Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm

In mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3′ untranslated region (UTR) of many short-lived mRNAs. AREs cause mRNAs to be degraded rapidly and thereby suppress gene expression at the posttranscriptional level. Based on the number of AUUUA pentamers, their proximity, and surrounding AU-rich regions, we generated an algorithm termed AREScore that identifies AREs and provides a numerical assessment of their strength. By analyzing the AREScore distribution in the transcriptomes of 14 metazoan species, we provide evidence that AREs were selected for in several vertebrates and Drosophila melanogaster. We then measured mRNA expression levels genome-wide to address the importance of AREs in SL2 cells derived from D. melanogaster hemocytes. Tis11, a zinc finger RNA–binding protein homologous to mammalian tristetraprolin, was found to target ARE–containing reporter mRNAs for rapid degradation in SL2 cells. Drosophila mRNAs whose expression is elevated upon knock down of Tis11 were found to have higher AREScores. Moreover high AREScores correlate with reduced mRNA expression levels on a genome-wide scale. The precise measurement of degradation rates for 26 Drosophila mRNAs revealed that the AREScore is a very good predictor of short-lived mRNAs. Taken together, this study introduces AREScore as a simple tool to identify ARE–containing mRNAs and provides compelling evidence that AREs are widespread regulatory elements in Drosophila

Estimation of chilling and heat requirements of six sweet cherry (Prunus avium L.) cultivars

Warmer winters without sufficient chilling due to climate change in Mediterranean regions represent a threat for deciduous fruit tree species such as sweet cherry (Prunus avium L.) with high chilling requirement, since it will affect fruit tree phenology leading to dramatic yield reduction and fruit industry income loss. Quantifying chilling requirements to overcome winter dormancy is crucial for identifying suitable cultivars for a given site, for predicting the necessity and timing applications of rest-breaking chemicals and the possible consequences of climate change. The aim of the following study was to determine the chilling and heat requirements of six sweet cherry cultivars grown in a germplasm collection field located in central Italy. The cultivars analyzed in this study were: ‘Kronio’, ‘Kordia’, ‘Galuciu Precoce’, ‘Ferrovia’, ‘Sandra’ and ‘Ciliegio D’Ottobre’. Historical temperature records and blooming dates were recorded in order to estimate the chilling and heat needs of each cultivar. Temperature-based models, developed by Richardson (1974) and Richardson et al. (1982) for peach, were used to calculate the chilling and heat requirement of the cultivars under investigation; the obtained results were compared with experimental data achieved from a parallel study conducted in controlled environment. The study in controlled environment was started using 2 years old cuttings collected in the abovementioned germplasm collection field. Several cuttings (50 for each cultivar) were artificially chilled in a refrigerated chamber at 6°C. Every 100 chilling hour intervals a sample of cuttings were transferred into a growing chamber at 26°C and flower development was rated weekly. ‘Galuciu Precoce’, ‘Kronio’, ‘Kordia’ and ‘Ciliegio D’Ottobre’ resulted to be the cultivars with low chilling requirements while ‘Ferrovia’ and ‘Sandra’ showed medium-high chilling requirements. Growth chamber experiment showed that, in all cultivars, the need of Growing degree hours (GDH) to achieve bloom was inversely related with chilling units (CU) accumulation. Only the cultivar ‘Ciliegio D’Ottobre’ showed an atypical pattern which required further investigation. From our field calculations, the specific chill accumulation requirements varied among cultivars, showing a minimum chill requirement value for ‘Kronio’ (700 CU) to a high chilling requirement of ‘Ferrovia’ (1200 CU). Field estimated chilling requirement values of each cultivar confirmed the growth chamber experiment results

The p38 MAPK pathway inhibits tristetraprolin-directed decay of interleukin-10 and pro-inflammatory mediator mRNAs in murine macrophages.

