Vitis OneGenE: a causality-based approach to generate gene networks in Vitis vinifera sheds light on the laccase and dirigent gene families

9openInternationalBothThe abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.openPilati, Stefania; Malacarne, Giulia; Navarro-Payá, David; Tomè, Gabriele; Riscica, Laura; Cavecchia, Valter; Matus, José Tomás; Moser, Claudio; Blanzieri, EnricoPilati, S.; Malacarne, G.; Navarro-Payá, D.; Tomè, G.; Riscica, L.; Cavecchia, V.; Matus, J.T.; Moser, C.; Blanzieri, E

Trends in Prevalence of Diabetes among Twin Pregnancies and Perinatal Outcomes in Catalonia between 2006 and 2015 : the DIAGESTCAT Study

The aims of our study were to evaluate the trends in the prevalence of diabetes among twin pregnancies in Catalonia, Spain between 2006 and 2015, to assess the influence of diabetes on perinatal outcomes of twin gestations and to ascertain the interaction between twin pregnancies and glycaemic status. A population-based study was conducted using the Spanish Minimum Basic Data Set. Cases of gestational diabetes mellitus (GDM) and pre-existing diabetes were identified using ICD-9-CM codes. Data from 743,762 singleton and 15,956 twin deliveries between 2006 and 2015 in Catalonia was analysed. Among twin pregnancies, 1088 (6.82%) were diagnosed with GDM and 83 (0.52%) had pre-existing diabetes. The prevalence of GDM among twin pregnancies increased from 6.01% in 2006 to 8.48% in 2015 (p < 0.001) and the prevalence of pre-existing diabetes remained stable (from 0.46% to 0.27%, p = 0.416). The risk of pre-eclampsia was higher in pre-existing diabetes (15.66%, p = 0.015) and GDM (11.39%, p < 0.001) than in normoglycaemic twin pregnancies (7.55%). Pre-existing diabetes increased the risk of prematurity (69.62% vs. 51.84%, p = 0.002) and large-for-gestational-age (LGA) infants (20.9% vs. 11.6%, p = 0.001) in twin gestations. An attenuating effect on several adverse perinatal outcomes was found between twin pregnancies and the presence of GDM and pre-existing diabetes. As a result, unlike in singleton pregnancies, diabetes did not increase the risk of all perinatal outcomes in twins and the effect of pre-existing diabetes on pre-eclampsia and LGA appeared to be attenuated. In conclusion, prevalence of GDM among twin pregnancies increased over the study period. Diabetes was associated with a higher risk of pre-eclampsia, prematurity and LGA in twin gestations. However, the impact of both, pre-existing diabetes and GDM, on twin pregnancy outcomes was attenuated when compared with its impact on singleton gestations

Immunological response against SARS-CoV-2 following full-dose administration of Comirnaty® COVID-19 vaccine in nursing home residents

Objectives: The current study was aimed at examining SARS-CoV-2 immune responses following two doses of Comirnaty® COVID-19 vaccine among elderly people in nursing homes. Methods: A prospective cohort study in a representative sample from nursing homes in Valencia (n ¼ 881; males: 271, females 610; median age, 86 years) recruited residents using a random one-stage cluster sampling approach. A lateral flow immunochromatography device (LFIC) (OnSite COVID-19 IgG/ IgM Rapid Test; CTK BIOTECH, Poway, CA, USA) was used as the front-line test for detecting SARS-CoV-2- Spike (S)-specific antibodies in whole blood obtained using a fingerstick. Residents returning negative LFIC results underwent venipuncture and testing for presence of SARS-CoV-2-S-reactive antibodies and T cells using the Roche Elecsys® Anti-SARS-CoV-2 S (Roche Diagnostics, Pleasanton, CA, USA), the LIAISON® SARS-CoV-2 TrimericS IgG assay (Diasorin S.p.A, Saluggia, Italy) and by flow cytometry, respectively. Results: The SARS-CoV-2-S antibody detection rate in nursing home residents was 99.6% (283/284) and 98.3% (587/597) for SARS-CoV-2 recovered and naïve residents, respectively, within a median of 99 days (range 17e125 days) after full vaccination. Three out of five residents lacking SARS-CoV-2-S antibodies had detectable S-reactive CD8þ and/or CD4þ T cells. In addition, 50/50 and 40/50 participants with detectable SARS-CoV-2 antibodies also had SARS-CoV-2-S-reactive interferon-g-producing CD4þ and CD8þ T cells, respectivelyMedicin

