Magnetic polarization effects of temperature sensors and heaters in LISA Pathfinder

Temperature sensors and heaters belong in the diagnostics subsystem of the LISA Technology Package (LTP) on board LISA Pathfinder, the technology demonstrator for LISA. A number of these diagnostics items are placed at short distances from the LTP proof masses and are negative temperature coefficient (NTC) thermistors. By design, these devices have tiny amounts of ferromagnetic materials, which therefore constitute a potential source of disturbance to the performance of the LTP. In this paper we report on detailed magnetic characterization of the NTCs and use the data to evaluate their impact on the acceleration noise budget of the LTP. The effect is seen to be small if the NTCs are submitted to a demagnetization process before they are attached. Remagnetization is unlikely, as rather strong fields (approximately millitesla) are required to produce enough NTC magnetic polarization. © 2008 American Institute of Physics

Long-term and transgenerational phenotypic, transcriptional and metabolic effects in rabbit males born following vitrified embryo transfer

[EN] The advent of assisted reproductive technologies (ART) in mammals involved an extraordinary change in the environment where the beginning of a new organism takes place. Under in vitro conditions, in which ART is currently being performed, it likely fails to mimic optimal in vivo conditions. This suboptimal environment could mediate in the natural developmental trajectory of the embryo, inducing lasting effects until later life stages that may be inherited by subsequent generations (transgenerational effects). Therefore, we evaluated the potential transgenerational effects of embryo exposure to the cryopreservation-transfer procedure in a rabbit model on the offspring phenotype, molecular physiology of the liver (transcriptome and metabolome) and reproductive performance during three generations (F1, F2 and F3). The results showed that, compared to naturally-conceived animals (NC group), progeny generated after embryo exposure to the cryopreservation-transfer procedure (VT group) exhibited lower body growth, which incurred lower adult body weight in the F1 (direct effects), F2 (intergenerational effects) and F3 (transgenerational effects) generations. Furthermore, VT animals showed intergenerational effects on heart weight and transgenerational effects on liver weight. The RNA-seq data of liver tissue revealed 642 differentially expressed transcripts (DETs) in VT animals from the F1 generation. Of those, 133 were inherited from the F2 and 120 from the F3 generation. Accordingly, 151, 190 and 159 differentially accumulated metabolites (DAMs) were detected from the F1, F2 and F3, respectively. Moreover, targeted metabolomics analysis demonstrated that transgenerational effects were mostly presented in the non-polar fraction. Functional analysis of molecular data suggests weakened zinc and fatty acid metabolism across the generations, associated with alterations in a complex molecular network affecting global hepatic metabolism that could be associated with the phenotype of VT animals. However, these VT animals showed proper reproductive performance, which verified a functional health status. In conclusion, our results establish the long-term transgenerational effects following a vitrified embryo transfer procedure. We showed that the VT phenotype could be the result of the manifestation of embryonic developmental plasticity in response to the stressful conditions during ART procedures.Funding from the Ministry of Economy, Industry and Competitiveness (Research project: AGL2014-53405-C2-1-P) and Generalitat Valenciana (Research project: Prometeo II 2014/036) is acknowledged. X.G.D. was supported by a research grant from the Ministry of Economy, Industry and Competitiveness (BES-2015-072429). English text version was revised by N. Macowan English Language Service.Garcia-Dominguez, X.; Marco-Jiménez, F.; Peñaranda, D.; Diretto, G.; García-Carpintero, V.; Cañizares Sales, J.; Vicente Antón, JS. (2020). Long-term and transgenerational phenotypic, transcriptional and metabolic effects in rabbit males born following vitrified embryo transfer. Scientific Reports. 10(1):1-15. https://doi.org/10.1038/s41598-020-68195-9S115101Canovas, S., Ross, P. J., Kelsey, G. & Coy, P. DNA methylation in embryo development: epigenetic impact of ART (assisted reproductive technologies). BioEssays 39, 1 (2017).García-Martínez, S. et al. Mimicking physiological O2 tension in the female reproductive tract improves assisted reproduction outcomes in pig. Mol. Hum. Reprod. 