p38 mitogen-activated protein kinase (MAPK) stabilises pro-inflammatory mediator mRNAs by inhibiting AU-rich element (ARE)-mediated decay. We show that in bone-marrow derived murine macrophages tristetraprolin (TTP) is necessary for the p38 MAPK-sensitive decay of several pro-inflammatory mRNAs, including cyclooxygenase-2 and the novel targets interleukin (IL)-6, and IL-1alpha. TTP(-/-) macrophages also strongly overexpress IL-10, an anti-inflammatory cytokine that constrains the production of the IL-6 despite its disregulation at the post-transcriptional level. TTP directly controls IL-10 mRNA stability, which is increased and insensitive to inhibition of p38 MAPK in TTP(-/-) macrophages. Furthermore, TTP enhances deadenylation of an IL-10 3'-untranslated region RNA in vitro

Retrospective Study on Breastfeeding Practices by SARS-COV-2 Positive Mothers in a High Risk Area for Coronavirus Infection

Background: During the pandemic of SARS-Cov-2, among other clinical and public health issues, a major concern raised by SARS-CoV-2 is the possibility of transmission of the infection from mother to child in the perinatal period. This has placed a question mark on the safety of breastfeeding, with ambiguity on the joint management of SARS-CoV-2 positive or suspected mothers and their children. It was aimed to evaluate breastfeeding rates for newborns of asymptomatic SARS-CoV-2 positive mothers who were temporarily separated from their babies at birth, compared to those who were not separated.Results: Babies who were not isolated from their mothers at delivery were significantly more likely to be breastfed and were at no higher risk of infection with SARS-CoV-2.Conclusion: Following the World Health Organization (WHO) recommendations and strict hand and mask hygiene measures, breastfeeding practices can be established and maintained through rooming-in, thus promoting the mother-child bond without compromising the safety of the newborn

Genetic diversity of fig (Ficus carica L.) genotypes grown in Southern Italy revealed by the use of SSR markers.

The genetic variability among 181 fig (Ficus carica L.) accessions found in small farms located in Campania, Basilicata, Apulia, Calabria and Sicily was investigated analysing the polymorphism of 18 simple sequence repeat (SSR) markers. The SSR analysis revealed a large genetic diversity among accessions. A total of 117 alleles were detected with a mean of 6.5 locus-1. The average expected (He) and observed heterozygosity (Ho) were 0.56 and 0.66, respectively. The mean polymorphic information content (PIC) was 0.51, suggesting a significant molecular diversity among the fig accessions taken into consideration. The UPGMA cluster analysis discriminated 174 genotypes and allowed to find 8 groups of identity. The genotype ‘Bianca di agosto’ was an “outgroup”. This study showed groups of fig accessions matching with their geographic or cultivation area, but also many genotypes, especially from Campania, with uneven distribution. The research evidenced the richness of the available fig genetic resources in Southern Italy, resolved cases of synonymies and homonymies and helped to characterize fig accessions, an important preliminary work for establishing core collections

PARP-14 combines with tristetraprolin in the selective posttranscriptional control of macrophage tissue factor expression.

Tissue factor (TF) (CD142) is a 47 kDa transmembrane cell surface glycoprotein that triggers the extrinsic coagulation cascade and links thrombosis with inflammation. Although macrophage TF expression is known to be regulated at the RNA level, very little is known about the mechanisms involved. Poly(adenosine 5'-diphosphate [ADP]-ribose)-polymerase (PARP)-14 belongs to a family of intracellular proteins that generate ADP-ribose posttranslational adducts. Functional screening of PARP-14-deficient macrophages mice revealed that PARP-14 deficiency leads to increased TF expression and functional activity in macrophages after challenge with bacterial lipopolysaccharide. This was related to an increase in TF messenger RNA (mRNA) stability. Ribonucleoprotein complex immunoprecipitation and biotinylated RNA pull-down assays demonstrated that PARP-14 forms a complex with the mRNA-destabilizing protein tristetraprolin (TTP) and a conserved adenylate-uridylate-rich element in the TF mRNA 3' untranslated region. TF mRNA regulation by PARP-14 was selective, as tumor necrosis factor (TNF)α mRNA, which is also regulated by TTP, was not altered in PARP-14 deficient macrophages. Consistent with the in vitro data, TF expression and TF activity, but not TNFα expression, were increased in Parp14(-/-) mice in vivo. Our study provides a novel mechanism for the posttranscriptional regulation of TF expression, indicating that this is selectively regulated by PARP-14