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Andrea Fulgione,1,* Flora Ianniello,1,* Marina Papaianni,1 Felice Contaldi,1 Tiziana Sgamma,2 Cinzia Giannini,3 Stella Pastore,3 Raffaele Velotta,4 Bartolomeo Della Ventura,5 Norberto Roveri,6 Marco Lelli,6 Federico Capuano,7 Rosanna Capparelli1 1Department of Agriculture, University of Naples “FedericoII”, Portici, Naples, Italy; 2Biomolecular Technology Group, School of Allied Health Sciences, De Montfort University, Leicester, UK; 3Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Bari, Italy; 4Department of Physics “Ettore Pancini”, University of Naples “Federico II”, Portici, Naples, Italy; 5Department of Physics, Politecnico di Milano, Milano, Italy; 6Chemical Center Srl, Granarolo dell’Emilia, Bologna, Italy; 7Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Naples, Italy *These authors contributed equally to this work Purpose: The use of bacteriophages represents a valid alternative to conventional antimicrobial treatments, overcoming the widespread bacterial antibiotic resistance phenomenon. In this work, we evaluated whether biomimetic hydroxyapatite (HA) nanocrystals are able to enhance some properties of bacteriophages. The final goal of this study was to demonstrate that biomimetic HA nanocrystals can be used for bacteriophage delivery in the context of bacterial infections, and contribute – at the same time – to enhance some of the biological properties of the same bacteriophages such as stability, preservation, antimicrobial activity, and so on. Materials and methods: Phage isolation and characterization were carried out by using Mitomycin C and following double-layer agar technique. The biomimetic HA water suspension was synthesized in order to obtain nanocrystals with plate-like morphology and nanometric dimensions. The interaction of phages with the HA was investigated by dynamic light scattering and Zeta potential analyses. The cytotoxicity and intracellular killing activities of the phage–HA complex were evaluated in human hepatocellular carcinoma HepG2 cells. The bacterial inhibition capacity of the complex was assessed on chicken minced meat samples infected with Salmonella Rissen. Results: Our data highlighted that the biomimetic HA nanocrystal–bacteriophage complex was more stable and more effective than phages alone in all tested experimental conditions. Conclusion: Our results evidenced the important contribution of biomimetic HA nanocrystals: they act as an excellent carrier for bacteriophage delivery and enhance its biological characteristics. This study confirmed the significant role of the mineral HA when it is complexed with biological entities like bacteriophages, as it has been shown for molecules such as lactoferrin. Keywords: biomimetic hydroxyapatite nanocrystals, Salmonella Rissen, bacteriophages, antibiotic resistance

Solanum commersonii is a potato species native to Central and South America. Despite being genetically isolated from cultivated potato, in the past few years it has garnered significant research interest because it exhibits high tolerance to both biotic and abiotic stresses. Among the abiotic stresses, particularly interesting are its freezing tolerance and capacity to cold acclimatize. Little is understood of the genetic determi- nants and mechanisms beyond its resistance traits. This is partially due to the lack of genomic resources for potato germplasm. The group at the University of Naples has recently decoded, for the first time, the genome of S. commersonii, ushering in a new era of whole-genome sequencing of wild potato relatives. After illustrating the genome structure and organization of this species and its intrigffuing evolutionary roots, this chapter describes findings relative to the identification of the candidate genes for cold stress tolerance. The genome sequence of S. commersonii will pave the way to an understanding of the molecular dynamics that have given this species so many adaptive characteristics.

Figure S2. Electrophoresis gel of PCR for detecting the presence of 5 kb region. Lines 1–5: RWϕ1+; lines 6–9: RWϕ1-; lines 10–14: RRϕ1+; lines 15–18: RSϕ1-; M = marker (100 kb). (PDF 35 kb)

Figure S1. Gas chromatography-mass spectrometry (GC-MS) analysis of the (A) RW, (B) RRϕ1+, and (C) RSϕ1-strains. All of the strains display the presence of glucose, glucosamine, heptose, and KDO. Acquisition of phage resistance by RRϕ1+ strain is associated with loss of mannose. Peaks marked with X represent methyl esters of fatty acids. (PDF 673 kb)

Table S1. SNPs detection analysis of RW and RRɸ1+ strains. (PDF 107 kb)