24, 260–270 (2018).Ng, K. Y. B., Mingels, R., Morgan, H., Macklon, N. & Cheong, Y. In vivo oxygen, temperature and pH dynamics in the female reproductive tract and their importance in human conception: a systematic review. Hum. Reprod. Update 24, 15–34 (2018).Roseboom, T. J. Developmental plasticity and its relevance to assisted human reproduction. Hum. Reprod. 33, 546–552 (2018).Feuer, S. & Rinaudo, P. From embryos to adults: a DOHaD perspective on in vitro fertilization and other assisted reproductive technologies. Healthcare 4, E51 (2016).Zandstra, H. et al. Association of culture medium with growth, weight and cardiovascular development of IVF children at the age of 9 years. Hum. Reprod. 33, 1645–1656 (2018).Chen, M. & Heilbronn, L. K. The health outcomes of human offspring conceived by assisted reproductive technologies (ART). J. Dev. Orig. Health Dis. 8, 388–402 (2017).Chen, L. et al. Birth prevalence of congenital malformations in singleton pregnancies resulting from in vitro fertilization/intracytoplasmic sperm injection worldwide: a systematic review and meta-analysis. Arch. Gynecol. Obstet. 297, 1115–1130 (2018).Zhang, W. Y. et al. Vascular health of children conceived via in vitro fertilization. J. Pediatr. 214, 47–53 (2019).Guo, X. Y. et al. Cardiovascular and metabolic profiles of offspring conceived by assisted reproductive technologies: a systematic review and meta-analysis. Fertil. Steril. 107, 622–631 (2017).Vrooman, L. A. & Bartolomei, M. S. Can assisted reproductive technologies cause adult-onset disease? Evidence from human and mouse. Reprod. Toxicol. 68, 72–84 (2017).Duranthon, V. & Chavatte-Palmer, P. Long term effects of ART: What do animals tell us?. Mol. Reprod. Dev. 85, 348–368 (2018).Ramos-Ibeas, P. et al. Embryo responses to stress induced by assisted reproductive technologies. Mol. Reprod. Dev. 86, 1292–1306 (2019).Feuer, S. K. et al. Transcriptional signatures throughout development: the effects of mouse embryo manipulation in vitro. Reproduction 153, 107–122 (2017).Feuer, S. K. & Rinaudo, P. F. Physiological, metabolic and transcriptional postnatal phenotypes of in vitro fertilization (IVF) in the mouse. J. Dev. Orig. Health Dis. 8, 403–410 (2017).Sparks, A. E. T. Human embryo cryopreservation-methods, timing, and other considerations for optimizing an embryo cryopreservation program. Semin. Reprod. Med. 33, 128–144 (2015).Dulioust, E. et al. Long-term effects of embryo freezing in mice. Proc. Natl. Acad. Sci. USA. 92, 589–593 (1995).Auroux, M., Cerutti, I., Ducot, B. & Loeuillet, A. Is embryo-cryopreservation really neutral? A new long-term effect of embryo freezing in mice: protection of adults from induced cancer according to strain and sex. Reprod. Toxicol. 18, 813–818 (2004).Vicente, J. S. et al. Rabbit morula vitrification reduces early foetal growth and increases losses throughout gestation. Cryobiology 67, 321–326 (2013).Saenz-De-Juano, M. D. et al. Vitrification alters rabbit foetal placenta at transcriptomic and proteomic level. Reproduction https://doi.org/10.1530/REP-14-0019 (2014).Saenz-de-Juano, M. D., Vicente, J. S., Hollung, K. & Marco-Jiménez, F. Effect of embryo vitrification on rabbit foetal placenta proteome during pregnancy. PLoS ONE 147, 789–801 (2015).Berntsen, S. & Pinborg, A. Large for gestational age and macrosomia in singletons born after frozen/thawed embryo transfer (FET) in assisted reproductive technology (ART). Birth Defects Res. 110, 630–643 (2018).Maheshwari, A. et al. Is frozen embryo transfer better for mothers and babies? Can cumulative meta-analysis provide a definitive answer?. Hum. Reprod. Update 24, 35–58 (2018).Garcia-Dominguez, X., Vicente, J. S. & Marco-Jiménez, F. Developmental plasticity in response to embryo cryopreservation: the importance of the vitrification device in rabbits. Animals 10, 804 (2020).Garcia-Dominguez, X., Marco-Jimenez, F., Viudes-de-Castro, M. P. & Vicente, J. S. Minimally invasive embryo transfer and embryo vitrification at the optimal embryo stage in rabbit model. J. Vis. Exp. 147, e58055 (2019).Garcia-Dominguez, X. et al. Long-term phenotypic effects following vitrified-thawed embryo transfer in a rabbit model. bioRxiv https://doi.org/10.1101/410514 (2018).Ventura-Juncá, P. et al. In vitro fertilization (IVF) in mammals: epigenetic and developmental alterations: scientific and bioethical implications for IVF in humans. Biol. Res. 48, 68 (2015).Calle, A. et al. Long-term and transgenerational effects of in vitro culture on mouse embryos. Theriogenology 77, 785–793 (2012).Calle, A. et al. Male mice produced by in vitro culture have reduced fertility and transmit organomegaly and glucose intolerance to their male Offspring1. Biol. Reprod. 