Selective Pressure and Evolution of SARS-CoV-2 Lineages BF.7 and BQ.1.1 Circulating in Italy from July to December 2022.

In this work, we studied the selective pressure and evolutionary analysis on the SARS-CoV-2 BF.7 and BQ.1.

Tracking the Selective Pressure Profile and Gene Flow of SARS-CoV-2 Delta Variant in Italy from April to October 2021 and Frequencies of Key Mutations from Three Representative Italian Regions.

The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions.

IRIDA-ARIES Genomics, a key player in the One Health surveillance of diseases caused by infectious agents in Italy.

Pathogen genomics is transforming surveillance of infectious diseases, deepening our understanding of evolution and diffusion of etiological agents, host-pathogen interactions and antimicrobial resistance. This discipline is playing an important role in the development of One Health Surveillance with public health experts of various disciplines integrating methods applied to pathogen research, monitoring, management and prevention of outbreaks. Especially with the notion that foodborne diseases may not be transmitted by food only, the ARIES Genomics project aimed to deliver an Information System for the collection of genomic and epidemiological data to enable genomics-based surveillance of infectious epidemics, foodborne outbreaks and diseases at the animal-human interface.

Exploring the nature of interaction between shiga toxin producing (STEC) and free-living amoeba - sp.

Free-living amoebae (FLA) are widely distributed protozoa in nature, known to cause severe eye infections and central nervous system disorders. There is growing attention to the potential role that these protozoa could act as reservoirs of pathogenic bacteria and, consequently, to the possibility that, the persistence and spread of the latter may be facilitated, by exploiting internalization into amoebae. Shiga toxin-producing strains of (STEC) are zoonotic agents capable of causing serious diseases, such as hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS).

Free-ranging red deer (Cervus elaphus) as carriers of potentially zoonotic Shiga toxin-producing Escherichia coli.

Shiga toxin-producing E. coli (STEC) are zoonotic foodborne pathogens of outmost importance and interest has been raised in recent years to define the potential zoonotic role of wildlife in STEC infection. This study aimed to estimate prevalence of STEC in free-ranging red deer (Cervus elaphus) living in areas with different anthropisation levels and describe the characteristics of strains in order to evaluate the potential risk posed to humans.

Genomic Characterization of hlyF-positive Shiga Toxin-Producing Escherichia coli, Italy and the Netherlands, 2000-2019.

Shiga toxin-producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E.

Tracing Back the Evolutionary Route of Enteroinvasive (EIEC) and Through the Example of the Highly Pathogenic O96:H19 EIEC Clone.

Enteroinvasive (EIEC) cause intestinal illness through the same pathogenic mechanism used by spp. The latter species can be typed through genomic and phenotypic methods used for and have been proposed for reclassification within species. Recently the first appearance of a highly pathogenic EIEC O96:H19 was described in Europe as the causative agent of two large outbreaks that occurred in Italy and in the United Kingdom.

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients.

The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens.

Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC).

Shiga-toxin producing Escherichia coli (STEC) strains possess a large accessory genome composed of virulence genes existing in multiple allelic variants, which sometimes segregate with specific STEC subpopulations. We analyzed the allelic variability of 91 virulence genes of STEC by Real Time PCR followed by melting curves analysis in 713 E. coli strains including 358 STEC.

Survival patterns in lung and pleural cancer in Europe 1999-2007: Results from the EUROCARE-5 study.

Background: Survival of patients diagnosed with lung and pleura cancer is a relevant health care indicator which is related to the availability and access to early diagnosis and treatment facilities. Aim of this paper is to update lung and pleural cancer survival patterns and time trends in Europe using the EUROCARE-5 database.

Methods: Data on adults diagnosed with lung and pleural cancer from 87 European cancer registries in 28 countries were analysed.

EUROCARE-4. Survival of cancer patients diagnosed in 1995-1999. Results and commentary.

EUROCARE-4 analysed about three million adult cancer cases from 82 cancer registries in 23 European countries, diagnosed in 1995-1999 and followed to December 2003. For each cancer site, the mean European area-weighted observed and relative survival at 1-, 3-, and 5-years by age and sex are presented. Country-specific 1- and 5-year relative survival is also shown, together with 5-year relative survival conditional to surviving 1-year.

