EBV persistence in gastric cancer cases conventionally classified as EBER-ISH negative.

BACKGROUND: The Epstein-Barr virus (EBV) causes various B-cell lymphomas and epithelial malignancies, including gastric cancer (GC) at frequencies ranging from 5 to 10% in adenocarcinomas (ADK) to 80% in GC with lymphoid stroma (GCLS). Using high-sensitivity methods, we recently detected EBV traces in a large cohort of EBV-negative B-cell lymphomas, suggesting a hit-and-run mechanism. METHODS: Here, we used routine and higher-sensitivity methods [droplet digital PCR (ddPCR) for EBV segments on microdissected tumour cells and RNAscope for EBNA1 mRNA] to assess EBV infection in a cohort of 40 GCs (28 ADK and 12 GCLS). RESULTS: ddPCR documented the presence of EBV nucleic acids in rare tumour cells of several cases conventionally classified as EBV-negative (ADK, 8/26; GCLS, 6/7). Similarly, RNAscope confirmed EBNA1 expression in rare tumour cells (ADK, 4/26; GCLS, 3/7). Finally, since EBV induces epigenetic changes that are heritable and retained after complete loss of the virus from the host cell, we studied the methylation pattern of EBV-specifically methylated genes (Timp2, Eya1) as a mark of previous EBV infection. Cases with EBV traces showed a considerable level of methylation in Timp2 and Eya1 genes that was similar to that observed in EBER-ISH positive cases and greater than cases not featuring any EBV traces. CONCLUSIONS: These findings suggest that: (a) EBV may contribute to gastric pathogenesis more widely than currently acknowledged and (b) indicate the methylation changes as a mechanistic framework for how EBV can act in a hit-and-run manner. Finally, we found that the viral state was of prognostic significance in univariate and multivariate analyses.

Integration of VarSome API in an existing bioinformatic pipeline for automated ACMG interpretation of clinical variants.

OBJECTIVE: While the bioinformatic workflow, from quality control to annotation, is quite standardized, the interpretation of variants is still a challenge. The decreasing cost of massively parallel NGS has produced hundreds of variants per patient to analyze and interpret. The ACMG "Standards and guidelines for the interpretation of sequence variants", widely adopted in clinical settings, assume that the clinician has a comprehensive knowledge of the literature and the disease. MATERIALS AND METHODS: To semi-automatize the application of the guidelines, we decided to develop an algorithm that exploits VarSome, a widely used platform that interprets variants on the basis of information from more than 70 genome databases. RESULTS: Here we explain how we integrated VarSome API into our existing clinical diagnostic pipeline for NGS data to obtain validated reproducible results as indicated by accuracy, sensitivity and specificity. CONCLUSIONS: We validated the automated pipeline to be sure that it was doing what we expected. We obtained 100% sensitivity, specificity and accuracy, confirming that it was suitable for use in a diagnostic setting.

CNV analysis in a diagnostic setting using target panel.

OBJECTIVE: Copy-number variation (CNV) is an important source of genetic diversity in humans. It can cause Mendelian or sporadic traits or be associated with complex diseases by various molecular mechanisms, including gene dosage, gene disruption, gene fusion and position effects. In clinical diagnostics, it is therefore fundamental to be able to identify such variations. The preferred techniques for CNV detection are MLPA, aCGH and qPCR, which have proven to be valuable, and they are complex, costly and require prior knowledge of the region to analyze. CNV calling from NGS data still suffers from data variability. Coverage can vary greatly from one region of the genome to another, depending on many factors like complexity, GC content, repeated regions and many others. In this paper, we describe how we developed a method for CNV detection. MATERIALS AND METHODS: Our method exploits CoNVaDING to detect single- and multiple-exon CNVs in targeted NGS data. RESULTS: We demonstrated that our CNV analysis has 100% specificity and 99.998% sensitivity. We also show how we evaluated the performance of this method based on internal analysis. CONCLUSIONS: The results indicate that the method can be used to screen prior to standard labs technologies, thus reducing the number of analyses, as well as costs, and increasing test conclusiveness.

