). The fading distinctions between classical patterns of ripening in climacteric and non-climacteric fruit and the ubiquity of ethylene—An overview. Journal of Food Science and Technology, 49(1), 1-21. doi:10.1007/s13197-011-0293-4Perotti, V. E., Moreno, A. S., & Podestá, F. E. (2014). Physiological aspects of fruit ripening: The mitochondrial connection. Mitochondrion, 17, 1-6. doi:10.1016/j.mito.2014.04.010ARAÚJO, W. L., NUNES-NESI, A., NIKOLOSKI, Z., SWEETLOVE, L. J., & FERNIE, A. R. (2011). Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues. Plant, Cell & Environment, 35(1), 1-21. doi:10.1111/j.1365-3040.2011.02332.xMelo, A. M. P., Bandeiras, T. M., & Teixeira, M. (2004). New Insights into Type II NAD(P)H:Quinone Oxidoreductases. Microbiology and Molecular Biology Reviews, 68(4), 603-616. doi:10.1128/mmbr.68.4.603-616.2004Møller, I. M. (2001). PLANT MITOCHONDRIA AND OXIDATIVE STRESS: Electron Transport, NADPH Turnover, and Metabolism of Reactive Oxygen Species. Annual Review of Plant Physiology and Plant Molecular Biology, 52(1), 561-591. doi:10.1146/annurev.arplant.52.1.561Fatland, B. L., Ke, J., Anderson, M. D., Mentzen, W. I., Cui, L. W., Allred, C. C., … Wurtele, E. S. (2002). Molecular Characterization of a Heteromeric ATP-Citrate Lyase That Generates Cytosolic Acetyl-Coenzyme A in Arabidopsis,. Plant Physiology, 130(2), 740-756. doi:10.1104/pp.008110Sánchez, L. B., Galperin, M. Y., & Müller, M. (2000). Acetyl-CoA Synthetase from the Amitochondriate EukaryoteGiardia lamblia Belongs to the Newly Recognized Superfamily of Acyl-CoA Synthetases (Nucleoside Diphosphate-forming). Journal of Biological Chemistry, 275(8), 5794-5803. doi:10.1074/jbc.275.8.5794Fraser, M. E., James, M. N. G., Bridger, W. A., & Wolodko, W. T. (1999). A detailed structural description of Escherichia coli succinyl-CoA synthetase 1 1Edited by D. Rees. Journal of Molecular Biology, 285(4), 1633-1653. doi:10.1006/jmbi.1998.2324Causse, M. (2008). Genetic background of flavour: the case of the tomato. Fruit and Vegetable Flavour, 229-253. doi:10.1533/9781845694296.4.229Nishimura, C., Ohashi, Y., Sato, S., Kato, T., Tabata, S., & Ueguchi, C. (2004). Histidine Kinase Homologs That Act as Cytokinin Receptors Possess Overlapping Functions in the Regulation of Shoot and Root Growth in Arabidopsis. The Plant Cell, 16(6), 1365-1377. doi:10.1105/tpc.021477Kieber, J. J. (2002). Journal of Plant Growth Regulation, 21(1), 1-2. doi:10.1007/s003440010059Zhang, Z., Jiang, S., Wang, N., Li, M., Ji, X., Sun, S., … Chen, X. (2015). Identification of Differentially Expressed Genes Associated with Apple Fruit Ripening and Softening by Suppression Subtractive Hybridization. PLOS ONE, 10(12), e0146061. doi:10.1371/journal.pone.0146061Girard, A.-L., Mounet, F., Lemaire-Chamley, M., Gaillard, C., Elmorjani, K., Vivancos, J., … Bakan, B. (2012). Tomato GDSL1 Is Required for Cutin Deposition in the Fruit Cuticle. The Plant Cell, 24(7), 3119-3134. doi:10.1105/tpc.112.101055Hayashi, S., Ishii, T., Matsunaga, T., Tominaga, R., Kuromori, T., Wada, T., … Hirayama, T. (2008). The Glycerophosphoryl Diester Phosphodiesterase-Like Proteins SHV3 and its Homologs Play Important Roles in Cell Wall Organization. Plant and Cell Physiology, 49(10), 1522-1535. doi:10.1093/pcp/pcn120Ge, W., Song, Y., Zhang, C., Zhang, Y., Burlingame, A. L., & Guo, Y. (2011). Proteomic analyses of apoplastic proteins from germinating Arabidopsis thaliana pollen. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1814(12), 1964-1973. doi:10.1016/j.bbapap.2011.07.013Rose, J. K. C., Hadfield, K. A., Labavitch, J. M., & Bennett, A. B. (1998). Temporal Sequence of Cell Wall Disassembly in Rapidly Ripening Melon Fruit1. Plant Physiology, 117(2), 345-361. doi:10.1104/pp.117.2.345Daminato, M., Guzzo, F., & Casadoro, G. (2013). A SHATTERPROOF-like gene controls ripening in non-climacteric strawberries, and auxin and abscisic acid antagonistically affect its expression. Journal of Experimental Botany, 64(12), 3775-3786. doi:10.1093/jxb/ert214Lu, W., Mao, L., Chen, J., Han, X., Ren, X., Ying, T., & Luo, Z. (2018). Interaction of abscisic acid and auxin on gene expression involved in banana ripening. Acta Physiologiae Plantarum, 40(3). doi:10.1007/s11738-018-2621-zBarry, C. S., Llop-Tous, M. I., & Grierson, D. (2000). The Regulation of 1-Aminocyclopropane-1-Carboxylic Acid Synthase Gene Expression during the Transition from System-1 to System-2 Ethylene Synthesis in Tomato. Plant Physiology, 123(3), 979-986. doi:10.1104/pp.123.3.979Wang, L., Zhang, X., Wang, L., Tian, Y., Jia, N., Chen, S., … Pang, X. (2017). Regulation of ethylene-responsive SlWRKYs involved in color change during tomato fruit ripening. Scientific Reports, 7(1). doi:10.1038/s41598-017-16851-yZhang, C., Hou, Y., Hao, Q., Chen, H., Chen, L., Yuan, S., … Huang, W. (2015). Genome-Wide Survey of the Soybean GATA Transcription Factor Gene Family and Expression Analysis under Low Nitrogen Stress. PLOS ONE, 10(4), e0125174. doi:10.1371/journal.pone.0125174Sharma, M. K., Kumar, R., Solanke, A. U., Sharma, R., Tyagi, A. K., & Sharma, A. K. (2010). Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato. Molecular Genetics and Genomics, 284(6), 455-475. doi:10.1007/s00438-010-0580-1Pirrello, J., Prasad, B. N., Zhang, W., Chen, K., Mila, I., Zouine, M., … Bouzayen, M. (2012). Functional analysis and binding affinity of tomato ethylene response factors provide insight on the molecular bases of plant differential responses to ethylene. BMC Plant Biology, 12(1). doi:10.1186/1471-2229-12-190Liu, M., Diretto, G., Pirrello, J., Roustan, J., Li, Z., Giuliano, G., … Bouzayen, M. (2014). The chimeric repressor version of an E thylene Response Factor ( ERF ) family member, Sl‐ ERF .B3 , shows contrasting effects on tomato fruit ripening. New Phytologist, 203(1), 206-218. doi:10.1111/nph.12771Jeong, M.-J., & Shih, M.-C. (2003). Interaction of a GATA factor with cis-acting elements involved in light regulation of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in Arabidopsis. Biochemical and Biophysical Research Communications, 300(2), 555-562. doi:10.1016/s0006-291x(02)02892-9Tarze, A., Deniaud, A., Le Bras, M., Maillier, E., Molle, D., Larochette, N., … Brenner, C. (2006). GAPDH, a novel regulator of the pro-apoptotic mitochondrial membrane permeabilization. Oncogene, 26(18), 2606-2620. doi:10.1038/sj.onc.1210074Zala, D., Hinckelmann, M.