The EUROCARE-4 database on cancer survival in Europe: data standardisation, quality control and methods of statistical analysis.

This paper describes the collection, standardisation and checking of cancer survival data included in the EUROCARE-4 database. Methods for estimating relative survival are also described. Incidence and vital status data on newly diagnosed European cancer cases were received from 93 cancer registries in 23 countries, covering 151,400,000 people (35% of the participating country population).

Metabolic alterations in K562 cells exposed to taxol and tyrphostin AG957: 1H NMR and biochemical studies.

K562 cells exposed for 3 h to taxol or taxol plus tyrphostin AG957 exhibited a significant variation in the concentration of the water-soluble metabolites glutathione, myo-inositol and phosphorylcholine, as evaluated by (1)H NMR up to 72 h incubation in drug-free medium. Cells treated with both drugs showed an increase of glutathione and glutathione reductase at 24 h and a sharp decrease of myo-inositol between 8 and 24 h. Phosphorylcholine increased at 8 h both in taxol and taxol plus AG957-treated cells, which was then abruptly inverted to a significantly lower concentration at 24 h, subsequently increasing again to values higher than those found in taxol-treated and control cells.

High-resolution proton NMR measures mobile lipids associated with Triton-resistant membrane domains in haematopoietic K562 cells lacking or expressing caveolin-1.

High-resolution proton NMR spectra of intact tumour cells generally exhibit intense signals due to isotropically mobile lipids (MLs) of still uncertain nature and origin. NMR studies performed on intact wild-type and caveolin-1-infected haematopoietic K562 cells showed that, under our experimental conditions, part of the ML signals are due to lipid complexes resistant to extraction in Triton X-100 at 4 degrees C. This evidence suggests that a portion of NMR-visible lipid structures are compatible with Triton-resistant membrane rafts and therefore biophysically distinct from NMR-visible Triton-soluble lipid bodies.

Two-step formation of 1H NMR visible mobile lipids during apoptosis of paclitaxel-treated K562 cells.

Despite increasing evidence on the formation of 1H NMR-detectable mobile lipid (ML) domains in cells induced to programmed cell death by continuous exposure to anticancer drugs, the time course of ML generation during the apoptotic cascade has not yet been fully elucidated. The present study shows that ML formation occurs at two different stages of apoptosis induced in human erythroleukemia K562 cells by a brief (3 hr) exposure to paclitaxel (Taxol), an antitumour drug with a stabilising effect on microtubules, or to paclitaxel plus tyrphostin AG957, a selective inhibitor of the p210(BCR-ABL) tyrosine kinase activity. A first wave of ML generation was in fact detected in paclitaxel-treated cells at the onset of the effector phase (8-24hr after exposure to the drug), plateaued at 24-48 hr and was eventually followed by further ML accumulation during the degradative phase (48-72 hr).

Detection of polyol accumulation in a new ovarian carcinoma cell line, CABA I: a(1)H NMR study.

Ovarian carcinomas represent a major form of gynaecological malignancies, whose treatment consists mainly of surgery and chemotherapy. Besides the difficulty of prognosis, therapy of ovarian carcinomas has reached scarce improvement, as a consequence of lack of efficacy and development of drug-resistance. The need of different biochemical and functional parameters has grown, in order to obtain a larger view on processes of biological and clinical significance.

1H NMR-visible mobile lipid domains correlate with cytoplasmic lipid bodies in apoptotic T-lymphoblastoid cells.

The presence of nuclear magnetic resonance (NMR)-visible mobile lipid (ML) domains in apoptotic lymphoblasts suggests alterations in neutral lipid metabolism and compartmentation during programmed cell death. The detection of similar ML signals in activated lymphocytes raises questions about common mechanisms of ML formation during apoptosis and upon lymphoblast stimulation. Structure and subcellular localization of ML domains were therefore investigated by NMR, fluorescence and electron microscopy in Jurkat T-lymphoblasts either induced to apoptosis (by anthracyclines or dexamethasone or by serum deprivation) or activated by phorbol myristate acetate (PMA) plus ionomycin.

