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Clams have long been a fisheries and aquaculture sector of great importance in Italy, the main resource of fisheries is the Chamelea gallina of indigenous origin, whereas clams breeding is supported almost entirely by the Tapes philippinarum, a species of Indo-Pacific origin. Bivalve molluscs quality depends mainly on the water quality, and then by a series of factors such as water temperature and salinity, gametogenic cycle, food availability, and environmental conditions, that affect the Condition Index. In this work crude extracts obtained from the edible part of Chamelea gallina and Tapes philippinarum were analyzed by a proteomic approach based on a two-dimensional gel electrophoresis followed by liquid chromatography-tandem mass spectrometry, in order to detect biomarkers useful for identification of the two kinds of clams and to assess their nutritional characteristics. As a result, four differentially expressed spots were found and identified, namely enolase, cyclophilin-A, ribosomal protein L13 and actin-1., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Crohn's disease (CD) is an inflammatory bowel disease (IBD) that can affect the whole gastrointestinal tract. The ileocolonic variant of CD, an inflammation of both the ileum and the large intestine, accounts for up to 50% of the cases with CD, whereas Crohn's ileitis affecting the ileum is diagnosed in about 30%. Crohn's colitis, which is confined to the large intestine and accounts for the remaining 20%, is difficult to distinguish from the large bowel inflammation seen in patients with ulcerative colitis (UC). The pathogenesis of CD is not yet completely understood. Autoimmunity is one factor that can partake in the triggering or modulation of inflammatory processes in IBD. The major zymogen-granule membrane glycoprotein 2 (GP2) has been recently identified as a major autoantigenic target in CD. Interestingly, GP2 is mainly expressed in the pancreas and has also been demonstrated to be a membrane-anchored receptor of microfold cells in the follicle-associated epithelium. Remarkably, GP2 is overexpressed at the site of CD inflammation in contrast to the one in UC. By utilizing novel enzyme-linked immunosorbent assays for the detection of GP2-specific IgA and IgG, the loss of tolerance to GP2 has been associated with a specific clinical phenotype in CD, in particular with the ileocolonic location of the disease.

An outbreak of tuberculosis (TB) in Italy involved 19 schoolchildren with active TB and 43 with latent infection. The source of the outbreak was a school assistant born in Italy who had a family history of TB. This outbreak highlights the need for maintaining clinical and public health expertise in countries with low TB incidence.

This study aimed to evaluate the incidence of Chlamydophila pneumoniae antibodies in patients with community acquired pneumonia (CAP) by a new ELISA test (EIA CP-IgG, IgA, IgM--Eurospital, Trieste, Italy). From January 1999 to July 2001 141 patients with clinical signs of CAP were enrolled in sixteen Italian Hospitals. Specific IgM and IgG antibodies anti-C. pneumoniae in serum and IgA in both serum and sputum were detected. At a primary inspection (time T-0) serum and sputum samples were taken from 115/141 patients, whereas serum was collected from only 100/141 patients after 30 days (time T-30). At T-0 24/115 (20.8%) patients showed serological markers thus suggesting an acute C. pneumoniae infection. In 23/24 patients the overall serological pattern found at T-0 was confirmed at T-30. In 32/115 patients (27.8%) serological markers of C. pneumoniae past infection were found positive and were confirmed 30 days later. These data support the role of C. pneumoniae as an important aetiological agent of CAP throughout different geographic areas of Italy. The test was suitable for the laboratory diagnosis of C. pneumoniae infection. In particular, the presence of specific IgA anti- C. pneumoniae in both serum and sputum proved useful to define different stages and evolution of infection.

All known DNA ligases catalyze the formation of a phosphodiester linkage between adjacent termini in double-stranded DNA via very similar mechanisms. The ligase family can, however, be divided into two classes: eubacterial ligases, which require NAD(+) as a cofactor, and other ligases, from viruses, archaea, and eukaryotes, which use ATP. Drugs that discriminate between DNA ligases from different sources may have antieubacterial activity. We now report that a group of arylamino compounds, including some commonly used antimalarial and anti-inflammatory drugs and a novel series of bisquinoline compounds, are specific inhibitors of eubacterial DNA ligases. Members of this group of inhibitors have different heterocyclic ring systems with a common amino side chain in which the two nitrogens are separated by four carbon atoms. The potency, but not the specificity of action, is influenced by the DNA-binding characteristics of the inhibitor, and the inhibition is noncompetitive with respect to NAD(+). The arylamino compounds appear to target eubacterial DNA ligase in vivo, since a Salmonella Lig(-) strain that has been rescued with the ATP-dependent T4 DNA ligase is less sensitive than the parental Salmonella strain.