87, 1–9 (2012).Mahsoudi, B., Li, A. & O’Neill, C. Assessment of the long-term and transgenerational consequences of perturbing preimplantation embryo development in Mice1. Biol. Reprod. 77, 889–896 (2007).Servick, K. Unsettled questions trail IVF’s success. Science (80-) 345, 744–746 (2014).Cifre, J., Baselga, M., Gómez, E. A. & De La Luz, G. M. Effect of embryo cryopreservation techniques on reproductive and growth traits in rabbits. Anim. Res. 48, 15–24 (1999).Lavara, R., Baselga, M., Marco-Jiménez, F. & Vicente, J. S. Embryo vitrification in rabbits: consequences for progeny growth. Theriogenology 84, 674–680 (2015).Nusbaumer, D., Da Cunha, L. M. & Wedekind, C. Sperm cryopreservation reduces offspring growth. Proc. R. Soc. B Biol. Sci. 286, 20191644 (2019).Feuer, S. K. et al. Sexually dimorphic effect of In Vitro Fertilization (IVF) on adult mouse fat and liver metabolomes. Endocrinology 155, 4554–4567 (2014).Feuer, S. K. et al. Use of a mouse in vitro fertilization model to understand the developmental origins of health and disease hypothesis. Endocrinology 155, 1956–1969 (2014).Velazquez, M. A. et al. Insulin and branched-chain amino acid depletion during mouse preimplantation embryo culture programmes body weight gain and raised blood pressure during early postnatal life. Biochim. Biophys. Acta Mol. Basis Dis. 1864, 590–600 (2018).Fernández-Gonzalez, R. et al. Long-term effect of in vitro culture of mouse embryos with serum on mRNA expression of imprinting genes, development, and behavior. Proc. Natl. Acad. Sci. U. S. A. 101, 5880–5885 (2004).Horsthemke, B. A critical view on transgenerational epigenetic inheritance in humans. Nat. Commun. 9, 2973 (2018).Perez, M. F. & Lehner, B. Intergenerational and transgenerational epigenetic inheritance in animals. Nat. Cell Biol. 21, 143–151 (2019).Lavara, R., Baselga, M., Marco-Jiménez, F. & Vicente, J. S. Long-term and transgenerational effects of cryopreservation on rabbit embryos. Theriogenology 81, 988–992 (2014).Rexhaj, E. et al. Mice generated by in vitro fertilization exhibit vascular dysfunction and shortened life span. J. Clin. Invest. 123, 5052–5060 (2013).Møller, S. & Bernardi, M. Interactions of the heart and the liver. Eur. Heart J. 34, 2804–2811 (2013).Hyatt, M. A., Budge, H. & Symonds, M. E. Early developmental influences on hepatic organogenesis. Organogenesis 4, 170–175 (2008).Skinner, M. K. What is an epigenetic transgenerational phenotype? F3 or F2. Reprod. Toxicol. 25, 2–6 (2008).Hajkova, P. Epigenetic reprogramming in the germline: towards the ground state of the epigenome. Philos. Trans. R. Soc. B Biol. Sci. 366, 2266–2273 (2011).Lacal, I. & Ventura, R. Epigenetic inheritance: concepts, mechanisms and perspectives. Front. Mol. Neurosci. 11, 292 (2018).Fraser, R. & Lin, C. J. Epigenetic reprogramming of the zygote in mice and men: on your marks, get set, go!. Reproduction 152, R211–R222 (2016).Adamek, A. & Kasprzak, A. Insulin-like growth factor (IGF) system in liver diseases. Int. J. Mol. Sci. 19, E1308 (2018).Kineman, R. D., del Rio-Moreno, M. & Sarmento-Cabral, A. 40 years of IGF1: understanding the tissue-specific roles of IGF1/IGF1R in regulating metabolism using the Cre/loxP system. J. Mol. Endocrinol. 61, T187–T198 (2018).Davis, S. R. & Cousins, R. J. Metallothionein expression in animals: a physiological perspective on function. J. Nutr. 130, 1085–1088 (2000).Günes, Ć et al. Embryonic lethality and liver degeneration in mice lacking the metal-responsive transcriptional activator MTF-1. EMBO J. 17, 2846–2854 (1998).Kambe, T., Tsuji, T., Hashimoto, A. & Itsumura, N. The physiological, biochemical, and molecular roles of zinc transporters in zinc homeostasis and metabolism. Physiol. Rev. 95, 749–784 (2015).Xia, X. et al. Serum levels of trace elements in children born after assisted reproductive technology. Clin. Chim. Acta 495, 664–669 (2019).Bird, A. J. Cellular sensing and transport of metal ions: Implications in micronutrient homeostasis. J. Nutr. Biochem. 26, 1103–1115 (2015).Meesapyodsuk, D. & Qiu, X. The front-end desaturase: Structure, function, evolution and biotechnological use. Lipids 47, 227–237 (2012).Chimhashu, T. et al. Sensitivity of fatty acid desaturation and elongation to plasma zinc concentration: a randomised controlled trial in Beninese children. Br. J. Nutr. https://doi.org/10.1017/S000711451700366X (2018).Wang, L. Y. et al. Alteration of fatty acid metabolism in the liver, adipose tissue, and testis of male mice conceived through assisted reproductive technologies: fatty acid metabolism in ART mice. Lipids Health Dis. 12, 5 (2013).Li, J., Yin, H., Bibus, D. M. & Byelashov, O. A. The role of Omega-3 docosapentaenoic acid in pregnancy and early development. Eur. J. Lipid Sci. Technol. 