Genetic structure of the Sardinian population at the D1S80 VNTR locus and population diversity

We typed the Sardinian population at the D1S80 VNTR locus. Nineteen alleles were detected in a sample of 92 unrelated individuals, allele frequency distribution showing a modal pattern mostly in agreement with other Caucasoid populations. A high degree of heterozygosity (observed value=80.4%) was present. Goodness-of-fit tests demonstrated no departure from Hardy-Weinberg expectations. Data regarding heterozygosity, number of alleles and singletons appeared in accordance with the IAM mutation-drift equilibrium model and showed no evidence of hidden substructuring. Allele 34 exhibited in Sardinians the highest frequency never observed in Caucasians. Nonetheless, the comparison with other European populations did not disclose Sardinian genetic peculiarity. Indeed, measures of genetic divergence among Europeans demonstrated definitely smaller values at the D1S80 locus in comparison with those calculated over a high number of (pre-DNA) polymorphic loci. High mutation rate and selective neutrality typical of VNTRs could account for the observed moderate genetic divergence. Isolation and genetic drift, on the other hand, may have determined certain deviations in allele frequency distribution, as occurred to allele 34 in the Sardinian population.     

Detection and enumeration of Arcobacter spp. in the coastal environment of the Straits of Messina (Italy)

Seawater and plankton samples from the Straits of Messina, Italy, were analysed to confirm the occurrence of potentially pathogenic Arcobacter butzleri, A. cryaerophilus and A. skirrowii. Both classical cultural methods and molecular techniques were used as confirmative steps of the growth in enrichment broth to enumerate and differentiate these bacteria. Only A. butzleri was isolated from seawater and plankton samples and was more abundant when associated with plankton than free-living. A. cryaerophilus was occasionally detected by PCR assay from environmental samples. The PCR procedure, used in a combined method, was useful in enumerating Arcobacter spp. in marine environment.     

Continuous cephalosporin C purification: dynamic modelling and parameter validation

A mathematical kinetic model for the adsorption and desorption of cephalosporin C on Amberlite XAD-2 resin is proposed. The model can represent Langmuir, Freundlich or linear isotherms at equilibrium. The intrinsic kinetic parameters and adsorption isotherms as well as physical parameters such as the effective diffusivity and the external mass transfer coefficient were obtained at different temperatures and ethanol concentrations. An unfavourable cephalosporin C adsorption occurred when ethanol was present in the solution. It has been shown that at 25 degrees C the ethanol, at concentrations from 1.5% to 2.5%, decreases the cephalosporin C adsorption. However, this behaviour was not observed at 10 degrees C. The kinetic model fitted the experimental data well under different conditions. The model was validated in a continuous process of cephalosporin C purification using the same resin. The model with the validated parameters is able to predict the behaviour of the reactor system. The continuous process is composed of two stirred tank reactors with adsorber recycle. The adsorption occurs in the first stage, and elution of the product takes place in the second stage with ethanol as eluent. The dynamic behaviour of the process was described using the following parameters: hydraulic residence time for the first (theta(h1)) and second stage (theta(h2)), solid residence time (theta(s)), initial concentration of CPC (C(0)), inlet ethanol concentration (C(ET0)) and kinetics parameters.     

Production of exopolysaccharides from a thermophilic microorganism isolated from a marine hot spring in flegrean areas

A thermophilic strain isolated from sea sand at Maronti, near Sant' Angelo (Ischia), is described. The organism grows well at an optimal temperature of 60 °C at pH 7.0. The thermophilic bacterium, named strain 4004, produces an exocellular polysaccharide (EPS) in yields of 90 mg/l. The EPS fraction was produced with all substrates tested, although a higher yield was obtained with sucrose or trehalose as sole carbon source. During growth, the EPS content was proportional to the biomass. Three fractions (EPS1, EPS2, EPS3) were obtained after purification. Quantitative monosaccharide analysis of the EPSs revealed the presence of mannose:glucose:galactose in a relative ratio of 0.5:1.0:0.3 in EPS1, mannose:glucose:galactose in a relative ratio of 1.0:0.3:trace in EPS2, and galactose:mannose:glucosamine:arabinose in a relative ratio of 1.0:0.8:0.4:0.2 in EPS3. The average molecular mass of EPS3 was determined to be 1×10⁶ Da. From comparison of the chemical shift values in ¹H and ¹³C spectra, we conclude that EPS3 presents a pentasaccharide repeating unit. Electronic Publication     