Induction and Repair of DNA DSB as Revealed by H2AX Phosphorylation Foci in Human Fibroblasts Exposed to Low- and High-LET Radiation: Relationship with Early and Delayed Reproductive Cell Death.

The spatial distribution of radiation-induced DNA breaks within the cell nucleus depends on radiation quality in terms of energy deposition pattern. It is generally assumed that the higher the radiation linear energy transfer (LET), the greater the DNA damage complexity. Using a combined experimental and theoretical approach, we examined the phosphorylation-dephosphorylation kinetics of radiation-induced γ-H2AX foci, size distribution and 3D focus morphology, and the relationship between DNA damage and cellular end points (i.e., cell killing and lethal mutations) after exposure to gamma rays, protons, carbon ions and alpha particles. Our results showed that the maximum number of foci are reached 30 min postirradiation for all radiation types. However, the number of foci after 0.5 Gy of each radiation type was different with gamma rays, protons, carbon ions and alpha particles inducing 12.64 ± 0.25, 10.11 ± 0.40, 8.84 ± 0.56 and 4.80 ± 0.35 foci, respectively, which indicated a clear influence of the track structure and fluence on the numbers of foci induced after a dose of 0.5 Gy for each radiation type. The γ-H2AX foci persistence was also dependent on radiation quality, i.e., the higher the LET, the longer the foci persisted in the cell nucleus. The γ-H2AX time course was compared with cell killing and lethal mutation and the results highlighted a correlation between cellular end points and the duration of γ-H2AX foci persistence. A model was developed to evaluate the probability that multiple DSBs reside in the same gamma-ray focus and such probability was found to be negligible for doses lower than 1 Gy. Our model provides evidence that the DSBs inside complex foci, such as those induced by alpha particles, are not processed independently or with the same time constant. The combination of experimental, theoretical and simulation data supports the hypothesis of an interdependent processing of closely associated DSBs, possibly associated with a diminished correct repair capability, which affects cell killing and lethal mutation.

Microbiological and fermentative properties of baker's yeast starter used in breadmaking.

This study assessed the levels of microbial contaminants in liquid, compressed and dry commercial baker's yeasts used as starters in breadmaking. Eumycetes, Enterobacteriaceae, total and fecal coliforms, Bacillus spp., and lactic acid bacteria (LAB), in particular enterococci, were quantified. Results obtained in this study highlighted that baker's yeast could represent a potential vehicle of spoilage and undesirable microorganisms into the baking environment, even if these do not influence the leavening activity in the dough, as ascertained by rheofermentometer analysis. Different microbial groups, such as spore-forming bacteria and moulds, were found in baker's yeast starters. Moreover, different species of LAB, which are considered the main contaminants in large-scale yeast fermentations, were isolated and identified by Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA sequencing. The most recurrent species were Lactobacillus plantarum, Enterococcus faecalis, and Enterococcus durans, isolated from both compressed and dry starters, whereas strains belonging to Leuconostoc and Pediococcus genera were found only in dry ones. Nested-Polymerase Chain Reaction (Nested-PCR) and Randomly Amplified Polymorphic DNA-PCR (RAPD-PCR) were also used to highlight the biodiversity of the different commercial yeast strains, and to ascertain the culture purity.

Critical thresholds for cerebrovascular reactivity after traumatic brain injury.