118, 1692–1701 (2016).Hadley, K. B., Ryan, A. S., Forsyth, S., Gautier, S. & Salem, N. The essentiality of arachidonic acid in infant development. Nutrients 8, 216 (2016).Makowski, L. & Hotamisligil, G. S. The role of fatty acid binding proteins in metabolic syndrome and atherosclerosis. Curr. Opin. Lipidol. 16, 543–548 (2005).Waynforth, D. Effects of conception using assisted reproductive technologies on infant health and development: An evolutionary perspective and analysis using UK millennium cohort data. Yale J. Biol. Med. 91, 225–235 (2018).Sullivan, E. M. et al. Mechanisms bywhich dietary fatty acids regulate mitochondrial structure-function in health and disease. Adv. Nutr. 9, 247–262 (2018).Richardson, U. I. & Wurtman, R. J. Polyunsaturated fatty acids stimulate phosphatidylcholine synthesis in PC12 cells. Biochim. Biophys. Acta Mol. Cell Biol. Lipids 1771, 558–563 (2007).Singh, A. et al. Human glutathione S-transferase enzyme gene polymorphisms and their association with neurocysticercosis. Mol. Neurobiol. 54, 2843–2851 (2017).Yu, H. F. et al. Malic enzyme 1 is important for uterine decidualization in response to progesterone/cAMP/PKA/HB-EGF pathway. FASEB J. 34, 3820–3837 (2020).Chen, M. et al. Altered glucose metabolism in mouse and humans conceived by IVF. Diabetes 63, 3189–3198 (2014).Auroux, M. Long-term effects in progeny of paternal environment and of gamete/embryo cryopreservation. Hum. Reprod. Update 6, 550–563 (2000).Belva, F. et al. Semen quality of young adult ICSI offspring: The first results. Hum. Reprod. 31, 2811–2820 (2016).Marco-Jiménez, F. & Vicente, J. S. Overweight in young males reduce fertility in rabbit model. PLoS ONE 12, e0180679 (2017).Laubach, Z. M. et al. Epigenetics and the maintenance of developmental plasticity: extending the signalling theory framework. Biol. Rev. 93, 1323–1338 (2018).Estany, J., Camacho, J., Baselga, M. & Blasco, A. Selection response of growth rate in rabbits for meat production. Genet. Sel. Evol. 24, 527–537 (1992).Vicente, J. S., Viudes-de-Castro, M. P., de la García, M. L. & Baselga, M. Effect of rabbit line on a program of cryopreserved embryos by vitrification. Reprod. Nutr. Dev. 43, 137–143 (2003).Zucker, I. & Beery, A. K. Males still dominate animal studies. Nature 465, 690 (2010).Vicente, J. S., Viudes-De-Castro, M. P. & García, M. L. In vivo survival rate of rabbit morulae after vitrification in a medium without serum protein. Reprod. Nutr. Dev. 39, 657–662 (1999).Besenfelder, U. & Brem, G. Laparoscopic embryo transfer in rabbits. J. Reprod. Fertil. 99, 53–56 (1993).Blasco, A. The use of Bayesian statistics in meat quality analyses: a review. Meat Sci. 69, 115–122 (2005).Andrews, S. FASTQC a quality control tool for high throughput sequence data. Babraham Institute (2015). Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc.Kim, D., Langmead, B. & Salzberg, S. L. HISAT: A fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2009).Wang, Y. E., Kutnetsov, L., Partensky, A., Farid, J. & Quackenbush, J. WebMeV: a cloud platform for analyzing and visualizing cancer genomic data. Cancer Res. 77, e11–e14 (2017).Metsalu, T. & Vilo, J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res. 44, 566–570 (2015).Heberle, H., Meirelles, V. G., da Silva, F. R., Telles, G. P. & Minghim, R. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 16, 169 (2015).Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).Diretto, G. et al. Tissue-specific accumulation of sulfur compounds and saponins in different parts of garlic cloves from purple and white ecotypes. Molecules 22, E1359 (2017).Cappelli, G. et al. A Corylus avellana L. extract enhances human macrophage bactericidal response against Staphylococcus aureus by increasing the expression of anti-inflammatory and iron metabolism genes. J. Funct. Foods 45, 499–511 (2018).Di Meo, F. et al. Anti-cancer activity of grape seed semi-polar extracts in human mesothelioma cell lines. J. Funct. Foods 61, 103515 (2019).Fiore, A. et al. A quadruple mutant of Arabidopsis reveals a β-carotene hydroxylation activity for LUT1/CYP97C1 and a regulatory role of xanthophylls on determination of the PSI/PSII ratio. BMC Plant Biol. 12, 50 (2012).Rambla, J. L. et al. Gene-metabolite networks of volatile metabolism in Airen and Tempranillo grape cultivars revealed a distinct mechanism of aroma bouquet production. Front. Plant Sci. 7, 1619 (2016).Sulli, M. et al. Molecular and biochemical characterization of a potato collection with contrasting tuber carotenoid content. PLoS ONE 12, e0184143 (2017)