The recruitment of DNA ligase I to replication foci in S phase depends on a replication factory targeting sequence that also mediates the interaction with proliferating cell nuclear antigen (PCNA) in vitro. By exploiting a monoclonal antibody directed at a phospho-epitope, we demonstrate that Ser66 of DNA ligase I, which is part of a strong CKII consensus site, is phosphorylated in a cell cycle-dependent manner. After dephosphorylation in early G(1), the level of Ser66 phosphorylation is minimal in G(1), increases progressively in S and peaks in G(2)/M phase. The analysis of epitope-tagged DNA ligase I mutants demonstrates that dephosphorylation of Ser66 requires both the nuclear localization and the PCNA-binding site of the enzyme. Finally, we show that DNA ligase I and PCNA interact in vivo in G(1) and S phase but not in G(2)/M. We propose that dephosphorylation of Ser66 is part of a novel control mechanism to establish the pre-replicative form of DNA ligase I.

In mammalian cells, DNA replication occurs at discrete nuclear sites termed replication factories. Here we demonstrate that DNA ligase I and the large subunit of replication factor C (RF-C p140) have a homologous sequence of approximately 20 amino acids at their N-termini that functions as a replication factory targeting sequence (RFTS). This motif consists of two boxes: box 1 contains the sequence IxxFF whereas box 2 is rich in positively charged residues. N-terminal fragments of DNA ligase I and the RF-C large subunit that contain the RFTS both interact with proliferating cell nuclear antigen (PCNA) in vitro. Moreover, the RFTS of DNA ligase I and of the RF-C large subunit is necessary and sufficient for the interaction with PCNA. Both subnuclear targeting and PCNA binding by the DNA ligase I RFTS are abolished by replacement of the adjacent phenylalanine residues within box 1. Since sequences similar to the RFTS/PCNA-binding motif have been identified in other DNA replication enzymes and in p21(CIP1/WAF1), we propose that, in addition to functioning as a DNA polymerase processivity factor, PCNA plays a central role in the recruitment and stable association of DNA replication proteins at replication factories.

Increased knowledge of the nature and biology of lymphoid cells has provided more rational classification schemes, and has improved therapeutic strategies. However, non-Hodgkin lymphomas (NHL) as well as Hodgkin's disease (HD) show a less favorable outcome in elderly compared to young patients. The poorer outcome in elderly patients with NHL is largely due to chemotherapy-related issues, although other age-related factors may contribute to determine a poor prognosis, such as the presence of more aggressive pathological subtypes and an increase in extranodal vs nodal presentations. Similarly, HD patients older than 50 years have higher rates of advanced disease, B symptoms, and histological types associated with poor prognosis at presentation. The poor prognosis in lymphoid malignancies also appears to be attributable to inadequate treatment. However, the inability to administer full therapy may be real, due to the high percentages of deaths caused by severe infections and intercurrent disease (cardiac, renal, lung) related to diminished organ function. The availability of growth factors may help to reduce the incidence of severe neutropenia and other related septic conditions.

ATP-dependent DNA ligases are essential enzymes in both DNA replication and DNA repair processes. Here we report a functional characterization of the T4 DNA ligase. One N-terminal and two C-terminal deletion mutants were expressed in Escherichia coli as histidine- tagged proteins. An additional mutant bore a substitution of Lys159 in the active site that abolished ATP binding. All the proteins were tested in biochemical assays for ATP-dependent self-adenylation, DNA binding, nick joining, blunt-end ligation and AMP- dependent DNA relaxation. From this analysis we conclude that binding to DNA is mediated by sequences at both protein ends and plays a key role in the reaction. The enzyme establishes two different complexes with DNA: (i) a transient complex (T.complex) involving the adenylated enzyme; (ii) a stable complex (S.complex) requiring the deadenylated T4 DNA ligase. The formation of an S. complex seems to be relevant during both blunt-end ligation and DNA relaxation. Moreover the inactive His-K159L substitution mutant, although unable to self-adenylate, still possesses AMP-dependent DNA nicking activity.