INTRODUCTION: Pressure-reactivity index (PRx) is a useful tool in brain monitoring of trauma patients, but the question remains about its critical values. Using our TBI database, we identified the thresholds for PRx and other monitored parameters that maximize the statistical difference between death/survival and favorable/unfavorable outcomes. We also investigated how these thresholds depend on clinical factors such as age, gender and initial GCS. METHODS: A total of 459 patients from our database were eligible. Tables of 2 × 2 format were created grouping patients according to survival/death or favorable/unfavorable outcomes and varying thresholds for PRx, ICP and CPP. Pearson's chi square was calculated, and the thresholds returning the highest score were assumed to have the best discriminative value. The same procedure was repeated after division according to clinical factors. RESULTS: In all patients, we found that PRx had different thresholds for survival (0.25) and for favorable outcome (0.05). Thresholds of 70 mmHg for CPP and 22 mmHg for ICP were identified for both survival and favorable outcomes. The ICP threshold for favorable outcome was lower (18 mmHg) in females and patients older than 55 years. In logistic regression models, independent variables associating with mortality and unfavorable outcome were age, GCS, ICP and PRx. CONCLUSION: The prognostic role of PRx is confirmed but with a lower threshold of 0.05 for favorable outcome than for survival (0.25). Results for ICP are in line with current guidelines. However, the lower value in elderly and in females suggests increased vulnerability to intracranial hypertension in these groups.

What comes first? The dynamics of cerebral oxygenation and blood flow in response to changes in arterial pressure and intracranial pressure after head injury.

BACKGROUND: Brain tissue partial oxygen pressure (Pbt(O(2))) and near-infrared spectroscopy (NIRS) are novel methods to evaluate cerebral oxygenation. We studied the response patterns of Pbt(O(2)), NIRS, and cerebral blood flow velocity (CBFV) to changes in arterial pressure (AP) and intracranial pressure (ICP). METHODS: Digital recordings of multimodal brain monitoring from 42 head-injured patients were retrospectively analysed. Response latencies and patterns of Pbt(O(2)), NIRS-derived parameters [tissue oxygenation index (TOI) and total haemoglobin index (THI)], and CBFV reactions to fluctuations of AP and ICP were studied. RESULTS: One hundred and twenty-one events were identified. In reaction to alterations of AP, ICP reacted first [4.3 s; inter-quartile range (IQR) -4.9 to 22.0 s, followed by NIRS-derived parameters and CBFV (10.9 s; IQR: -5.9 to 39.6 s, 12.1 s; IQR: -3.0 to 49.1 s, 14.7 s; IQR: -8.8 to 52.3 s for THI, CBFV, and TOI, respectively), with Pbt(O(2)) reacting last (39.6 s; IQR: 16.4 to 66.0 s). The differences in reaction time between NIRS parameters and Pbt(O(2)) were significant (P<0.001). Similarly when reactions to ICP changes were analysed, NIRS parameters preceded Pbt(O(2)) (7.1 s; IQR: -8.8 to 195.0 s, 18.1 s; IQR: -20.6 to 80.7 s, 22.9 s; IQR: 11.0 to 53.0 s for THI, TOI, and Pbt(O(2)), respectively). Two main patterns of responses to AP changes were identified. With preserved cerebrovascular reactivity, TOI and Pbt(O(2)) followed the direction of AP. With impaired cerebrovascular reactivity, TOI and Pbt(O(2)) decreased while AP and ICP increased. In 77% of events, the direction of TOI changes was concordant with Pbt(O(2)). CONCLUSIONS: NIRS and transcranial Doppler signals reacted first to AP and ICP changes. The reaction of Pbt(O(2)) is delayed. The results imply that the analysed modalities monitor different stages of cerebral oxygenation.

Production of functional probiotic, prebiotic, and synbiotic ice creams.

In this work, 3 types of ice cream were produced: a probiotic ice cream produced by adding potentially probiotic microorganisms such as Lactobacillus casei and Lactobacillus rhamnosus; a prebiotic ice cream produced by adding inulin, a prebiotic substrate; and a synbiotic ice cream produced by adding probiotic microorganisms and inulin in combination. In addition to microbial counts, pH, acidity, and physical and functional properties of the ice creams were evaluated. The experimental ice creams preserved the probiotic bacteria and had counts of viable lactic acid bacteria after frozen storage that met the minimum required to achieve probiotic effects. Moreover, most of the ice creams showed good nutritional and sensory properties, with the best results obtained with Lb. casei and 2.5% inulin.

