Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping.

Organisms engage in extensive cross-species molecular dialog, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of 98 isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites. The effects of parasite genotypes on plant gene expression were often substantial, with up to 90-fold (P = 3.2 × 10-52) changes in expression levels caused by individual parasite loci. Mapped loci included a number of pleiotropic sites, including one 87-kb parasite locus that modulated expression of >60 host genes. The 213 host genes identified were substantially enriched for transcription factors. We distilled higher-order connections between polymorphisms and genes from both species via network inference. To replicate our results and test whether effects were conserved across a broader host range, we performed a confirmatory experiment using M. hapla-infected tomato. This revealed that homologous genes were similarly affected. Finally, to validate the broader utility of cross-species eQTL mapping, we applied the strategy to data from a Salmonella infection study, successfully identifying polymorphisms in the human genome affecting bacterial expression

Early gene expression events in the laminar abscission zone of abscission-promoted citrus leaves after a cycleof water stress/rehydration: involvement of CitbHLH1

[EN] Leaf abscission is a common response of plants to drought stress. Some species, such as citrus, have evolved a specific behaviour in this respect, keeping their leaves attached to the plant body during water stress until this is released by irrigation or rain. This study successfully reproduced this phenomenon under controlled conditions (24h of water stress followed by 24h of rehydration) and used it to construct a suppression subtractive hybridization cDNA library enriched in genes involved in the early stages of rehydration-promoted leaf abscission after water stress. Sequencing of the library yielded 314 unigenes, which were spotted onto nylon membranes. Membrane hybridization with petiole (Pet)- and laminar abscission zone (LAZ)-enriched RNA samples corresponding to early steps in leaf abscission revealed an almost exclusive preferential gene expression programme in the LAZ. The data identified major processes such as protein metabolism, cell-wall modification, signalling, control of transcription and vesicle production, and transport as the main biological processes activated in LAZs during the early steps of rehydration-promoted leaf abscission after water stress. Based on these findings, a model for the early steps of citrus leaf abscission is proposed. In addition, it is suggested that CitbHLH1, the putative citrus orthologue of Arabidopsis BIGPETAL, may play major roles in the control of abscission-related events in citrus abscission zonesWork at the Centre de Genomica was supported by INIA grant RTA08-00065-00-00 and Ministerio de Ciencia e Innovacion-FEDER grants AGL2007-65437-C04-01, PSG-06-0000-2009-8, IPT-01-0000-2010-43, and AGL2011-30240. J.A. and P. M. were recipients of INIA predoctoral fellowships and M. C. and A. C. of INIA/CCAA and 'Ramon y Cajal' postdoctoral contracts, respectively. The help and expertise of E. Blazquez, I. Sanchis, and A. Boix are gratefully acknowledged.Agustí, J.; Gimeno, J.; Merelo, P.; Serrano Salom, R.; Cercós, M.; Conesa, A.; Talón, M.... (2012). Early gene expression events in the laminar abscission zone of abscission-promoted citrus leaves after a cycleof water stress/rehydration: involvement of CitbHLH1. Journal of Experimental Botany. 63:6079-6091. https://doi.org/10.1093/jxb/ers270S607960916

ECMO for COVID-19 patients in Europe and Israel

Since March 15th, 2020, 177 centres from Europe and Israel have joined the study, routinely reporting on the ECMO support they provide to COVID-19 patients. The mean annual number of cases treated with ECMO in the participating centres before the pandemic (2019) was 55. The number of COVID-19 patients has increased rapidly each week reaching 1531 treated patients as of September 14th. The greatest number of cases has been reported from France (n = 385), UK (n = 193), Germany (n = 176), Spain (n = 166), and Italy (n = 136) .The mean age of treated patients was 52.6 years (range 16–80), 79% were male. The ECMO configuration used was VV in 91% of cases, VA in 5% and other in 4%. The mean PaO2 before ECMO implantation was 65 mmHg. The mean duration of ECMO support thus far has been 18 days and the mean ICU length of stay of these patients was 33 days. As of the 14th September, overall 841 patients have been weaned from ECMO support, 601 died during ECMO support, 71 died after withdrawal of ECMO, 79 are still receiving ECMO support and for 10 patients status n.a. . Our preliminary data suggest that patients placed on ECMO with severe refractory respiratory or cardiac failure secondary to COVID-19 have a reasonable (55%) chance of survival. Further extensive data analysis is expected to provide invaluable information on the demographics, severity of illness, indications and different ECMO management strategies in these patients

Respuesta transcripcional al estrés hídrico en mandarino. Estudio genómico-funcional con micromatrices de cDNA

