Ectopic expression of the erythrocyte band 3 anion exchange protein, using a new avian retrovirus vector

12 pages, 5 figures, 3 tables.A retrovirus vector was constructed from the genome of avian erythroblastosis virus ES4. The v-erbA sequences of avian erythroblastosis virus were replaced by those coding for neomycin phosphotransferase, creating a gag-neo fusion protein which provides G418 resistance as a selectable marker. The v-erbB sequences following the splice acceptor were replaced by a cloning linker allowing insertion of foreign genes. The vector has been tested in conjunction with several helper viruses for the transmission of G418 resistance, titer, stability, transcription, and the transduction and expression of foreign genes in both chicken embryo fibroblasts and the QT6 quail cell line. The results show that the vector is capable of producing high titers of Neor virus from stably integrated proviruses. These proviruses express a balanced ratio of genome length to spliced transcripts which are efficiently translated into protein. Using the Escherichia coli beta-galactosidase gene cloned into the vector as a test construct, expression of enzyme activity could be detected in 90 to 95% of transfected target cells and in 80 to 85% of subsequently infected cells. In addition, a cDNA encoding the avian erythrocyte band 3 anion exchange protein has been expressed from the vector in both chicken embryo fibroblasts and QT6 cells and appears to function as an active, plasma membrane-based anion transporter. The ectopic expression of band 3 protein provides a visual marker for vector function in these cells.The support of the European Molecular Biology Laboratory during the initial phases of this work is acknowledged. S.F. was supported by the Swedish Medical Research Foundation, and A.M. was supported by the Juan March Foundation. Grants were obtained from the Swedish Cancer Society, the Wallenberg Foundation, the Children's Cancer Fund, and Kjell and Marta Beijer's Foundation.Peer reviewe

Effect of fluorine and nitrogen content on the properties of Ca-Mg-Si-Al-O-(N)-(F) glasses

X-ray amorphous glasses of composition (in equivalent percent) 15Ca:15Mg: 55Si:15Al:(100-x-y)O:xN:yF with x=0, 10, 15 and y=0, 1, 3, 5, were prepared by melting and casting. The effects of oxygen substitution by fluorine and/or nitrogen on the physical, mechanical, thermal and optical properties of the glasses have been investigated. Molar volume, fractional glass compactness, microhardness, Young's Modulus, glass-transition temperature, dilatometric-softening point and refractive index increased linearly with nitrogen substitution for oxygen, whereas molar volume and thermal expansion coefficient decreased linearly with nitrogen increase. In contrast, all properties except glass-transition temperature and dilatometric-softening point, are virtually unaffected by fluorine substitution for oxygen. Significant and linear, decreases in thermal properties occurred with increasing fluorine substitution level. All the data collected and its analysis clearly showed that the substitution effects of fluorine for oxygen on the studied properties of the glasses of the system with general formula Ca-Mg-Si-Al-O-(N)-(F) are totally independent and additive with respect to the substitution effects of nitrogen for oxygen on glass properties

Cabut, a C₂H₂ zinc finger transcription factor, is required during <em>Drosophila</em> dorsal closure downstream of JNK signaling

AbstractDuring dorsal closure, the lateral epithelia on each side of the embryo migrate dorsally over the amnioserosa and fuse at the dorsal midline. Detailed genetic studies have revealed that many molecules are involved in this epithelial sheet movement, either with a signaling function or as structural or motor components of the process. Here, we report the characterization of cabut (cbt), a new Drosophila gene involved in dorsal closure. cbt is expressed in the yolk sac nuclei and in the lateral epidermis. The Cbt protein contains three C2H2-type zinc fingers and a serine-rich domain, suggesting that it functions as a transcription factor. cbt mutants die as embryos with dorsal closure defects. Such embryos show defects in the elongation of the dorsal-most epidermal cells as well as in the actomyosin cable assembly at the leading edge. A combination of molecular and genetic analyses demonstrates that cbt expression is dependent on the JNK cascade during dorsal closure, and it functions downstream of Jun regulating dpp expression in the leading edge cells

Factors Controlling Properties of Ca-Mg, Ca-Er, Ca-Nd, or Ca-Y-Modified Aluminosilicate Glasses Containing Nitrogen and Fluorine