-V., Yu, H., Lyra da Cunha, M. M., Liot, G., Cordelières, F. P., … Saudou, F. (2013). Vesicular Glycolysis Provides On-Board Energy for Fast Axonal Transport. Cell, 152(3), 479-491. doi:10.1016/j.cell.2012.12.029YANAKA, N. (2007). Mammalian Glycerophosphodiester Phosphodiesterases. Bioscience, Biotechnology, and Biochemistry, 71(8), 1811-1818. doi:10.1271/bbb.70062Zhu, M., Chen, G., Zhou, S., Tu, Y., Wang, Y., Dong, T., & Hu, Z. (2013). A New Tomato NAC (NAM/ATAF1/2/CUC2) Transcription Factor, SlNAC4, Functions as a Positive Regulator of Fruit Ripening and Carotenoid Accumulation. Plant and Cell Physiology, 55(1), 119-135. doi:10.1093/pcp/pct162Jaakola, L., Poole, M., Jones, M. O., Kämäräinen-Karppinen, T., Koskimäki, J. J., Hohtola, A., … Seymour, G. B. (2010). A SQUAMOSA MADS Box Gene Involved in the Regulation of Anthocyanin Accumulation in Bilberry Fruits    . Plant Physiology, 153(4), 1619-1629. doi:10.1104/pp.110.158279Seymour, G. B., Ryder, C. D., Cevik, V., Hammond, J. P., Popovich, A., King, G. J., … Manning, K. (2010). A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria×ananassa Duch.) fruit, a non-climacteric tissue*. Journal of Experimental Botany, 62(3), 1179-1188. doi:10.1093/jxb/erq360Obando-Ulloa, J. M., Ruiz, J., Monforte, A. J., & Fernández-Trujillo, J. P. (2010). Aroma profile of a collection of near-isogenic lines of melon (Cucumis melo L.). Food Chemistry, 118(3), 815-822. doi:10.1016/j.foodchem.2009.05.068Gaude, N., Nakamura, Y., Scheible, W.-R., Ohta, H., & Dörmann, P. (2008). Phospholipase C5 (NPC5) is involved in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis. The Plant Journal, 56(1), 28-39. doi:10.1111/j.1365-313x.2008.03582.xLi, M., Qin, C., Welti, R., & Wang, X. (2005). Double Knockouts of Phospholipases Dζ1 and Dζ2 in Arabidopsis Affect Root Elongation during Phosphate-Limited Growth But Do Not Affect Root Hair Patterning. Plant Physiology, 140(2), 761-770. doi:10.1104/pp.105.070995Nakamura, Y., Koizumi, R., Shui, G., Shimojima, M., Wenk, M. R., Ito, T., & Ohta, H. (2009). Arabidopsis lipins mediate eukaryotic pathway of lipid metabolism and cope critically with phosphate starvation. Proceedings of the National Academy of Sciences, 106(49), 20978-20983. doi:10.1073/pnas.0907173106Nakamura, Y., Awai, K., Masuda, T., Yoshioka, Y., Takamiya, K., & Ohta, H. (2005). A Novel Phosphatidylcholine-hydrolyzing Phospholipase C Induced by Phosphate Starvation in Arabidopsis. Journal of Biological Chemistry, 280(9), 7469-7476. doi:10.1074/jbc.m408799200Tang, Y., Zhang, C., Cao, S., Wang, X., & Qi, H. (2015). The Effect of CmLOXs on the Production of Volatile Organic Compounds in Four Aroma Types of Melon (Cucumis melo). PLOS ONE, 10(11), e0143567. doi:10.1371/journal.pone.0143567Zhang, C., Cao, S., Jin, Y., Ju, L., Chen, Q., Xing, Q., & Qi, H. (2017). Melon13-lipoxygenase CmLOX18 may be involved in C6 volatiles biosynthesis in fruit. Scientific Reports, 7(1). doi