High relative expression of two genes of a melon near-isogenic line versus its parental during ripening

[SPA] Con el fin de comparar la expresión génica de una línea casi isogénica (NIL) SC10-2 de melón y su Piel de Sapo (PS) parental durante la maduración y para comprender los mecanismos de diferenciación, se realizó una secuenciación de transcriptoma. Los genes CmTCP15 (Factor de actividad de transcripción) y CmGDSL (actividad de la esterasa y la lipasa) tenían una alta expresión diferencial en el NIL SC10-2 en comparación con el PS debido a la introgresión en LG X. En consecuencia, algunos atributos de calidad de fruto como el aroma, dulzura y, probablemente otros pueden estar afectados por tales genes. [ENG] In order to compare the gene expression of a melon Near-isogenic Line (NIL) SC10-2 and its parental Piel de Sapo (PS) during ripening and to understand the differentiate mechanisms, a transcriptome sequencing was performed. CmTCP15 (Transcription factor activity) and CmGDSL (Esterase and lipase activity) genes were high differentially expressed in the NIL SC10-2 compared with PS due to the introgression in LG X. Consequently, some fruit quality traits such as aroma, sweetness and probably others can be affected by such genes.Financial support: Fundación Séneca de la Región de Murcia (11784/PI/09), MINECO & UE-FEDER funds (AGL2010-20858). Thanks for the technical assistance to P. Varó and his team in CIFEA-Torre Pacheco (Consejería de Agricultura, Región de Murcia), N. Dos-Santos, E. Cuadros, M. García-Gutiérrez, A. Hakmaoui (UPCT), M.J. Roca (SAIT-UPCT), and IRTA-CRAG for the seeds of the NIL

