Transcriptomic and volatilomic profiles reveal Neofabraea vagabunda infection-induced changes in susceptible and resistant apples during storage

Bull’s eye rot is one of the most severe diseases that may affect apple fruit during post-harvest storage. It is caused by the fungus Neofabraea vagabunda, and the mechanism by which the pathogen infects the fruits is only partially understood. In particular, very little is known about the molecular mechanisms regulating the interaction between the pathogen and the host during symptoms development. Despite different apple cultivars show divergent levels of resistance to the pathogen, the genetic basis of these responses is still unknown. In order to better understand the molecular mechanisms occurring in the apple fruit during N. vagabunda infection, a large-scale transcriptome study by RNA-Seq analysis was performed, comparing fruits of the sensitive ‘Roho’ cultivar and the resistant cultivar ‘Ariane’ after artificial infection with N. vagabunda and a storage period of four months. Transcriptomic analyses revealed the regulation of several classes of genes during this period, some of which may be involved in apple-pathogen interaction, such as superoxide dismutases and heat shock proteins (HSPs), ethylene-responsive transcription factors (ERFs), carboxylesterases and NAC transcription factors gene families. Moreover, a volatile analysis was performed, revealing differences in the volatile profile between the resistant and the susceptible cultivar that may help to elucidate the resistance mechanism. RNA-Seq data highlighted several classes of pathogen-related genes, such as genes coding for enzymes involved in cell wall disruption and in reactive oxygen species (ROS) homeostasis, being differentially regulated between resistant and susceptible fruits and between diseased and healthy fruits of the same cultivar, indicating that apples are capable of perceiving and triggering a molecular response to N. vagabunda infection. Some volatiles, as ethanol and methanol, but also furan and formaldehyde, might be potential markers for N. vagabunda infection; others, such as hexenal and methyl acetate, were found to be putatively involved in regulating apple-fungi interactio

Long term nucleotide and nucleoside analogs treatment in chronic hepatitis B HBeAg negative genotype D patients and risk for hepatocellular carcinoma

Background and rationale of the study. Effect of Long-term nucleoside/nucleotide (NUC) on hepatocellular carcinoma (HCC) incidence in a population of HBeAg-negative genotype D patients has not been adequately studied in real-life cohorts. Our aim was to evaluate the impact of liver fibrosis and other variables on HCC incidence in this population of patients. Of 745 patients with chronic hepatitis B (CHB), 306 HBeAg-negative genotype D were selected and included in this study. All patients received treatment with NUC for at least 18 months. Patients with CHB or compensated cirrhosis were included. Patients with HCC diagnosed before or during the first 18 months of NUC therapy were excluded. Results. HCC was diagnosed in 2 CHB patients (1.0%) and 23 cirrhosis patients (20%) (OR = 24.41, 95% CI 5.40 < OR < 153.2; p < 0.0001). Multivariate analysis revealed that HCC risk was independently associated with age ≥ 60 years (OR = 6.45, 95% CI 1.22 to 34.0; p = 0.02) and liver cirrhosis (OR = 12.1, 95% CI 1.39 to 106.2; p = 0.02), but not with virological response (VR), and previous resistance to NUC, or rescue therapy. Multivariate analysis in cirrhosis patients revealed that only age ≥ 60 years was an independent risk factor associated with HCC (p = 0.003). Conclusions. Liver cirrhosis and age ≥ 60 years are the stronger risk factors for HCC in genotype D HBeAgnegative patients. Previous resistance to NUC in patients that achieved a VR after rescue therapy was not a predictive factor regarding HCC. VR does not appear to significantly reduce the overall incidence of HCC when a patient has already progressed to liver cirrhosis

Identification and molecular characterization of LTR and LINE retrotransposable elements in Fagus sylvatica L.

Retrotransposable elements are important and peculiar genetic components derived from ancient retrovirus insertion inside plants genome. Their ability to move and/or replicate inside the genome is an important evolutionary force, responsible for the increase of genome size and the regulation of gene expression. Retrotransposable elements are well characterized in model or crop species like Arabidopsis thaliana and Oryza sativa, but are poorly known in forest tree species. In this paper the molecular identification of retrotransposable elements in Fagus sylvatica L. is reported. Two retrotransposons, belonging to the two major classes of LTR and non-LTR elements, were characterized trough a SCAR (Sequence Characterized Amplified Region) strategy. The analysis demonstrated the presence of multiple copies of retrotransposable elements inside the genome of beech, in accordance with the viral quasi-species theory of retrotransposon evolution. The cloning and sequencing of amplification products and a Cleaved Amplified Polymorphisms (CAPs) approach on the identified retrotransposons, showed a high level of diversity among the multiple copies of both elements. The identification of retrotransposable elements in forest trees represents an important step toward the understanding of mechanisms of genome evolution. Furthermore, the high polymorphism of retrotransposable elements can represent a starting point for the development of new genetic variability markers