Tallimustine, an alkylating benzoyl mustard derivative of distamycin A (FCE 24517), is a novel anti-tumor agent. Both its cytotoxic activity against human LoVo cells and nicking efficiency on isolated plasmid DNA were studied in relation to hyperthermic treatment and compared to the effect of doxorubicin, a known non-alkylating anti-tumor agent. The results of this analysis indicate that the cytotoxic activity of tallimustine reflects its direct interaction with the DNA target. The ability of tallimustine to induce DNA repair in human primary normal fibroblasts was monitored by determining both the stimulation of unscheduled DNA synthesis (UDS) and the ability to reactivate a plasmid containing a reporter gene, treated in vitro with tallimustine, in comparison with the effect of UV-C irradiation. The results suggest that human cells able to repair UV-damage arc unable to overcome DNA damage induced by tallimustine. Therefore, the hypothesis that the biological activity of tallimustine is related to its alkylating properties is further supported by the temperature studies and strengthened by the observed inability of cells to repair tallimustine-induced DNA damage.

The baculovirus expression system was used to overexpress human DNA ligase I (hLig I). Approx. 2 mg of recombinant hLig I was produced per 10(8) Spodoptera frugiperda Sf9 insect cells infected with the recombinant baculovirus. The optimum time point for the production of biologically active recombinant hLig I was 48 h post-infection. Lig I activity was demonstrated by auto-adenylating, polynucleotide joining and DNA relaxation assays. The baculovirus system has the advantage over previously described methods for producing hLig I of generating large amounts of a full-length active protein.

DNA replication in mammalian cells occurs in discrete nuclear foci called 'replication factories'. Here we show that DNA ligase I, the main DNA ligase activity in proliferating cells, associates with the factories during S phase but displays a diffuse nucleoplasmic distribution in non-S phase nuclei. Immunolocalization analysis of both chloramphenicol acetyltransferase (CAT)-DNA ligase I fusion proteins and epitope tagged DNA ligase I mutants allowed the identification of a 13 amino acid functional nuclear localization signal (NLS) located in the N-terminal regulatory domain of the protein. Furthermore, the NLS is immediately preceded by a 115 amino acid region required for the association of the enzyme with the replication factories. We propose that in vivo the activity of DNA ligase I could be modulated through the control of its sub-nuclear compartmentalization.

5-Iodo-2'-deoxy-L-uridine (L-IdU) and (E)-5-(2-bromovinyl)-2'-deoxy-L-uridine (L-BVdU) have been prepared and found to inhibit herpes simplex virus type 1 (HSV-1) thymidine kinase (TK) with activities comparable to those of their analogs with the natural D-sugar configuration. The mechanism of inhibition is purely competitive for L-IdU (Ki = 0.24 microM) and mixed-type for L-BVdU (Ki = 0.13 microM). High performance liquid chromatographic analysis of the reaction products demonstrated that the viral enzyme phosphorylates both L-enantiomers to their corresponding monophosphates with efficiency comparable to that for D-enantiomers. Neither L-enantiomer inhibits the human cytosolic TK. In contrast to their D-enantiomers, L-IdU and L-BVdU have no effect on human thymidylate synthase, either in HeLa cells or in TK-deficient HeLa cells transformed with the HSV-1 TK gene. Both L-enantiomers (i) have no effect on HeLa cell growth, (ii) are 1000-fold less cytotoxic toward TK-deficient HeLa cells transformed with the HSV-1 TK gene than are their D-enantiomers, (iii) in contrast to their D-enantiomers, are fully resistant to hydrolysis by nucleoside phosphorylase, and, (iv) in spite of their much lower cytotoxicity, most probably due to the very low affinity of L-BVdU monophosphate and L-IdU monophosphate for thymidylate synthase, are only 1 or 2 orders of magnitude less potent than their D-enantiomers in inhibiting viral growth, with potency comparable to that of acyclovir.

We have studied the regulation of DNA ligase I gene expression in UV-C irradiated human primary fibroblasts. An increase of approximately 6-fold both in DNA ligase I messenger and activity levels was observed 24 h after UV treatment, when nucleotide excision repair (NER) is no longer operating. DNA ligase I induction is serum-independent and is controlled mainly by the steady-state level of its mRNA. The activation is a function of the UV dose and occurs at lower doses in cells showing UV hypersensitivity. No increase in replicative DNA polymerase alpha activity was found, indicating that UV induction of DNA ligase I occurs through a pathway that differs from the one causing activation of the replication machinery. These data suggest that DNA ligase I induction could be linked to the repair of DNA damage not removed by NER.