Long-term benefits of nevirapine-containing regimens: multicenter study with 506 patients, followed-up a median of 9 years

[Abstract] OBJECTIVE: To evaluate long-term outcomes in patients maintaining a nevirapine (NVP)-based regimen. METHODS: Retrospective, multicenter, cohort study including patients currently receiving an NVP regimen that had been started at least 5 years previously. Demographic, clinical, and analytical variables were recorded. RESULTS: Median follow-up was 8.9 (5.7-11.3) years. Baseline characteristics: 74% men, 47 years old, 36% drug users, 40% AIDS, 40% HCV+, 51.4% detectable HIV-1 viral load, CD4 count 395 (4-1,421)/μL, 19% CD4 3.37 mmol/L significantly decreased in a subsample with available values. A significant decrease in transaminases, alkaline phosphatase, and Fib4 score was observed, mainly in HCV+ and ARV-naive patients. CONCLUSIONS: In patients who tolerate NVP therapy, (even those with HCV coinfection), long term benefits may be significant in terms of a progressive improvement in general health status markers and CD4 response, a favorable lipid profile, and good liver tolerability

Boceprevir plus pegylated interferon/ribavirin to re-treat hepatitis C virus genotype 1 in HIV-HCV co-infected patients: final results of the Spanish BOC HIV-HCV Study

Introduction Boceprevir (BOC) was one of the first oral inhibitors of hepatitis C virus (HCV) NS3 protease to be developed. This study assessed the safety and efficacy of BOC + pegylated interferon-α2a/ribavirin (PEG-IFN/RBV) in the retreatment of HIV-HCV co-infected patients with HCV genotype 1. Methods This was a phase III prospective trial. HIV-HCV (genotype 1) co-infected patients from 16 hospitals in Spain were included. These patients received 4 weeks of PEG-IFN/RBV (lead-in), followed by response-guided therapy with PEG-IFN/RBV plus BOC (a fixed 44 weeks was indicated in the case of cirrhosis). The primary endpoint was the sustained virological response (SVR) rate at 24 weeks post-treatment. Efficacy and safety were evaluated in all patients who received at least one dose of the study drug. Results From June 2013 to April 2014, 102 patients were enrolled, 98 of whom received at least one treatment dose. Seventy-three percent were male, 34% were cirrhotic, 23% had IL28b CC, 65% had genotype 1a, and 41% were previous null responders. The overall SVR rate was 67%. Previous null-responders and cirrhotic patients had lower SVR rates (57% and 51%, respectively). Seventy-six patients (78%) completed the therapy scheme; the most common reasons for discontinuation were lack of response at week 12 (12 patients) and adverse events (six patients). Conclusions Response-guided therapy with BOC in combination with PEG-IFN/RBV led to an overall SVR rate of 67%, but an SVR rate of only 51% in patients with cirrhosis. The therapy was generally well tolerated. Although the current standards of care do not include BOC + PEG-IFN/RBV, the authors believe that this combination can be beneficial in situations where new HCV direct antiviral agent interferon-free therapies are not available yet

Graph based study of allergen cross-reactivity of plant lipid transfer proteins (LTPs) using microarray in a multicenter study.

The study of cross-reactivity in allergy is key to both understanding. the allergic response of many patients and providing them with a rational treatment In the present study, protein microarrays and a co-sensitization graph approach were used in conjunction with an allergen microarray immunoassay. This enabled us to include a wide number of proteins and a large number of patients, and to study sensitization profiles among members of the LTP family. Fourteen LTPs from the most frequent plant food-induced allergies in the geographical area studied were printed into a microarray specifically designed for this research. 212 patients with fruit allergy and 117 food-tolerant pollen allergic subjects were recruited from seven regions of Spain with different pollen profiles, and their sera were tested with allergen microarray. This approach has proven itself to be a good tool to study cross-reactivity between members of LTP family, and could become a useful strategy to analyze other families of allergens

COVID-19 in hospitalized HIV-positive and HIV-negative patients: A matched study

Objectives: We compared the characteristics and clinical outcomes of hospitalized individuals with COVID-19 with [people with HIV (PWH)] and without (non-PWH) HIV co-infection in Spain during the first wave of the pandemic. Methods: This was a retrospective matched cohort study. People with HIV were identified by reviewing clinical records and laboratory registries of 10 922 patients in active-follow-up within the Spanish HIV Research Network (CoRIS) up to 30 June 2020. Each hospitalized PWH was matched with five non-PWH of the same age and sex randomly selected from COVID-19@Spain, a multicentre cohort of 4035 patients hospitalized with confirmed COVID-19. The main outcome was all-cause in-hospital mortality. Results: Forty-five PWH with PCR-confirmed COVID-19 were identified in CoRIS, 21 of whom were hospitalized. A total of 105 age/sex-matched controls were selected from the COVID-19@Spain cohort. The median age in both groups was 53 (Q1-Q3, 46-56) years, and 90.5% were men. In PWH, 19.1% were injecting drug users, 95.2% were on antiretroviral therapy, 94.4% had HIV-RNA < 50 copies/mL, and the median (Q1-Q3) CD4 count was 595 (349-798) cells/μL. No statistically significant differences were found between PWH and non-PWH in number of comorbidities, presenting signs and symptoms, laboratory parameters, radiology findings and severity scores on admission. Corticosteroids were administered to 33.3% and 27.4% of PWH and non-PWH, respectively (P = 0.580). Deaths during admission were documented in two (9.5%) PWH and 12 (11.4%) non-PWH (P = 0.800). Conclusions: Our findings suggest that well-controlled HIV infection does not modify the clinical presentation or worsen clinical outcomes of COVID-19 hospitalization.This work was supported by the Instituto de Salud Carlos III (ISCII) (grant no. COV20/00108) and the Spanish AIDS Research Network (RD16/0025), which is included in the Spanish I+D+I Plan and is co- funded by ISCIII- Subdirección General de Evaluación and European Funding for Regional Development (FEDER)S