La citricultura es una de las ramas de la fruticultura de mayor producción a nivel mundial, siendo España el cuarto productor y primer país exportador mundial de cítricos para consumo en fresco (FAO, 2005). La obtención de nuevas variedades que se adapten a las exigencias de mercado y de cultivo es la clave para continuar siendo competitivos. La reducción de las precipitaciones en muchas zonas agrícolas provoca que el estrés hídrico sea uno de los estreses abióticos que más limita la producción de los cultivos, entre ellos los cítricos. Aunque son numerosos los estudios orientados a conocer mejor la respuesta de la planta ante el estrés hídrico a nivel molecular en especies modelo, son pocos los trabajos realizados en relación a la respuesta al estrés hídrico en cítricos. Este trabajo tiene como objetivo el desarrollo de herramientas que nos permitan conocer mejor la respuesta de los cítricos frente a este estrés que en un futuro puedan utilizarse para conseguir cítricos que sean capaces de aprovechar mejor el agua disponible en condiciones adversas, evitando las importantes pérdidas de cosecha. El análisis global de la respuesta a estrés hídrico en cítricos se ha llevado a cabo a través de un estudio del transcriptoma de los cítricos sometidos a este estrés. Para ello se han utilizado dos abordajes, la generación de ESTs y la hibridación de micromatrices de cDNA, que han permitido identificar genes candidatos a estar implicados en la respuesta a estrés hídrico. La generación de ESTs se ha realizado a partir de la secuenciación de un total de 2296 clones aislados de dos bibliotecas de cDNA sustraido, Drought1 y Drought2, construidas a partir de hojas y raíces de plantas sometidas a estrés hídrico respectivamente. Las ESTs obtenidas han pasado a formar parte de la colección del CFGP (Citrus Functional Genomics Project). Como resultado del estudio de los unigenes resultantes de las bibliotecas construidas con material sometido a estrés hídrico, en relación con el rGimeno Romeu, J. (2007). Respuesta transcripcional al estrés hídrico en mandarino. Estudio genómico-funcional con micromatrices de cDNA [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/1993Palanci

Selection and Validation of Reference Genes for Gene Expression Analysis in Switchgrass (<i>Panicum virgatum</i>) Using Quantitative Real-Time RT-PCR

<div><p>Switchgrass (<i>Panicum virgatum</i>) has received a lot of attention as a forage and bioenergy crop during the past few years. Gene expression studies are in progress to improve new traits and develop new cultivars. Quantitative real time PCR (qRT-PCR) has emerged as an important technique to study gene expression analysis. For accurate and reliable results, normalization of data with reference genes is essential. In this work, we evaluate the stability of expression of genes to use as reference for qRT-PCR in the grass <i>P. virgatum</i>. Eleven candidate reference genes, including <i>eEF-1α</i>, <i>UBQ6</i>, <i>ACT12</i>, <i>TUB6</i>, <i>eIF-4a</i>, <i>GAPDH</i>, <i>SAMDC</i>, <i>TUA6</i>, <i>CYP5</i>, <i>U2AF</i>, and <i>FTSH4</i>, were validated for qRT-PCR normalization in different plant tissues and under different stress conditions. The expression stability of these genes was verified by the use of two distinct algorithms, geNorm and NormFinder. Differences were observed after comparison of the ranking of the candidate reference genes identified by both programs but <i>eEF-1α</i>, <i>eIF-4a</i>, <i>CYP5</i> and <i>U2AF</i> are ranked as the most stable genes in the samples sets under study. Both programs discard the use of <i>SAMDC</i> and <i>TUA6</i> for normalization. Validation of the reference genes proposed by geNorm and NormFinder were performed by normalization of transcript abundance of a group of target genes in different samples. Results show similar expression patterns when the best reference genes selected by both programs were used but differences were detected in the transcript abundance of the target genes. Based on the above research, we recommend the use of different statistical algorithms to identify the best reference genes for expression data normalization. The best genes selected in this study will help to improve the quality of gene expression data in a wide variety of samples in switchgrass.</p></div

Expression stability values of <i>P. virgatum</i> candidate reference genes as calculated by the NormFinder software.

<p><b>Note</b>: Genes are ranked according to their stability values from the most stable genes to the least stable.</p

Primer sequences and amplicons of the 11 candidate reference genes evaluated in this study.

<p>Primer sequences and amplicons of the 11 candidate reference genes evaluated in this study.</p

Description of candidate reference genes selected for evaluation of expression stability in <i>Panicum virgatum</i>.

<p><b>Note</b>: <b>a</b>. All Switchgrass sequences were named according on similarity to <i>Arabidopsis thaliana</i> proteins determined with BLASTX. <b>b</b>. Accession number of the most similar EST to the rice protein according to the Switchgrass GenBank dbEST. <b>c</b>. TIGR rice genome identifier of the rice proteins used to identify Switchgrass reference genes sequences via TBLASTN among the Switchgrass GenBank dbEST.</p