Glasses with composition (in eq.%) (30 − x)Ca:xM:55Si:15Al:80O:15N:5F have been prepared with different levels of substitution of Ca2+ cations by Mg2+, Y3+, Er3+, or Nd3+. The properties of these glasses are examined in detail and changes observed in molar volume (MV), free volume, fractional glass compactness, Young's modulus, microhardness, glass transition temperature, and thermal expansion as a function of M content are presented. Using linear regression analysis, evidence is presented which clearly shows that these glass properties are either solely dependent on the effective cation field strength, if modifier cation valency is the same (e.g., Mg substitution for Ca), or dependent on the effective cation field strength and the number of (Si, Al) (O, N, F) tetrahedra associated with each modifier when Ca is replaced by the trivalent modifiers. Combining these correlations with those observed previously relating glass properties to N and F substitution for O, it becomes apparent that glass properties for Ca–M–Si–Al–O–N–F glasses can be described by correlations which involve independent, but additive contributions by N and F substitution levels, effective cation field strength, and the number of tetrahedra associated with each modifier ion

La agricultura ecológica a largo plazo en plantaciones de cítricos permite la recuperación del carbono orgánico del suelo

[ES] Se ha demostrado que el manejo del suelo bajo agricultura ecológica puede aumentar el contenido de carbono orgánico en el suelo moderando el incremento de los gases de efecto invernadero, pero hasta la fecha las evaluaciones cuantitativas basadas en mediciones a largo plazo han sido escasas, especialmente bajo condiciones mediterráneas. En esta investigación se examinaron los cambios en el contenido de carbono orgánico como respuesta a la agricultura ecológica con cobertura vegetal en una plantación de cítricos en el área mediterránea, utilizando una base de datos de 21 años. El incremento de contenido de carbono orgánico en el suelo fue más evidente tras cinco años desde el cambio del manejo del suelo, sugiriendo que, para plantaciones de cítricos en ambientes mediterráneos, los estudios deberían tener una duración superior a cinco años. La sata de secuestro de carbono orgánico no cambió significativamente durante los 21 años de observaciones, con valores que oscilaron entre -1.10 Mg C ha-1 a-1 y 1.89 Mg C ha-1 a-1. Tras 21 años, un total de 61 t CO2 ha-1 fueron secuestradas en las áreas de acumulación de carbono en el suelo. Estos resultados demuestran que la agricultura ecológica es una estrategia efectiva para restaurar o incrementar los niveles de carbono orgánico en el suelo en los sistemas de cítricos mediterráneos.[EN] It has been shown that soil management under organic farming can enhance soil organic carbon, thereby mitigating atmospheric greenhouse gas increases, but until now quantitative evaluations based on long term experiments are scarce, especially under Mediterranean conditions. Changes in soil organic carbon (SOC) content were examined in response to organic management with cover crops in a Mediterranean citrus plantation using 21 years of survey data. Soil organic carbon increase was more apparent 5 years after a land management change suggesting that, for citrus plantations on Mediterranean conditions, studies should be longer than five years in duration. Soil organic carbon sequestration rate did not significantly change during the 21 years of observation, with values ranging from -1.10 Mg C ha(-1) y(-1) to 1.89 Mg C ha(-1) y(-1). After 21 years, 61 Mg CO2 ha(-1) were sequestered in long-lived soil C pools. These findings demonstrate that organic management is an effective strategy to restore or increase SOC content in Mediterranean citrus systems.This research was funded by the European Union Seventh Framework Program (FP7/2007-2013) under grant no. 603498 (RECARE Project) and the research projects GL2008-02879/BTE and LEDDRA 243857.Novara, A.; Pulido, M.; Rodrigo-Comino, J.; Di Prima, S.; Smith, P.; Gristina, L.; Giménez Morera, A.... (2019). Long-term organic farming on a citrus plantation results in soil organic carbon recovery. Cuadernos de Investigación Geográfica. 45(1):271-286. https://doi.org/10.18172/cig.3794S27128645

Properties of Ca–(Y)–Si–Al–O–N–F Glasses: Independent and Additive Effects of Fluorine and Nitrogen

