The fine tuning of metabolism, autophagy and differentiation during in vitro myogenesis.

Although the mechanisms controlling skeletal muscle homeostasis have been identified, there is a lack of knowledge of the integrated dynamic processes occurring during myogenesis and their regulation. Here, metabolism, autophagy and differentiation were concomitantly analyzed in mouse muscle satellite cell (MSC)-derived myoblasts and their cross-talk addressed by drug and genetic manipulation. We show that increased mitochondrial biogenesis and activation of mammalian target of rapamycin complex 1 inactivation-independent basal autophagy characterize the conversion of myoblasts into myotubes. Notably, inhibition of autophagic flux halts cell fusion in the latest stages of differentiation and, conversely, when the fusion step of myocytes is impaired the biogenesis of autophagosomes is also impaired. By using myoblasts derived from p53 null mice, we show that in the absence of p53 glycolysis prevails and mitochondrial biogenesis is strongly impaired. P53 null myoblasts show defective terminal differentiation and attenuated basal autophagy when switched into differentiating culture conditions. In conclusion, we demonstrate that basal autophagy contributes to a correct execution of myogenesis and that physiological p53 activity is required for muscle homeostasis by regulating metabolism and by affecting autophagy and differentiation.

Ethnobotanical study on the medicinal plants in the Mainarde Mountains (central-southern Apennine, Italy).

ETHNOPHARMACOLOGICAL RELEVANCE: New documentation of the uses of plants in the popular medicine of the Mainarde Mountain, a protected area of the central-southern Apennine characterised by a high floristic richness, is here reported. MATERIALS AND METHODS: Field data were collected through semi-structured and open interviews with native People between 2011 and 2014. The plants were identified and vouchers specimens were scanned to create a Virtual Herbarium. The Ethnobotanicity Index (EI), the Relative Importance Index (RI) and the Fidelity Level Index (FL) were calculated. The plant uses surveyed in the study area were compared with those described in medical and ethnobotanical literature. RESULTS: Seventy-one interviews were conducted, the age range of the informants was between 21 and 98 years. The inventory included 106 taxa belonging to 45 families; among these, 87 were wild species and 20 were cultivated species. The uses recorded were 429, among these, 69.1% of the uses concerned internal applications to treat digestive system disorders, infections and respiratory system disorders mainly, while 31.9% concerned external applications, especially to treat skin/subcutaneous cellular tissue disorders and injuries. In particular, 17 new uses and 16 unusual and rarely mentioned plants are documented. CONCLUSION: The data collected support evidence on traditional uses for plant in the Apennine. Findings from medical flora and from new or rare medical uses reinforce the usefulness of such research efforts.

DNA damage response by single-strand breaks in terminally differentiated muscle cells and the control of muscle integrity.

DNA single-strand breaks (SSB) formation coordinates the myogenic program, and defects in SSB repair in post-mitotic cells have been associated with human diseases. However, the DNA damage response by SSB in terminally differentiated cells has not been explored yet. Here we show that mouse post-mitotic muscle cells accumulate SSB after alkylation damage, but they are extraordinarily resistant to the killing effects of a variety of SSB-inducers. We demonstrate that, upon SSB induction, phosphorylation of H2AX occurs in myotubes and is largely ataxia telangiectasia mutated (ATM)-dependent. However, the DNA damage signaling cascade downstream of ATM is defective as shown by lack of p53 increase and phosphorylation at serine 18 (human serine 15). The stabilization of p53 by nutlin-3 was ineffective in activating the cell death pathway, indicating that the resistance to SSB inducers is due to defective p53 downstream signaling. The induction of specific types of damage is required to activate the cell death program in myotubes. Besides the topoisomerase inhibitor doxorubicin known for its cardiotoxicity, we show that the mitochondria-specific inhibitor menadione is able to activate p53 and to kill effectively myotubes. Cell killing is p53-dependent as demonstrated by full protection of myotubes lacking p53, but there is a restriction of p53-activated genes. This new information may have important therapeutic implications in the prevention of muscle cell toxicity.

Mechanisms of dealing with DNA damage in terminally differentiated cells.