Double-resonance J-edited (1)H-NMR detection of 6-(13)C-D-2-deoxyglucose uptake in glioma cells.

The C6 methylene protons were selectively detected in (1)H-NMR spectra of intact glioma cells incubated with 6-(13)C-D-2-deoxyglucose (6-(13)C-2dG), a (13)C-enriched glucose analog that is suitable for monitoring glucose utilization in brain tumors. Spectral editing via (1)H-(13)C scalar coupling was performed with twin spin-echo double resonance (T-SEDOR), a pulse sequence which combines chemical specificity and high sensitivity, requires no solvent pre-saturation, and can easily be adapted to imaging protocols. This work demonstrates the suitability of the pulse sequence for monitoring 6-(13)C-2dG uptake in living cells in vitro, in spite of line-broadening and the occurrence of other strong signals in the spectral region of interest (3.

Biophysical and structural characterization of 1H-NMR-detectable mobile lipid domains in NIH-3T3 fibroblasts.

Nature and subcellular localization of 1H-NMR-detectable mobile lipid domains (ML) were investigated by NMR, Nile red fluorescence and electron microscopy, in NIH-3T3 fibroblasts and their H-ras transformants (3T3ras) transfected with a high number of oncogene copies. Substantial ML levels (ratio of (CH2)n/CH3 peak areas R=1. 56+/-0.

Absolute metabolite quantification by in vivo NMR spectroscopy: V. Multicentre quantitative data analysis trial on the overlapping background problem.

The goal of this study was to establish the best approach for quantifying nuclear magnetic resonance (NMR) lines, that in the frequency domain are overlapping with broad, unwanted background features. To perform the quantitative data analysis in a controlled way, test signals were designed and utilised, derived from two different real-world in vivo nuclear magnetic resonance signals. One of the main conclusions of the study was that the quantification methods currently available to the biomedical research groups can deliver the correct values of the quantitative parameters, but that great care should be taken in using optimal input parameters for the computer programs concerned.

Absolute metabolite quantification by in vivo NMR spectroscopy: IV. Multicentre trial on MRSI localisation tests.

The difference between the experimental and theoretical spatial response function (SRF) of a narrow tube with water is used for a localization test for magnetic resonance spectroscopic imaging (MRSI). From this difference a quantitative performance parameter is derived for the relative amount of signal within a limited region in the field of view. The total signal loss by the MRSI experiment and eddy currents is described by a parameter SL derived from the signal intensities of two echoes.

Lower levels of 1H MRS-visible mobile lipids in H-ras transformed tumorigenic fibroblasts with respect to their untransformed parental cells.

High resolution 1H MRS studies report increased mobile neutral lipid (MNL) signals in transformed and malignant as well as in some in vitro cultured embryonic cells. Nature, subcellular localization and biological function of MNL are still under debate. This work was aimed at assessing alterations induced in MNL signals of NIH-3T3 mouse embryo fibroblasts by transformation with human HJ-ras oncogene.

Potential role of in vitro 1H magnetic resonance spectroscopy in the definition of malignancy grading of human neuroepithelial brain tumours.

The increasing sensitivity of neuro-imaging in the diagnosis of brain expanding lesions is not directly related to biopathological specificity and new technological approaches are under study. In particular Magnetic Resonance Spectroscopy (MRS) allows evaluation of some biochemical pathways whose metabolic alterations may be correlated with the nature and malignancy grading of primary brain tumours. In the present study the author performed an in vitro high field 1H MRS (9.

Evaluation of signal processing methods for the quantification of a multi-exponential signal: the glycogen 13C-1 NMR signal.

The 13C-1 NMR peak in proton-decoupled spectra of liver glycogen solution was quantitatively analyzed by three types of model-function fitting algorithms: iterative line-fitting in the frequency domain (MDCON); iterative least-squares fitting (VARPRO) in the time domain; and noniterative singular value decomposition-based analysis (HTLS), also in the time domain. Quantification results were compared with manual integration values. Performance of the algorithms was tested at different signal-to-noise ratios (S/N) of the glycogen C-1 peak.