Interactions between Lactobacillus sakei and CNC (Staphylococcus xylosus and Kocuria varians) and their influence on proteolytic activity.

AIMS: To evaluate interactions between Lactobacillus sakei and coagulase negative cocci (CNC) (Staphylococcus xylosus and Kocuria varians) and to investigate the influence of these interactions on their own proteolytic activity. METHODS AND RESULTS: Interactions occurring between strains of Lact. sakei and CNC were assessed by spectrophotometric analysis. The growth of 35 strains of Lact. sakei, used as indicators, was compared to that obtained combining the same strains with growing cells or cell-free supernatants of 20 CNC (18 Staph. xylosus and 2 K. varians). The proteolytic activity expressed by single strains or by their combinations was assessed on sarcoplasmic protein extracts by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The results evidenced that interactions are able to affect not only the growth but also the in vitro proteolytic activity of Lact. sakei and CNC used in combination. CONCLUSIONS: A relationship between the presence of interactions among useful strains and the strength of technological characteristics, such as proteolysis, was defined. SIGNIFICANCE AND IMPACT OF THE STUDY: The study highlighted that CNC are able to stimulate the growth of some Lact. sakei strains. At the same time, this interaction positively influences the proteolytic activity of strains used in combination. Given the importance of proteolysis during the ripening of fermented meats, this phenomenon should be taken into account to select meat starter cultures.

Risk of Salmonella transmission via cryopreserved semen in turkey flocks.

To investigate the possibility to carry pathogen bacteria in turkey flocks via cryopreserved semen, research was carried out 1) to investigate the microbial contamination of fresh and frozen thawed turkey semen and 2) to evaluate the effect of the freezing-thawing process on the survival of 3 serovars of Salmonella spp. experimentally inoculated in turkey semen. Five pools of semen diluted 4-fold were cooled, added with 8% of dimethylacetamide as a cryoprotectant, and aliquots of 80 muL were directly plunged into liquid nitrogen to form frozen pellets. Mesophilic viable counts, total and fecal coliforms, Enterobacteriaceae, enterococci, Campylobacter spp., and Salmonella spp. were investigated on fresh and thawed samples. Further, 5 pools of diluted semen were each divided into 3 subsamples, inoculated with 7.8 +/- 0.2 log cfu.mL(-1) of Salmonella Liverpool, Salmonella Montevideo, and Salmonella Braenderup, respectively, and cryopreserved before to assess the postthaw viability of Salmonella spp. strains. Fresh semen was highly contaminated by all of the saprophytic bacteria investigated and the cryopreservation process reduced the amount of mesophilic viable count and total coliforms (P < 0.05) and fecal coliforms, Enterobacteriaceae, and enterococci (P < 0.01) by about 1 log cfu.mL(-1). Conversely, neither Campylobacter spp. nor Salmonella spp. were found as endogenous bacteria in semen. In the inoculated semen, both Salmonella Liverpool, Salmonella Montevideo, and Salmonella Braenderup colonies were recovered postthaw, showing a significant reduction of 2.03 +/- 0.28, 3.08 +/- 0.22, and 2.72 +/- 0.23 log cfu.mL(-1), respectively, compared with the fresh semen (P < 0.001). In conclusion, the cryopreservation process allowed us to obtain a low reduction of microbial count both in endogenous saprophytic bacteria and artificially inoculated Salmonella spp. strains; therefore, the possibility of Samonella spp. transmission to flocks through the use of infected cryopreserved semen does exist.

Fatal subarachnoid hemorrhage from mycotic aneurysm ruptures in an immunocompetent patient with aspergillosis: a case report.