Distribution of potentially pathogenic bacteria as free living and plankton associated in a marine coastal zone

AIMS: To determine the abundance of faecal and nonfaecal bacteria related to human and animal health, as free living or associated with small (>64 microm) and large (>200 microm) plankton, samples were collected monthly from the coastal zone at Messina (Italy). METHODS AND RESULTS: Different enrichment and selective cultural methods were used to determine the abundance of bacteria in sea water and plankton. The bacteria were more frequently isolated from water and large plankton than from small plankton. Vibrio and Aeromonas spp. showed different distribution patterns in water and plankton. Faecal indicators were always present in water and the large size class plankton samples. Enterococci associated with large plankton were more abundant than E. coli in the winter. Vibrio species distributions were different in water and plankton samples. Among arcobacters only A. butzleri was isolated from water and plankton samples. Campylobacter spp. was always absent in small plankton and more frequent in large plankton than in water. CONCLUSIONS: The colonization of zooplankton by potentially pathogenic bacteria is a widespread phenomenon. SIGNIFICANCE AND IMPACT OF THE STUDY: The presence of potentially pathogenic bacteria in sea water and associated with plankton can have ecological and epidemiological implications.     

Differential expression of PARK2 splice isoforms in an in vitro model of dopaminergic‐like neurons exposed to toxic insults mimicking Parkinson's disease

Mutations in PARK2 (or parkin) are responsible for 50% of cases of autosomal‐recessive juvenile‐onset Parkinson's disease (PD). To date, 21 alternative splice variants of the human gene have been cloned. Yet most studies have focused on the full‐length protein, whereas the spectrum of the parkin isoforms expressed in PD has never been investigated. In this study, the role of parkin proteins in PD neurodegeneration was explored for the first time by analyzing their expression profile in an in vitro model of PD. To do so, undifferentiated and all‐trans‐retinoic‐acid (RA)‐differentiated SH‐SY5Y cells (which thereby acquire a PD‐like phenotype) were exposed to PD‐mimicking neurotoxins: 1‐methyl‐4‐phenylpyridinium (MPP⁺) and 6‐hydroxydopamine (6‐OHDA) are widely used in PD models, whereas carbonyl cyanide m‐chlorophenyl hydrazone (CCCP) and carbobenzoxy‐Leu‐Leu‐leucinal (MG132) interfere, respectively, with mitochondrial mitophagy and proteasomal degradation. Following treatment with each neurotoxin H1, the first parkin isoform to be cloned, was down‐regulated compared to the respective controls both in undifferentiated and RA‐differentiated cells. In contrast, the expression pattern of the minor splice isoforms varied as a function of the compound used: it was largely unchanged in both cell cultures (eg, H21‐H6, H12, XP isoform) or it showed virtually opposite alterations in undifferentiated and RA‐differentiated cells (eg, H20 and H3 isoform). This complex picture suggests that up‐ or down‐regulation may be a direct effect of toxin exposure, and that the different isoforms may exert different actions in neurodegeneration via modulation of different molecular pathways.     

Submarine Hydrothermal Vents of the Aeolian Islands: Relationship Between Microbial Communities and Thermal Fluids

The relationship between fluid geochemistry and microbial communities was investigated for shallow (< 25 m) submarine hydrothermal vents in the Aeolian Islands (Southern Italy). Thermal waters, gases, and deposits of white filamentous material were collected from 11 sites. The geochemical analyses showed a magmatic component was present in all sampled fluids. The total microbial abundances, evaluated as direct counts of picoplanktonic cells (ranging from 0.2 to 2 mu m in diameter), were between 1.55 107 and 4.18 108 cells per liter. Picophytoplankton (total autofluorescent cells) ranged from 9.6 105 to 7.88 106 cells per liter. Yellow-orange autofluorescent prokaryotes belonging to the cyanobacteria were more abundant than red autofluorescent eukaryotic cells. Chemolithoautotrophic, sulfur-oxidizing, rod-shaped Bacteria were isolated from venting water samples and identified as Thiobacillus -like. Microscopic examination of the white mat deposits showed the presence of filamentous microorganisms.     