To characterize nucleotide excision repair properties of cells from trichothiodystrophy (TTD) patients genetically-related to the xeroderma pigmentosum (XP) group D, TTD skin fibroblasts from two unrelated patients (TTD1VI and TTD2VI) belonging to the TTD/XPD group were transformed with a plasmid containing SV40 large T antigen-coding sequences and some DNA repair properties, such as unscheduled DNA synthesis (UDS), UV-survival, in vitro repair synthesis of cell extracts and reactivation of UV-irradiated reporter plasmid were studied. Results showed that: a) both untransformed and transformed TTD cells present a reduced UV-survival, compared to wild-type cells, but at significantly less reduced levels than XP-D cells; b) reduced repair activities were detected in both TTD and XP-D transformed cells by using in vitro cell free extract repair and reactivation of UV-irradiated plasmid procedures, and these relative reduced extents correlated with respective UV-survival; c) surprisingly, near wild-type UDS levels were detected in TTD2VILas transformed cells at different passages after the crisis, suggesting a phenotypic reversion of this transformed cell line; d) fluoro-cytometric analysis of TTD2VILas cells revealed a strong increase of a cell population containing a DNA amount more than twice as high than that of untransformed cells; finally, e) when UDS data were normalized to the DNA content in TTD2VILas cells, it appeared that the repair efficiency was only slightly higher than in untransformed cells. This implies that in transformed cells DNA repair properties should be evaluated, taking into account additional parameters. We obtained an immortalized TTD cell line which maintains DNA repair properties similar to those of parental untransformed cells and may be used to characterize the TTD defect at genetic, molecular and biochemical levels.

A complementary DNA (2961 bp) containing the complete coding sequence for murine DNA ligase I was isolated from a mouse fibroblast cDNA library using a cDNA encoding the human protein as a probe. An open reading frame of 2748 bp, encoding a protein of 916 amino acids (aa), was identified. Northern blot analysis of total RNA extracted from mouse fibroblasts showed a single band with a mobility corresponding to a size of 3.2 kb whose level increases upon serum stimulation of quiescent mouse NIH-3T3 cells. Alignment of the murine and human deduced aa sequences showed an overall 83% identity, that rises to 91% if only the sequence on the C-terminal portion of the protein containing the active site is considered.

The number of DNA single strand breaks generated by FCE24517 increases exponentially while covalent adducts linearly accumulate at a higher rate. Kinetics studies indicate that the rate of DNA fragmentation is temperature-dependent. The sites of DNA strand breaks do not change in the 30-65 degrees C range. The cytotoxic potency of FCE24517 is also affected by temperature, since a shift up of 6 degrees C during the 4 h exposure of human colon carcinoma cells raises the cytotoxic efficiency fivefold. These results are consistent with the hypothesis that the biological activity of this new drug relates to its electrophilic properties.

Both bacteriophage T4 and human type I DNA ligases in the presence of a mixture of ATP, AMP and PPi altered the topological properties of a supercoiled substrate by a step-wise reaction eventually leading to a population of fully relaxed, covalently closed products. In the presence of only AMP and PPi DNA products containing nicks with 3'OH/5'P termini accumulated in the presence of bacteriophage T4 DNA ligase, suggesting reversal of the entire joining reaction, but not in the presence of human DNA ligase I. Both DNA ligases became deoxyadenylylated in the presence of dATP, but the joining reaction did not proceed to completion. However, with both enzymes the full relaxing reaction took place in the presence of dAMP alone and in the presence of a mixture of dATP, dAMP and PPi. In no case could the joining reaction be reversed by dAMP and PPi. Related experiments with modified derivatives of deoxyribonucleoside 5'-triphosphates and PPi gave results in accord with these observations. The AMP dependent DNA relaxation catalysed by DNA ligases was insensitive to the presence of exonuclease III. These results indicate that controlled relaxation of the substrate by both DNA ligases occurs as a separate reaction rather than by simple reversal of the joining reaction. These findings support the hypothesis that in vivo the DNA topoisomerising ligases relax their substrate at the replication fork both during and separately from ligation of a pre-existing nick.

We have measured the effects of eight distamycin and two anthracycline derivatives on polynucleotide joining and self-adenylating activities of human DNA ligase I and rat DNA ligases I and III. All test drugs show good inhibitory activity against the three enzymes in the poly[d(A-T)] joining assay. Several distamycins also inhibit the DNA-independent self-adenylation reaction catalysed by the human enzyme and, to a lesser extent, by rat DNA ligases. These results confirm that anthracyclines and distamycins express their inhibitory action against DNA joining activities mainly via specific interactions with the substrate, and suggest that the three test DNA ligases utilize similar, if not identical, mechanisms of recognition and interaction with DNA-drug complexes. Our findings also indicate that distamycins have a greater affinity for human DNA ligase I than for rat enzymes, suggesting that, in this respect, rat DNA ligase I is more similar to rat DNA ligase III than to human DNA ligase I.