Cerebral aspergillosis is a rare condition usually encountered in severely immunodepressed patients. We review the case of an immunocompetent patient who developed a fulminant form of cerebral aspergillosis which led to death due to the rapid formation and rupture of multiple mycotic aneurysms in the cerebral arteries. We suggest the possible role of genetic factors in causing this unusual clinical history and we propose that cerebral aspergillosis should be taken into consideration early in the process of diagnosis in order to allow for timely treatment.

DNA fragmentation induced in human fibroblasts by 56Fe ions: experimental data and Monte Carlo simulations.

We studied the DNA fragmentation induced in human fibroblasts by iron-ion beams of two different energies: 115 MeV/nucleon and 414 MeV/nucleon. Experimental data were obtained in the fragment size range 1-5700 kbp; Monte Carlo simulations were performed with the PARTRAC code; data analysis was also performed through the Generalized Broken Stick (GBS) model. The comparison between experimental and simulated data for the number of fragments produced in two different size ranges, 1-23 kbp and 23-5700 kbp, gives a satisfactory agreement for both radiation qualities. The Monte Carlo simulations also allow the counting of fragments outside the experimental range: The number of fragments smaller than 1 kbp is large for both beams, although with a strong difference between the two cases. As a consequence, we can compute different RBEs depending on the size range considered for the fragment counting. The PARTRAC evaluation takes into account fragments of all sizes, while the evaluation from the experimental data considers only the fragments in the range of 1-5700 kbp. When the PARTRAC evaluation is restricted to this range, the agreement between experimental and computed RBE values is again good. When fragments smaller than 1 kbp are also considered, the RBE increases considerably, since gamma rays produce a small number of such fragments. The analysis performed with the GBS model proved to be quite sensitive to showing, with a phenomenological single parameter, variations in double-strand break (DSB) correlation.

Tetraplegia and respiratory failure following mild cervical trauma in a child with Cornelia De Lange syndrome.

Here we report a 6-year-old female patient with Cornelia de Lange syndrome who developed tetraplegia and respiratory failure after a seemingly trivial spinal trauma due to an spinal malformation that has not yet been described.

The Cosmic Silence experiment: on the putative adaptive role of environmental ionizing radiation.

Previously we reported that yeast and Chinese hamster V79 cells cultured under reduced levels of background environmental ionizing radiation show enhanced susceptibility to damage caused by acute doses of genotoxic agents. Reduction of environmental radiation dose rate was achieved by setting up an underground laboratory at Laboratori Nazionali del Gran Sasso, central Italy. We now report on the extension of our studies to a human cell line. Human lymphoblastoid TK6 cells were maintained under identical in vitro culture conditions for six continuous months, at different environmental ionizing radiation levels. Compared to "reference" environmental radiation conditions, we found that cells cultured in the underground laboratories were more sensitive to acute exposures to radiation, as measured both at the level of DNA damage and oxidative metabolism. Our results are compatible with the hypothesis that ultra-low dose rate ionizing radiation, i.e. environmental radiation, may act as a conditioning agent in the radiation-induced adaptive response.

NMR metabolic profiling of organic and aqueous sea bass extracts: implications in the discrimination of wild and cultured sea bass.

The nuclear magnetic resonance (NMR) technique was used as analytical tool to determine the complete metabolic profiling of sea bass extracts: water-soluble metabolites belonging to different classes such as sugars, amino acids, dipeptides and organic acids as well as metabolites soluble in organic solvent such as lipids, sterols and fatty acids were identified. The metabolite profiling together with a suitable statistical analysis were used to discriminate between wild and cultured sea bass samples. Preliminary results show that discrimination between wild and cultured sea bass was obtained not only using fatty acid composition but also cholesterol and phosphatidylethanolamine and some water-soluble metabolites such as choline, trimethylamine oxide, glutamine, fumaric and malic acids.

Interactions between strains of Staphylococcus xylosus and Kocuria varians isolated from fermented meats.