Thirty glasses of composition (in equivalent percent) 20-xCa:xY:50Si:30Al:(100-y-z)O:yN:zF, with x = 0, 10; y = 0, 10, 20, and z = 0, 1, 3, 5, 7 were prepared by melting and casting. All glasses were X-ray amorphous. Glass molar volumes (MV) decreased with nitrogen substitution for oxygen for all fluorine contents and, correspondingly, glass fractional compactness increased. Fluorine substitution of oxygen had virtually no effect on molar volume or fractional glass compactness for the three nitrogen contents tested. Young's modulus and microhardness were virtually unaffected by fluorine substitution for oxygen while nitrogen substitution for oxygen caused increases in these two properties. Glass-transition temperature and dilatometric-softening point values all decreased with increasing fluorine substitution levels, while increasing nitrogen substitution caused values for these thermal properties to increase. Correspondingly, the thermal expansion coefficient increased with fluorine and decreased with nitrogen substitution levels. Using property value differences between glasses containing fluorine and the corresponding glass containing 0 eq.% F enabled 24 data points to be used to determine the effect of fluorine on Tg,dil and TDS. The trends were linear with a gradient for both properties of the order of −22°C (eq.% F)−1. For the nitrogen effect, 20 data points were analyzed for trend effects. As expected from earlier work, all trends had good linearity. Gradients were for Tg,dil and TDS +2.5°C (eq.% N)−1, which are fairly similar to previous results in oxynitride systems. All of the data collected and its analysis clearly shows that the substitution effects of fluorine for oxygen and nitrogen for oxygen are independent and additive with the fluorine substitution. The property trends of the glasses are discussed in terms of their implications for glass structure.The authors wish to acknowledge Science Foundation Ireland and Valencian Small and Medium Enterprise Institute for financial support of this research and to thank colleagues in Materials Ireland and the Materials and Surface Science Institute for their help and advice

Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series

[EN] Motivation: The widespread adoption of RNA-seq to quantitatively measure gene expression has increased the scope of sequencing experimental designs to include time-course experiments. maSigPro is an R package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data. Results: We have updated maSigPro to support RNA-seq time series analysis by introducing generalized linear models in the algorithm to support the modeling of count data while maintaining the traditional functionalities of the package. We show a good performance of the maSigPro-GLM method in several simulated time-course scenarios and in a real experimental dataset. Availability and implementation: The package is freely available under the LGPL license from the Bioconductor Web site (http:// bioconductor.org)This work has been funded by the FP7 STATegra [GA-30600] project, EU FP7 [30600] and the Spanish MINECO [BIO2012-40244].Nueda, MJ.; Tarazona Campos, S.; Conesa, A. (2014). Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series. Bioinformatics. 30(18):2598-2602. https://doi.org/10.1093/bioinformatics/btu333S259826023018Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11(10). doi:10.1186/gb-2010-11-10-r106Bullard, J. H., Purdom, E., Hansen, K. D., & Dudoit, S. (2010). Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 11(1). doi:10.1186/1471-2105-11-94Conesa, A., Nueda, M. J., Ferrer, A., & Talon, M. (2006). maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics, 22(9), 1096-1102. doi:10.1093/bioinformatics/btl056Hacquard, S., Kracher, B., Maekawa, T., Vernaldi, S., Schulze-Lefert, P., & Ver Loren van Themaat, E. (2013). Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proceedings of the National Academy of Sciences, 110(24), E2219-E2228. doi:10.1073/pnas.1306807110Hoogerwerf, W. A., Sinha, M., Conesa, A., Luxon, B. A., Shahinian, V. B., Cornélissen, G., … Cassone, V. M. (2008). Transcriptional Profiling of mRNA Expression in the Mouse Distal Colon. Gastroenterology, 135(6), 2019-2029. doi:10.1053/j.gastro.2008.08.048Levin, A. M., de Vries, R. P., Conesa, A., de Bekker, C., Talon, M., Menke, H. H., … Wösten, H. A. B. (2007). Spatial Differentiation in the Vegetative Mycelium ofAspergillus niger. Eukaryotic Cell, 6(12), 2311-2322. doi:10.1128/ec.00244-07Liu, Y., Zhou, J., & White, K. P. (2013). RNA-seq differential expression studies: more sequence or more replication? Bioinformatics, 30(3), 301-304. doi:10.1093/bioinformatics/btt688Maekawa, T., Kracher, B., Vernaldi, S., Ver Loren van Themaat, E., & Schulze-Lefert, P. (2012). Conservation of NLR-triggered immunity across plant lineages. Proceedings of the National Academy of Sciences, 109(49), 20119-20123. doi:10.1073/pnas.1218059109Medina, I., Carbonell, J., Pulido, L., Madeira, S. C., Goetz, S., Conesa, A., … Dopazo, J. (2010). Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research, 38(suppl_2), W210-W213. doi:10.1093/nar/gkq388Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5(7), 621-628. doi:10.1038/nmeth.1226Nueda, M. j., Ferrer, A., & Conesa, A. (2011). ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments. Biostatistics, 13(3), 553-566. doi:10.1093/biostatistics/kxr042Risso, D., Schwartz, K., Sherlock, G., & Dudoit, S. (2011). GC-Content Normalization for RNA-Seq Data. BMC Bioinformatics, 12(1), 480. doi:10.1186/1471-2105-12-480Roberts, A., & Pachter, L. (2012). Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods, 10(1), 71-73. doi:10.1038/nmeth.2251Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11(3), R25. doi:10.1186/gb-2010-11-3-r25Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2009). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616Sims, D., Sudbery, I., Ilott, N. E., Heger, A., & Ponting, C. P. (2014). Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics, 15(2), 121-132. doi:10.1038/nrg3642Tarazona, S., Garcia-Alcalde, F., Dopazo, J., Ferrer, A., & Conesa, A. (2011). Differential expression in RNA-seq: A matter of depth. Genome Research, 21(12), 2213-2223. doi:10.1101/gr.124321.111Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., … Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7(3), 562-578. doi:10.1038/nprot.2012.016Terol, J., Conesa, A., Colmenero, J. M., Cercos, M., Tadeo, F., Agustí, J., … Talon, M. (2007). BMC Genomics, 8(1), 31. doi:10.1186/1471-2164-8-3