Graph based study of allergen cross-reactivity of plant lipid transfer proteins (LTPs) using microarray in a multicenter study.

The study of cross-reactivity in allergy is key to both understanding. the allergic response of many patients and providing them with a rational treatment In the present study, protein microarrays and a co-sensitization graph approach were used in conjunction with an allergen microarray immunoassay. This enabled us to include a wide number of proteins and a large number of patients, and to study sensitization profiles among members of the LTP family. Fourteen LTPs from the most frequent plant food-induced allergies in the geographical area studied were printed into a microarray specifically designed for this research. 212 patients with fruit allergy and 117 food-tolerant pollen allergic subjects were recruited from seven regions of Spain with different pollen profiles, and their sera were tested with allergen microarray. This approach has proven itself to be a good tool to study cross-reactivity between members of LTP family, and could become a useful strategy to analyze other families of allergens

Effects of Spatial Dispersion on the Casimir Force between Graphene Sheets

The Casimir force between graphene sheets is investigated with emphasis on the effect from spatial dispersion using a combination of factors, such as a nonzero chemical potential and an induced energy gap. We distinguish between two regimes for the interaction - T=0 $K$ and $T\neq 0$ $K$. It is found that the quantum mechanical interaction (T=0 $K$) retains its distance dependence regardless of the inclusion of dispersion. The spatial dispersion from the finite temperature Casimir force is found to contribute for the most part from $n=0$ Matsubara term. These effects become important as graphene is tailored to become a poor conductor by inducing a band gap.Comment: 6 pages, 9 figures. Submitted to EP

Clinical experience with integrase inhibitors in HIV-2-infected individuals in Spain.

Background: HIV-2 is a neglected virus despite estimates of 1–2 million people being infected worldwide. The virus is naturally resistant to some antiretrovirals used to treat HIV-1 and therapeutic options are limited for patients with HIV-2. Methods: In this retrospective observational study, we analysed all HIV-2-infected individuals treated with inte- grase strand transfer inhibitors (INSTIs) recorded in the Spanish HIV-2 cohort. Demographics, treatment modal- ities, laboratory values, quantitative HIV-2 RNA and CD4 counts as well as drug resistance were analysed. Results: From a total of 354 HIV-2-infected patients recruited by the Spanish HIV-2 cohort as of December 2017, INSTIs had been given to 44, in 18 as first-line therapy and in 26 after failing other antiretroviral regimens. After a median follow-up of 13 months of INSTI-based therapy, undetectable viraemia for HIV-2 was achieved in 89% of treatment-naive and in 65.4% of treatment-experienced patients. In parallel, CD4 gains were 82 and 126cells/mm3, respectively. Treatment failure occurred in 15 patients, 2 being treatment-naive and 13 treatment-experienced. INSTI resistance changes were recognized in 12 patients: N155H (5), Q148H/R (3), Y143C/G (3) and R263K (1). Conclusions: Combinations based on INSTIs are effective and safe treatment options for HIV-2-infected individ- uals. However, resistance mutations to INSTIs are selected frequently in failing patients, reducing the already limited treatment options

