In vitro zika virus infection of human neural progenitor cells: Meta-analysis of RNA-seq assays

The Zika virus (ZIKV) is an emergent arthropod-borne virus (arbovirus) responsible for congenital Zika syndrome (CZS) and a range of other congenital malformations. Evidence shows that ZIKV infects human neural progenitor cells (hNPCs) in the fetal brain, prompting inflammation and tissue damage/loss. Despite recent advances, little is known about the pathways involved in CZS pathogenesis. We performed a meta-analysis, gene ontology (GO), and pathway analysis of whole transcriptome studies with the aim of clarifying the genes and pathways potentially altered during hNPCs infection with ZIKV. We selected three studies (17 samples of infected hPNCs compared to hPNCs uninfected controls) through a systematic search of the Gene Expression Omnibus (GEO) database. The raw reads were trimmed, counted, and normalized. Next, we performed a rank product meta-analysis to detect consistently differentially expressed genes (DEGs) in these independent experiments. We detected 13 statistically significant DEGs. GO ontology and reactome analysis showed an enrichment of interferon, pro-inflammatory, and chemokines signaling and apoptosis pathways in ZIKV-infected cells. Moreover, we detected three possible new candidate genes involved in hNPCs infection: APOL6, XAF1, and TNFRSF1. Our results confirm that interferon (IFN) signaling dominates the ZIKV response, and that a crucial contribution is given by apoptotic pathways, which might elicit the CZS phenotype

Plant colonization of brownfield soil and post-washing sludge: effect of organic amendment and environmental conditions

This paper analyses the effects of substrate properties and environmental conditions on spontaneous vegetation of soil and sludges from a dismantled steel plant moderately polluted by heavy metals and polycyclic aro- matic hydrocarbons. Plant colonization was monitored in the presence or absence of acidic peat for 5 years both inside the degraded brownfield site and after transferral into a nearby Oak Park environment. Overall, 57 plant species grew healthily on the substrates, with peat enhancing plant growth in the unfavourable brownfield site. Most of the species were found in the park (91 %), showing plant colonization was mainly affected by the immediate environment rather than by substrate properties. Restricted metal uptake and tissue accumulation by selec- ted plants were measured, with only Daucus carota showing a higher ability to translocate metals to shoots (shoot/root metal concentration quotient [1 with peat). Phytostabilization with native plants represents an eco- nomically more realistic and cost-effective option than excavation, soil washing and sludge disposal, especially for vast industrial sites. Addition of organic matter and planting strategically selected vegetation islands could facilitate the spontaneous recovery of such highly degraded environments

Mutational landscape of Zika virus strains worldwide and its structural impact on proteins

Zika virus (ZIKV)has spread globally and has been linked to the onset of microcephaly and other brain abnormalities. The ZIKV genome consists of an ~10.7 kb positive-stranded RNA molecule that encodes three structural (C, prM and E)and seven nonstructural (5\u2032-NS1\u2013NS2A\u2013NS2B\u2013NS3\u2013 NS4A/2K\u2013NS4B\u2013NS5-3\u2032)proteins. In this work, we looked for genetic variants in 485 ZIKV complete genomes from GenBank (NCBI)and performed a computational systematic approach using MAESTROweb server to assess the impact of nonsynonymous mutations in ZIKV proteins (C, M, E, NS1, NS2A, NS2B-NS3 protease, NS3 helicase and NS5). Then, we merged the data and correlated it with the phenotypic reports of ZIKV circulating strains. The sensitivity profile of the proteins showed 96 mutational hotspots. We found 22 relevant mutations in proteins C (I80T), NS2A (I34M/T/V, I45V, I80T/V, L113F, A117V, I118V, L128P, V143A, T151A, M199I/V, R207K and L208I)and NS3 helicase (D436G, Y498H, R525K, Q528R and R583K)of the circulating strains. Our analysis exploited the impact of nonsynonymous mutations on ZIKV proteins, their structural and functional insights. The results presented here could advance our current understanding on ZIKV proteins functions and pathogenesis

Production system effects on growth, pod yield and seed quality of organic faba bean in southern Italy

Research was carried out in southern Italy in order to evaluate the effects of two farming systems (open field, greenhouse) and five transplanting times (27 September, 11 October, 25 October, 8 November, 22 November) on plant growth, harvest precocity, fresh pod yield and seed quality of organic faba bean. Crop biomass and root expansion were higher in open field than in greenhouse. The fourth planting time resulted in the highest crop biomass, whereas the second crop cycle showed the highest leaf area index. Greenhouse crops showed higher precocity than the open field ones by about two weeks, as well as the first transplant; the delay in harvest beginning increased from the second to the fourth planting time. Fresh pod yield in open field was significantly higher than that obtained under protected environment with the third and fourth planting times. Seed yield was higher in greenhouse grown crops than in open field, with the third to fifth planting time. Seed fiber and protein content showed higher values in greenhouse compared to open field and increased with the transplant delay. Seed polyphenols attained higher concentration in open field and with the two earliest planting times. Overall, 25 October to 8 November planting times in open field best fitted the southern Italy growing conditions in terms of pod yield, but the 27 September to 11 October planting times resulted in the highest harvest precocity, remarkably enhanced under greenhouse growing, whereas seed quality was controversial