The tetraploid cultivated potato (Solanum tuberosum, 2n=4x=48) is the fourth most important crop for humans. Since the cultivated varieties are derived from a small number of genotypes, potato is characterized by a low genetic variability. Fortunately, it has about 200 wild tuber-bearing relatives that represent an incredible source of genetic variation and a reservoir of useful genes for the development of new varieties with improved resistance, nutrient content and productivity. However, several constrains hamper wild germplasm utilization. Among them, sexual incompatibility between wild and cultivated species and linkage drag make classical breeding methods time-consuming and laborious. In addition, few genomic resources ara available that can help breeders in their work of producing genetic variability and select superior clones. For all these reasons there has been an under-utilization of the potato genetic resources. The objective of this research was to develop new genomic tools that enable the expansion of the existing breeding strategies for an efficient exploitation of potato genetic resources. Nowadays, sequencing technology combined with the availability of the S. tuberosum reference genome allows the characterization of the genetic variations affecting the cultivated potato. However, no genome sequence is available for a wild potato species. Therefore our study was addressed to sequence the genome of one of the most important tuber-bearing species, S. commersonii (2n=2x=24), that possesses several resistances to biotic and abiotic stresses. We de novo sequenced the genome of S. commersonii to 103x coverage using Illumina technology producing a 862 Mb genome. On the basis of sequence homology, 39,290 protein-coding genes were predicted and supported by transcript data and further annotation. We used the orthology and paralogy proteins relationships for the reconstruction of the complete collection of evolutionary histories of all S. commersonii protein-coding genes across a phylogeny of 12 sequenced plants. Interestingly, we discovered 8,578 S. commersonii-specific gene families lacking in S. tuberosum. HMM models and manual curation were used to annotate 2,523 non-redundant NBS-encoding R gene candidates, and comparison analysis with potato R-genes supported the idea that a locus rearrangement occurred during evolution. In order to find out the genetic determinants of S. commersonii resistance to low temperatures and capacity to cold harden, we focused on genes involved in abiotic stress response. Out of roughly 2,800 cold resistance genes, we found that 126 were unique in S. commersonii. To investigate further, a transcriptome analysis by using a custom microarray chip was carried out in two different experimental conditions. This allowed us to detect all the expressed genes involved in cold acclimation and to hypothesize the molecular dinamics at the basis of the different response to low temperature in S. commersonii vs. S. tuberosum. The experimental work carried out in this PhD reports the first genome sequence for a wild relative of the cultivated potato The genome sequence of S. commersonii has substantially increased our understanding on wild potatoes and these information might be used to overcome the limitations due to the low variability of domesticated germplasm. It will also offer the potential of better using wild relatives for potato breeding and evolutionary studies.

Background The study describes the Salmonella Rissen phage ϕ1 isolated from the ϕ1-sensitive Salmonella Rissen strain RW. The same phage was then used to select the resistant strain RRϕ1+, which can harbour or not ϕ1. Results Following this approach, we found that ϕ1, upon excision from RW cells with mitomycin, behaves as a temperate phage: lyses host cells and generates phage particles; instead, upon spontaneous excision from RRϕ1+ cells, it does not generate phage particles; causes loss of phage resistance; switches the O-antigen from the smooth to the rough phenotype, and favors the transition of Salmonella Rissen from the planktonic to the biofilm growth. The RW and RRϕ1+ strains differ by 10 genes; of these, only two (phosphomannomutase_1 and phosphomannomutase_2; both involved in the mannose synthesis pathway) display significant differences at the expression levels. This result suggests that phage resistance is associated with these two genes. Conclusions Phage ϕ1 displays the unusual property of behaving as template as well as lytic phage. This feature was used by the phage to modulate several phases of Salmonella Rissen lifestyle. Electronic supplementary material The online version of this article (10.1186/s12866-018-1360-z) contains supplementary material, which is available to authorized users.

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.

There is epidemiological evidence that H. pylori might predispose to Alzheimer’s disease. To understand the cellular processes potentially linking such unrelated events, we incubated the human gastric cells MNK-28 with the H. pylori peptide Hp(2-20). We then monitored the activated genes by global gene expression. The peptide modulated 77 genes, of which 65 are listed in the AlzBase database and include the hallmarks of Alzheimer’s disease: APP, APOE, PSEN1, and PSEN2. A large fraction of modulated genes (30 out of 77) belong to the inflammation pathway. Remarkably, the pathways dis-regulated in Alzheimer’s and Leasch-Nyhan diseases result dis-regulated also in this study. The unsuspected links between such different diseases – though still awaiting formal validation – suggest new directions for the study of neurological diseases.

The cultivated potato Solanum tuberosum is unrivalled among crop plants for its wild relatives, which potentially represent an important source of genetic diversity to improve the nutritional value of potato varieties and understand metabolism regulation. The main aim of this research was to profile human health-related metabolites in a number of clones from 13 Solanum species. Results from HPLC-DAD and LC-ESI-MS analyses highlighted a high interspecific variability in the level of metabolites analysed. Ascorbic acid was confirmed to be the most abundant antioxidant in potato and chlorogenic acid the primary polyphenol. Generally, metabolite-based hierarchical clustering (HCL) and correlation networks did not group clones of identical species in the same cluster. This might be due to various factors, including the outcrossing nature of potato species, gene expression level and metabolic profiling techniques. Access to the genome sequence of S. tuberosum and S. commersonii allowed comparison of the genes involved in ascorbic acid, aromatic amino acid, phenylpropanoid and glycoalkaloid biosynthesis and helped interpret their respective pathways.