Espècie porcina: manual lesional de suport per al dictamen de carns fresques

Escorxador; Porcí; Carn; Control oficialMatadero; Porcino; Carne; Control oficialSlaughterhouse; Swine; Meat; Official controlLa inspecció post mortem que efectua el col·lectiu de veterinaris oficials d’escorxador és una part important dels controls oficials relatius a la carn fresca i, com a tal, és un dels elements que condiciona que es dictamini com a apta o no per al consum humà i que s’hagin de notificar les malalties de declaració obligatòria. Els escorxadors són entorns òptims per observar i registrar les particularitats de la variada patologia animal que s’hi presenta. Aquesta informació, si és compartida, pot esdevenir una eina molt útil i interessant per al col·lectiu de professionals. En conseqüència, es va crear una comunitat de pràctica (CoP) per a l’espècie porcina. L’autoria d’aquest manual és de veterinaris oficials d’escorxador de la Generalitat de Catalunya. El contingut s’ha volgut transmetre per mitjà de fitxes que contenen informació científica, tècnica i legal per a cada una de les malalties i lesions que s’hi descriuen. Alhora, les fitxes s’il·lustren amb imatges obtingudes als diferents escorxadors de Catalunya. Així, doncs, sabem que els manuals es presenten encara incomplets i, per això, es preveu poder completar-los en futures edicions.La inspección post mortem que efectúa el colectivo de veterinarios oficiales de matadero es una parte importante de los controles oficiales relativos a la carne fresca y, como tal, es uno de los elementos que condiciona que se dictamine como apta o no para el consumo humano y que deban notificarse las enfermedades de declaración obligatoria. Los mataderos son entornos óptimos para observar y registrar las particularidades de la variada patología animal que se presenta. Esta información, si es compartida, puede convertirse en una herramienta muy útil e interesante para el colectivo de profesionales. En consecuencia, se creó una comunidad de práctica (CoP) para la especie porcina. La autoría de este manual es de veterinarios oficiales de matadero de la Generalitat de Catalunya. El contenido se ha querido transmitir por medio de fichas que contienen información científica, técnica y legal para cada una de las enfermedades y lesiones que se describen. Asimismo, las fichas se ilustran con imágenes obtenidas en los diferentes mataderos de Cataluña. Así pues, sabemos que los manuales se presentan todavía incompletos y, por eso, se prevé poder completarlos en futuras ediciones.The post-mortem inspection carried out by the group of official slaughterhouse veterinarians is an important part of the official controls related to fresh meat and, as such, is one of the elements that determines whether or not it is deemed fit for human consumption and Notifiable diseases must be notified. Slaughterhouses are optimal environments to observe and record the particularities of the varied animal pathology that occurs. This information, if shared, can become a very useful and interesting tool for the group of professionals. Accordingly, a community of practice (CoP) for swine was created. The authorship of this manual is official slaughterhouse veterinarians of the Generalitat de Catalunya. The content has been conveyed through sheets containing scientific, technical and legal information for each of the diseases and injuries described. Likewise, the sheets are illustrated with images obtained in the different slaughterhouses in Catalonia. Thus, we know that the manuals are still incomplete and, therefore, it is expected to be able to complete them in future editions

HTLV-1 infection in solid organ transplant donors and recipients in Spain

HTLV-1 infection is a neglected disease, despite infecting 10-15 million people worldwide and severe illnesses develop in 10% of carriers lifelong. Acknowledging a greater risk for developing HTLV-1 associated illnesses due to immunosuppression, screening is being widely considered in the transplantation setting. Herein, we report the experience with universal HTLV testing of donors and recipients of solid organ transplants in a survey conducted in Spain. All hospitals belonging to the Spanish HTLV network were invited to participate in the study. Briefly, HTLV antibody screening was performed retrospectively in all specimens collected from solid organ donors and recipients attended since the year 2008. A total of 5751 individuals were tested for HTLV antibodies at 8 sites. Donors represented 2312 (42.2%), of whom 17 (0.3%) were living kidney donors. The remaining 3439 (59.8%) were recipients. Spaniards represented nearly 80%. Overall, 9 individuals (0.16%) were initially reactive for HTLV antibodies. Six were donors and 3 were recipients. Using confirmatory tests, HTLV-1 could be confirmed in only two donors, one Spaniard and another from Colombia. Both kidneys of the Spaniard were inadvertently transplanted. Subacute myelopathy developed within 1 year in one recipient. The second recipient seroconverted for HTLV-1 but the kidney had to be removed soon due to rejection. Immunosuppression was stopped and 3 years later the patient remains in dialysis but otherwise asymptomatic. The rate of HTLV-1 is low but not negligible in donors/recipients of solid organ transplants in Spain. Universal HTLV screening should be recommended in all donor and recipients of solid organ transplantation in Spain. Evidence is overwhelming for very high virus transmission and increased risk along with the rapid development of subacute myelopathy