The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement

Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species' pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important, Vitis vinifera species has driven the need for a standardised collection of genes within the grapevine community. In an effort led by the Integrape COST Action CA17111, we have recently developed the first grape gene reference catalogue, where genes are ascribed to functional data, including their accession identifiers from different genome-annotation versions (https://integrape.eu/resources/genes-genomes/). We present and discuss this gene repository together with a validation-level scheme based on varied supporting evidence found in current literature. The catalogue structure and online submission form provided permits community curation. Finally, we present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data. This perspective article aims to present these resources to the community as well as highlight their potential use, in particular for plant-breeding applications

Orchestration of the stilbene synthase gene family and their regulators by subgroup 2 MYB genes

The control of plant specialised metabolism is exerted by transcription factors and co-regulators acting on cis-regulatory DNA sequences of pathway-structural genes, determining when, where, and how metabolites are accumulated. A particularly interesting case for studying the transcriptional control of metabolism is represented by stilbenoids, produced within the phenylpropanoid pathway, as their ability to inhibit infection by coronaviruses MERS-CoV and SARS-CoV has been recently demonstrated in vitro. Integrative omic studies in grapevine (Vitis vinifera L.), including gene co-expression networks, have previously highlighted several transcription factors (TFs) from different gene families as potential modulators of stilbenoid accumulation, offering an ideal framework for gene function characterisation using genome-wide approaches. In the context of non-model plant species, DNA affinity purification sequencing (DAP-Seq) results a novel and potentially powerful tool for the analysis of novel uncharacterised regulators, however, it has not yet been applied in fruit crops. Accordingly, we tested as a proof-of-concept the binding of two previously characterised R2R3-MYB TFs to their known targets of the stilbene pathway, MYB14 and MYB15, obtaining 5,222 and 4,502 binding events assigned to 4,038 and 3,645 genes for each TF, respectively. Bound genes (putative targets) were overlapped with aggregated gene centred co-expression networks resulting in shared and exclusive High Confidence Targets (HCTs) suggesting a high, but not complete, redundancy. Our results show that in addition to the previously known but few STS targets, these regulators bind to almost half of the complete STS family in addition to other phenylpropanoid- and stilbenoid-related genes. We also suggest they are potentially involved in other processes such as the circadian rhythm or the synthesis of biotin. We searched the activated transcriptomes of transiently MYB15-overexpressing grapevine plants and observed a large activation of its high confidence targets, validating our methodological approach. Our results also show that MYB15 seems to play a role in regulating other stilbenoid-related TFs such as WRKY03.This work was supported by Grant PGC2018-099449-A-I00 and by the Ramón y Cajal program grant RYC-2017-23645, both awarded to J.T.M. and to the FPI scholarship PRE2019-088044 granted to L.O. from the Ministerio de Ciencia, Innovaci´on y Universidades (MCIU, Spain), Agencia Estatal de Investigaci´on (AEI, Spain), and Fondo Europeo de Desarrollo Regional (FEDER, European Union). C.Z. is supported by China Scholarship Council (CSC) no. 201906300087. This article is based upon work from COST Action CA 17111 INTEGRAPE, supported by COST (European Cooperation in Science and Technology). Data has been treated and uploaded in public repositories according to the FAIR principles.N

Descripción en un programa de empoderamiento para el desarrollo de competencias socioemocionales en Educación Superior

El objetivo del presente trabajo versa sobre la descripción de los objetivos, contenidos, metodología y evaluación de un programa de empoderamiento para el desarrollo de competencias socioemocionales en estudiantes universitarios vehiculado a través de las TICs. Se establecen siete bloques de trabajo impartidos en formación presencial mediatizada transversalmente en una plataforma virtual de enseñanza y aprendizaje paralela. Las temáticas abordadas son las siguientes: la experiencia de fluidez, inteligencias múltiples y talentos, fortalezas personales, creatividad, comprensión y gestión de emociones, búsqueda de la excelencia y, por último, empoderamiento y establecimiento de sinergias positivas en entornos de alto rendimiento. Las competencias trabajadas durante la formación son de carácter socioemocional y, más específicamente, autoconocimiento, habilidades intrapersonales e interpersonales, gestión de emociones, motivación por alcanzar metas, manejo del estrés, búsqueda de la excelencia, la calidad y la mejora, determinación, capacidad de gestión y solución de problemas y capacidad de adaptación al cambio, afrontamiento de la adversidad y resiliencia. La metodología se basa en una combinación de sesiones grupales, tutorías individuales y trabajo e-learning. Por último, la evaluación estriba en la calidad de las tareas y aportaciones compartidas en el espacio moodle, a través de una construcción conjunta y proactiva de los contenidos trabajados

Global analysis of alternative splicing events based on long- and short-read RNA sequencing during grape berry development