Tillage versus no-tillage. soil properties and hydrology in an organic persimmon farm in eastern Iberian Peninsula

There is an urgent need to implement environmentally friendly agriculture management practices to achieve the Sustainable Goals for Development (SDGs) of the United Nations by 2030. Mediterranean agriculture is characterized by intense and millennia-old tillage management and as a consequence degraded soil. No-Tillage has been widely examined as a solution for soil degradation but No-Tillage relies more on the application of herbicides that reduce plant cover, which in turn enhances soil erosion. However, No-Tillage with weed cover should be researched to promote organic farming and sustainable agriculture. Therefore, we compare Tillage against No-Tillage using weed cover as an alternative strategy to reduce soil losses in persimmon plantations, both of them under organic farming management. To achieve these goals, two plots were established at "La Canyadeta" experimental station on 25-years old Persimmon plantations, which are managed with Tillage and No-Tillage for 3 years. A survey of the soil cover, soil properties, runoff generation and initial soil losses using rainfall simulation experiments at 55 mm h-1 in 0.25 m2 plot was carried out. Soils under Tillage are bare (96.7%) in comparison to the No-Tillage (16.17% bare soil), with similar organic matter (1.71 vs. 1.88%) and with lower bulk densities (1.23 vs. 1.37 g cm3). Tillage induces faster ponding (60 vs. 92 s), runoff (90 vs. 320 s) and runoff outlet (200 vs. 70 s). The runoff discharge was 5.57 times higher in the Tillage plots, 8.64 for sediment concentration and 48.4 for soil losses. We conclude that No-tillage shifted the fate of the tilled field after 3 years with the use of weeds as a soil cover conservation strategy. This immediate effect of No-Tillage under organic farming conditions is very promising to achieve the SDGs

Recent reforms in Spanish housing markets: an evaluation using a DSGE model

After a long academic debate, Spain finally repealed in 2012 the deduction for home purchase. The abrogation took effect in 2013. In parallel, the VAT for the purchase of new housing was increased after a short period in which it had a reduced rate. The aim of this paper is to assess the macroeconomic effects of these two relevant housing market reforms. In order to do that, we use a dynamic stochastic general equilibrium (DSGE) model calibrated to capture the key ratios of the Spanish economy. The model includes a housing market, covering both the rental market side and the property market side and credit-constrained agents. We find that these measures drive down housing prices and have a negative impact on output and employment in the construction sector. However, in the long run, this last effect is offset by the benefits of a reduction in distortionary taxes