Diversity of Prokaryotic Community at a Shallow Marine Hydrothermal Site Elucidated by Illumina Sequencing Technology

To investigate the prokaryotic community structure and composition in an active hydrothermal site, named Black Point, off Panarea Island (Eolian Islands, Italy), we examined sediment and fluid samples, differing in temperature, by a massive parallel sequencing (Illumina) technique targeting the V3 region of the 16S rRNA gene. The used technique enabled us to detect a greater prokaryotic diversity than that until now observed and to reveal also microorganisms occurring at very low abundance (≤0.01 %). Most of sequences were assigned to Bacteria while Archaea were a minor component of the microbial community in both low- and high-temperature samples. Proteobacteria (mainly consisting of Alpha-, Gamma-, and Epsilonproteobacteria) dominated among all samples followed by Actinobacteria and Bacteroidetes. Analyzed DNA obtained from samples taken at different temperatures indicated the presence of members of different dominant genera. The main differences were observed between sediment samples where Rhodovulum and Thiohalospira prevailed at high temperature, while Thalassomonas and Sulfurimonas at low temperature. Chlorobium, Acinetobacter, Sulfurimonas, and Brevundimonas were abundant in both low- and high-temperature fluid samples. Euryarchaeota dominated the archaeal community in all samples. Classes of Euryarchaeota embracing hyperthermophilic members (Thermococci and Thermoplasmata) and of Crenarchaeota (Thermoprotei) were more abundant in high-temperature samples. A great number of sequences referred to Bacteria and Archaea still remained unaffiliated, indicating that Black Point site represents a rich source of so-far uncharted prokaryotic diversity.     

LINE-1 Hypomethylation in Blood and Tissue Samples as an Epigenetic Marker for Cancer Risk: A Systematic Review and Meta-Analysis

Objective

A systematic review and a meta-analysis were carried out in order to summarize the current published studies and to evaluate LINE-1 hypomethylation in blood and other tissues as an epigenetic marker for cancer risk.

Methods

A systematic literature search in the Medline database, using PubMed, was conducted for epidemiological studies, published before March 2014. The random-effects model was used to estimate weighted mean differences (MDs) with 95% Confidence Intervals (CIs). Furthermore, subgroup analyses were conducted by sample type (tissue or blood samples), cancer types, and by assays used to measure global DNA methylation levels. The Cochrane software package Review Manager 5.2 was used.

Results

A total of 19 unique articles on 6107 samples (2554 from cancer patients and 3553 control samples) were included in the meta-analysis. LINE-1 methylation levels were significantly lower in cancer patients than in controls (MD: −6.40, 95% CI: −7.71, −5.09; p<0.001). The significant difference in methylation levels was confirmed in tissue samples (MD −7.55; 95% CI: −9.14, −65.95; p<0.001), but not in blood samples (MD: −0.26, 95% CI: −0.69, 0.17; p = 0.23). LINE-1 methylation levels were significantly lower in colorectal and gastric cancer patients than in controls (MD: −8.33; 95% CI: −10.56, −6.10; p<0.001 and MD: −5.75; 95% CI: −7.75, −3.74; p<0.001) whereas, no significant difference was observed for hepatocellular cancer.

Conclusions

The present meta-analysis adds new evidence to the growing literature on the role of LINE-1 hypomethylation in human cancer and demonstrates that LINE-1 methylation levels were significantly lower in cancer patients than in control samples, especially in certain cancer types. This result was confirmed in tissue samples, both fresh/frozen or FFPE specimens, but not in blood. Further studies are needed to better clarify the role of LINE-1 methylation in specific subgroups, considering both cancer and sample type, and the methods of measurement.