This study was supported by Natural Science Foundation of China (NSFC: U1904113), National Key Research and Development Program of China (2018YFD1000105) and Program for Innovative Research Team (in Science and Technology) in University of Henan Province (21IRTSTHN021).Peer reviewe

Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by subgroup 2 R2R3-MYBs in grapevine

The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.This work was supported by Grant PGC2018-099449-A-I00 and by the Ramón y Cajal program (grant RYC-2017-23 645), both awarded to JTM, and to the FPI scholarship (PRE2019-088044) granted to LO from the Ministerio de Ciencia, Innovación y Universidades (MCIU, Spain), Agencia Estatal de Investigación (AEI, Spain), and Fondo Europeo de Desarrollo Regional (FEDER, European Union). CZ is supported by China Scholarship Council (CSC; no. 201906300087). KG and ZR were supported by the Slovenian Research Agency (grants P4-0165 and Z7-1888). SCH is partially supported by the National Science Foundation (grant PGRP IOS-1916804). This article is based upon work from COST Action CA 17111 INTEGRAPE, supported by COST (European Cooperation in Science and Technology).Peer reviewe

SARS-CoV-2 adaptive immunity in nursing home residents following a third dose of the Comirnaty® COVID-19 vaccine

A third Comirnaty® vaccine dose increased SARS-CoV-2-receptor binding domain antibody levels (median of 93-fold) and neutralizing antibody titers against Wuhan-Hu-1 (median, 57-fold), Beta (median, 22-fold), Delta, (median, 43-fold) and Omicron (median, 8-fold) variants, particularly in SARS-CoV-2-naïve individuals, but had a negligible impact on S-reactive T-cell immunity in nursing home residents.Peer reviewe

Cumulative incidence of SARS-CoV-2 infection in the general population of the Valencian Community (Spain) after the surge of the Omicron BA.1 variant

Background Studies investigating the cumulative incidence of and immune status against SARS-CoV-2 infection provide valuable information for shaping public health decision-making. Methods The current cross-sectional, population-based study, conducted in April 2022 in the Valencian Community (VC), recruited 935 participants of all ages. Anti-SARS-CoV-2-Receptor Binding Domain-RBD-total antibodies and anti-Nucleocapsid (N)- IgGs were measured by electrochemiluminescence assays. To account for past SARS-CoV-2 infection the VC microbiology registry (RedMiVa) was interrogated. |Quantitation of neutralizing antibodies (NtAb) against the ancestral and Omicron BA.1 and BA.2 (sub)variants by an S-pseudotyped neutralization assay and for enumeration of SARS-CoV-2-S specific-IFNγ-producing CD4+ and CD8+ T cells by Intracellular Cytokine Staining assay was performed in a subset of participants (n=100 and 137, respectively). Findings The weighted cumulative incidence was 51□9% (95% CI, 48□7–55□1), and was inversely related to age. Anti-RBD total antibodies were detected in 906/931 (97□3%) participants, those vaccinated and SARS-CoV-2-experienced (VAC-ex;=442) displaying higher levels (P<0.001) than vaccinated/naïve (VAC-n;(n=472) and non-vaccinated/experienced (UNVAC-ex; n(n=63). Antibody levels correlated inversely with the time elapsed since receipt of last vaccine dose in VAC-n (Rho, -0□52; 95% CI, -0□59 to -0□45; P<0.001) but not in VAC-ex. NtAbs against Omicron BA.1 were detected in 94%, 75% and 50% of VAC-ex, VAC-n and UNVAC-ex groups, respectively, while in 97%, 84% and 40%, against Omicron BA.2. SARS-CoV-2-S-reactive IFN-γ T cells were detected in 73%, 75%, and 64% for VAC-ex, VAC-n, UNVAC-ex, respectively. Interpretation By April 2022 around half of the VC population had been infected with SARS-CoV-2 and due to extensive vaccination display hybrid immunity. The large percentage of participants with detectable functional antibody and T-cell responses against SARS-CoV-2, which may be cross-reactive to some extent, points towards lower expected severity than in previous waves.We also thank Ana Berenguer, General Director of Analysis and Public Policies of the Presidency of the Generalitat. Eliseo Albert (Juan Rodés Contract; JR20/00011) Estela Giménez (Juan Rodés Contract, JR18/00053) and Ignacio Torres (Río Hortega Contract; CM20/00090) hold contracts funded by the Carlos III Health Institute (co-financed by the European Regional Development Fund, ERDF/FEDER). Ron Geller holds a Ramon y Cajal fellowship from the Spanish Ministry of Economics and Competitiveness (RYC-2015-17517).N