AIMS: To evaluate the interactions of Staphylococcus xylosus on Kocuria varians strains isolated from fermented meat products. METHODS AND RESULTS: Interactions were assessed in vitro by agar spot test, agar well diffusion assay and spectrophotometric assay. The growth of K. varians (five strains) alone was compared with that in the presence of growing cells of S. xylosus (50 strains) or in the presence of heat-treated or untreated supernatants of S. xylosus. Sixteen strains stimulated the growth of K. varians K4, while four strains inhibited the K4 strain. Heated cell-free supernatants of S. xylosus did not have any effect on K. varians. The proteolytic activity of single strains or their combinations was assessed in vitro and in vivo by sodiumdodecylsulfate-polyacrylamide gel electrophoresis of sarcoplasmic protein extracts. Combinations of stimulatory strains of S. xylosus and K. varians showed a higher proteolytic activity compared with that of S. xylosus or K. varians alone. CONCLUSIONS: The interactions between strains may influence both the growth of the co-cultured strains and proteolysis, technologically relevant characteristics. SIGNIFICANCE AND IMPACT OF THE STUDY: The study of interactions between coagulase-negative cocci may guide the formulation of mixed strain starters for the production of fermented sausages.

DNA fragments induction in human fibroblasts by radiations of different qualities.

Experimental data on DNA double strand break (DSB) induction in human fibroblasts (AG1522), following irradiation with several radiation qualities, namely gamma rays, 0.84 MeV protons, 58.9 MeV u(-1) carbon ions, iron ions of 115 MeV u(-1), 414 MeV u(-1), 1 GeV u(-1), and 5 GeV u(-1), are presented. DSB yields were measured by calibrated Pulsed Field Gel Electrophoresis in the DNA fragment size range 0.023-5.7 Mbp. The DSB yields show little LET dependence, in spite of the large variation of the latter among the beams, and are slightly higher than that obtained using gamma rays. The highest yield was found for the 5 GeV u(-1) iron beam, that gave a value 30% higher than the 1 GeV u(-1) iron beam. A phenomenological method is used to parametrise deviation from randomness in fragment size spectra.

A 244Cm irradiator for protracted exposure of cultured Mammalian cells with alpha particles.

A 244Cm alpha-particle irradiator was designed and constructed for radiobiological studies where protracted exposure at a low dose rate of cultured mammalian cells is required. It allows irradiation of a cell monolayer attached to the Mylar bottom of a specially designed Petri dish of 56 mm diameter (approximately 25 cm(2) area). The irradiator is based on a 20-mm-diameter stainless steel chamber containing a 148 kBq 244Cm source. The chamber, flushed with helium gas at a pressure kept slightly above the external pressure, is inserted into a cell incubator where temperature and CO2 concentration are controlled. Spectrometric and dosimetric characterization of the irradiator was carried out by means of an ion-implanted-silicon charged-particle detector, CR39 detectors, and Monte Carlo simulations with the TRIM code. Average LET of particles incident on the cells at the center of the Petri dish was evaluated to be 120 keV microm(-1) at 59 mm from the source, and the average dose rate was 5.69 x 10 Gy s(-1), with +12% and -8% variations at the center and the edge, respectively. The irradiator has been successfully tested and used for several experiments involving 16-d exposure of human fibroblasts monolayers.

Shelf life of fresh sausages stored under modified atmospheres.

The aim of this study was to investigate differences in modified atmosphere packaging (MAP) for the improvement of the shelf life of fresh meat products. Three different conditions for preserving fresh sausages were tested: MAP1 (20% CO2, 70% O2, and 10% N2), MAP2 (40% CO2 and 60% O2), and MAP3 (40% CO2, 30% O2, and 30% N2). Samples from the MAP2 group had fewer spoilage bacteria, stable red color (no change of a* value), and good physical attributes (high water-holding capacity, little loss from cooking, and low shear force needed for cutting) compared with samples from other treatment groups. Thus, high concentrations of CO2 (40%) and O2 (60%) resulted in a longer shelf life for fresh sausages.