Gene expression and volatile production during melon ripening

[SPA] Se realizó una secuenciación de transcriptoma para analizar los genes implicados en la formación de aromas expresados durante la maduración y para comprender los mecanismos moleculares que diferencian una línea casi isogénica (NIL) SC10-2 de melón y su parental Piel de Sapo (PS). El gen CmLOX18 (similar a la lipoxigenasa 4) se expresó diferencialmente comparando la NIL SC10-2 y PS y se asoció a la producción de hexanal, un compuesto diana e indicador del proceso de maduración no climatérica. La expresión del gen de la CmACO1 (1-aminocyclopropane-1-carboxylate oxidase 1) implicado en la biosíntesis de etileno no manifestó diferencias durante la maduración. La introgresión en LG X estuvo asociada a la diferente producción de hexanal entre la NIL y PS. Se propone un eQTL en el LG X que controla la producción de aromas del gen CmLOX18 localizado en LG I. [ENG] Transcriptome sequencing was performed in order to analyze the genes associated to volatile synthesis expressed during ripening and to understand the molecular mechanisms that differentiate a melon Near-isogenic Line (NIL) SC10-2 and its parental Piel de Sapo (PS). CmLOX18 gene (Similar to Lipoxygenase 18) was differentially expressed in the NIL SC10-2 compared with PS associated with the aroma volatile compound hexanal as a target compound of the non-climacteric ripening. The expression of CmACO1 (1-aminocyclopropane-1-carboxylate oxidase 1) gene associated with ethylene biosynthesis did not change during ripening. The introgression in LG X was associated with the differential hexanal production of the NIL and PS. An eQTL located in LG X is probably controlling the production of aroma volatiles due to CmLOX18 in LG I.Financial support: Fundación Séneca de la Región de Murcia (11784/PI/09), MINECO & UE-FEDER funds (AGL2010-20858). Thanks for the technical assistance to P. Varó and his team in CIFEA-Torre Pacheco (Consejería de Agricultura, Región de Murcia), N. Dos-Santos, E. Cuadros, M. García-Gutiérrez, A. Hakmaoui (UPCT), M.J. Roca (SAIT-UPCT), and IRTA-CRAG for the seeds of the NIL

Lower relative differential expression of two genes is associated with delayed ripening in melon

