Search results for " meta-analysis."

Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq …

2019

Background Our study is the first to provide RNA-Seq data analysis related to transcriptomic responses towards drought across different crops. The aim was to identify and map which genes play a key role in drought response on leaves across different crops. Forty-two RNA-seq samples were analyzed from 9 published studies in 7 plant species (Arabidopsis thaliana, Solanum lycopersicum, Zea mays, Vitis vinifera, Malus X domestica, Solanum tuberosum, Triticum aestivum). Results Twenty-seven (16 up-regulated and 11 down-regulated) drought-regulated genes were commonly present in at least 7 of 9 studies, while 351 (147 up-regulated and 204 down-regulated) were commonly drought-regulated in 6 of 9 …

Transcriptomic responses to biotic stresses in Malus x domestica: a meta-analysis study.

2017

AbstractRNA-Seq analysis is a strong tool to gain insight into the molecular responses to biotic stresses in plants. The objective of this work is to identify specific and common molecular responses between different transcriptomic data related to fungi, virus and bacteria attacks in Malus x domestica. We analyzed seven transcriptomic datasets in Malus x domestica divided in responses to fungal pathogens, virus (Apple Stem Grooving Virus) and bacteria (Erwinia amylovora). Data were dissected using an integrated approach of pathway- and gene- set enrichment analysis, Mapman visualization tool, gene ontology analysis and inferred protein-protein interaction network. Our meta-analysis revealed…

Gaining Insight into Exclusive and Common Transcriptomic Features Linked with Biotic Stress Responses in Malus

2017

Identifying key information in transcriptomic data is very important, especially when the “omic” study deals with plant responses to stresses in field conditions where a high number of variables and disturbing factors may affect the analysis. In this meta-analysis we collected 12 transcriptomic works in Malus in order to identify which key genes, proteins, gene categories are involved in general plant pathological conditions and those features linked with exclusive biotic stress responses. Those genes that are only related with molecular responses to pathogen attacks and those linked with other plant physiological processes were identified. A pipeline composed by pathway and gene set enrich…

Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species

2020

As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visuali…

Gaining Insight into Exclusive and Common Transcriptomic Features Linked to Drought and Salinity Responses across Fruit Tree Crops

2020

The present study aimed at identifying and mapping key genes expressed in root tissues involved in drought and salinity tolerance/resistance conserved among different fruit tree species. Twenty-six RNA-Seq samples were analyzed from six published studies in five plant species (Olea europaea, Vitis riparia Michx, Prunus mahaleb, Prunus persica, Phoenix dactylifera). This meta-analysis used a bioinformatic pipeline identifying 750 genes that were commonly modulated in three salinity studies and 683 genes that were commonly regulated among three drought studies, implying their conserved role in resistance/tolerance/response to these environmental stresses. A comparison was done on the genes th…

Anthocyanins: Biosynthesis, Distribution, Ecological Role, and Use of Biostimulants to Increase Their Content in Plant Foods—A Review

2021

In the past century, plant biostimulants have been increasingly used in agriculture as innovative and sustainable practice. Plant biostimulants have been mainly investigated as potential agents able to mitigate abiotic stress. However, few information is available about their ability to influence fruit quality or change fruit phytochemical composition. In particular, very little is known about their effects on anthocyanin synthesis and accumulation. Due to the increasing demand of consumers for healthier foods with high nutraceutical values, this review tries to fill the gap between anthocyanin content and biostimulant application. Here, we elucidate the chemical structure, biosynthetic pat…

Effectiveness of European Atlanto-Mediterranean MPAs: Do they accomplish the expected effects on populations, communities and ecosystems?

2008

The success of MPAs in conserving fishing resources and protecting marine biodiversity relies strongly on how well they meet their planned (or implicit) management goals. From a review of empirical studies aiming at assessing the ecological effects of Mediterranean and Macaronesian MPAs, we conclude that establishing an MPA is successful for (i) increasing the abundance/biomass, (ii) increasing the proportion of larger/older individuals, and (iii) enhancing the fecundity of commercially harvested populations; also, MPAs demonstrated to be effective for (iv) augmenting local fishery yields through biomass exportation from the protected area, and (v) inducing shifts in fish assemblage structu…

Marine reserves: size and age do matter

2008

Marine reserves are widely used throughout the world to prevent overfishing and conserve biodiversity, but uncertainties remain about their optimal design. The effects of marine reserves are heterogeneous. Despite theoretical findings, empirical studies have previously found no effect of size on the effectiveness of marine reserves in protecting commercial fish stocks. Using 58 datasets from 19 European marine reserves, we show that reserve size and age do matter: Increasing the size of the no-take zone increases the density of commercial fishes within the reserve compared with outside; whereas the size of the buffer zone has the opposite effect. Moreover, positive effects of marine reserve…

Untargeted Antifungal Treatment in Nonneutropenic Critically Ill Patients: Should Further Studies Be Performed Based on Trial Sequential Analysis Res…

2018

Ceftazidime-Avibactam Combination Therapy Compared to Ceftazidime-Avibactam Monotherapy for the Treatment of Severe Infections Due to Carbapenem-Resi…

2020

Ceftazidime-avibactam (CZA) is a novel beta-lactam beta-lactamase inhibitor combination approved for the treatment of complicated urinary tract infections, complicated intra-abdominal infections, and for hospital-acquired/ventilator-associated pneumonia. The aim of this systematic review (PROSPERO registration number: CRD42019128927) was to evaluate the effectiveness of CZA combination therapy versus CZA monotherapy in the treatment of severe infections. The databases included in the search, until February 12th, 2020, were MEDLINE by PubMed, EMBASE, and The Cochrane Central Register of Controlled Trials. We included both randomized controlled trials (RCTs) and non-randomized studies publish…