[SPA] Con el fin de comparar la expresión génica de un melón cerca de la línea isogénica (NIL) SC10-2 y su parental Piel de Sapo (PS) durante la maduración y para comprender los mecanismos de diferenciación, se realizó una secuenciación transcriptoma. Dos genes de CmGGP (GDP-L-galactosa fosforilasa 1) y CmRAP2-11 (factor de transcripción sensible al etileno RAP2-11) mostraron menor expresión relativa en la NIL SC10 -2 versus PS debido a la introgresión en LG X. Sin embargo, no existieron diferencias en expresión de CmAP2-like X1 (factor de transcripción sensible al etileno, similar a AP2 TOE3 isoforma X1). En consecuencia, la expresión de genes que mapearon en el grupo de ligamiento X como un factor de transcripción de respuesta a etileno o del metabolismo del ácido ascórbico estuvieron probablemente asociados con el retraso de maduración. [ENG] The expression of selected genes during ripening was studied considering a melon Near-isogenic Line (NIL) SC10-2 and its parental “Piel de Sapo” (PS). The expression of CmGGP (GDP-L-galactose phosphorylase 1), CmAP2-like X1 (AP2-like ethylene-responsive transcription factor TOE3 isoform X1) and CmRAP2-11 (ethylene-responsive transcription factor RAP2-11) were differentially expressed in the NIL SC10-2 compared with PS. Consequently, expression of genes that mapped in LG X such as one ethylene response transcription factors or ascorbic acid metabolism gene were probably associated with delayed ripening.Financial support: Fundación Séneca de la Región de Murcia (11784/PI/09), MINECO & UE-FEDER funds (AGL2010-20858). Thanks for the technical assistance to P. Varó and his team in CIFEA-Torre Pacheco (Consejería de Agricultura, Región de Murcia) for crop management and IRTA-CRAG for the seeds of the NIL

s-s*-d-wave superconductor on a square lattice and its BCs phase diagram

We study an extended Hubbard model with on-site repulsion and nearest neighbors attraction which tries to mimic some of the experimental features of doped cuprates in the superconducting state. We draw and discuss the phase diagram as a function of the effective interactions among electrons for a wide range of doping concentrations. We locate the region which is relevant for the cuprates setting some constraints on the parameters which may be used in this kind of effective models. We also study the effects of temperature and orthorrombicity on the symmetry and magnitude of the gap function, and map the model onto a simpler linearized hamiltonian, which produces similar phase diagrams.Comment: 4 pages, 3 figures included. Accepted for publication in Phys. Rev.

A novel technique for detoxification of phenol from wastewater: Nanoparticle Assisted Nano Filtration (NANF)

© 2016 Naidu et al. Background: Phenol is one of the most versatile and important organic compound. It is also a growing concern as water pollutants due to its high persistence and toxicity. Removal of Phenol from wastewaters was investigated using a novel nanoparticle adsorption and nanofiltration technique named as Nanoparticle Assisted Nano Filtration (NANF). Methods: The nanoparticle used for NANF study were silver nanoparticles and synthesized to three distinct average particle sizes of 10 nm, 40 nm and 70 nm. The effect of nanoparticle size, their concentrations and their tri and diparticle combinations upon phenol removal were studied. Results: Total surface areas (TSA) for various particle size and concentrations have been calculated and the highest was 4710 × 1012 nm2 for 10 nm particles and 180 ppm concentration while the lowest was for 2461 × 1011 for 70 nm and 60 ppm concentrations. Tri and diparticle studies showed more phenol removal % than that of their individual particles, particularly for using small particles on large membrane pore size and large particles at low concentrations. These results have also been confirmed with COD and toxicity removal studies. Conclusions: The combination of nanoparticles adsorption and nanofiltration results in high phenol removal and mineralization, leading to the conclusion that NANF has very high potential for treating toxic chemical wastewaters

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

Background: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding.Results: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions.Conclusion: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties. © 2011 Blanca et al; licensee BioMed Central Ltd.Blanca Postigo, JM.; Cañizares Sales, J.; Roig Montaner, MC.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Picó Sirvent, MB. (2011). Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 12:104-117. doi:10.1186/1471-2164-12-104S1041171

Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) a-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of “extra-target” RAS suggests the need for RAS screening in all three DAA target regions