To protect genomic integrity living cells that are continuously exposed to DNA-damaging insults are equipped with an efficient defence mechanism termed the DNA damage response. Its function is to eliminate DNA damage through DNA repair and to remove damaged cells by apoptosis. The DNA damage response has been investigated mainly in proliferating cells, in which the cell cycle machinery is integrated with the DNA damage signalling. The current knowledge of the mechanisms of DNA repair, DNA damage signalling and cell death of post-mitotic cells that have undergone irreversible cell cycle withdrawal will be reviewed. Evidence will be provided that the protection of the genome integrity in terminally differentiated cells is achieved by different strategies than in proliferating cells.

Upper limits on gravitational-wave emission in association with the 27 Dec 2004 giant flare of SGR1806-20.

At the time when the giant flare of SGR1806-20 occurred, the AURIGA "bar" gravitational-wave (GW) detector was on the air with a noise performance close to stationary Gaussian. This allows us to set relevant upper limits, at a number of frequencies in the vicinities of 900 Hz, on the amplitude of the damped GW wave trains, which, according to current models, could have been emitted, due to the excitation of normal modes of the star associated with the peak in x-ray luminosity.

The "T" vein of the leg.

BACKGROUND: We frequently observe a tributary of the saphenous vein with the origin in the saphenous compartment of the medial aspect of the upper third of the leg. It runs transversally in the interfascial compartment toward the lateral aspect of the leg. Constantly it feeds by reflux varicose veins clinically visible in the paratibial region and/or in the lateral aspect of the leg. For the peculiarity of its anatomical shape as well as duplex appearance, we defined it as the "T" vein. OBJECTIVES: To assess how frequently the "T" vein of the leg is involved in varicose networks. METHODS: A total of 218 consecutive patients affected by primary varicose veins have been evaluated by the means of duplex scanning. We assessed both the presence of the above-mentioned tributary and the frequency of its hemodynamic involvement in the varicose network. RESULTS: In 15 of 218 cases (7%) we demonstrated the above-mentioned tributary with an interfascial length ranging between 5 and 12 cm involved in varicose networks. CONCLUSIONS: The anterior tributary of the saphenous vein of the anterolateral aspect of the leg is a neglected clinical entity, whose existence is important to know for the treatment of varicose veins of the lateral aspect of the leg.

8-Oxoguanine DNA damage: at the crossroad of alternative repair pathways.

Radical oxygen species (ROS) generate various modified DNA bases. Among them 8-oxo-7,8-dihydroguanine (8oxoG) is the most abundant and seems to play a major role in mutagenesis and in carcinogenesis. 8oxoG is removed from DNA by the specific glycosylase OGG1. An additional post-replication repair is needed to correct the 8oxoG/A mismatches that are produced by persistent 8oxoG residues. This review is focused on the mechanisms of base excision repair (BER) of this oxidized base. It is shown that, in vitro, efficient and complete repair of 8oxoG/C pairs requires a core of four proteins, namely OGG1, APE1, DNA polymerase (Pol) beta, and DNA ligase I. Repair occurs predominantly by one nucleotide replacement reactions (short-patch BER) and Pol beta is the polymerase of election for the resynthesis step. However, alternative mechanisms can act on 8oxoG residues since Pol beta-null cells are able to repair these lesions. 8oxoG/A mismatches are repaired by human cell extracts via two BER events which occur sequentially on the two strands. The removal of the mismatched adenine is followed by preferential insertion of a cytosine leading to the formation of 8oxoG/C pairs which are then corrected by OGG1-mediated BER. Both repair events are inhibited by aphidicolin, suggesting that a replicative DNA polymerase is involved in the repair synthesis step. We propose that Pol delta/epsilon-mediated BER (long-patch BER) is the mode of repair when lesions persist or are formed at replication. Finally, we address the issues of the relative contribution of the two BER pathways to oxidative damage repair in vivo and the possible role of BER gene variants as cancer susceptibility genes.

The base excision repair: mechanisms and its relevance for cancer susceptibility.

Base damage or loss occurs at high frequency in the cells (almost 10(4) bases are damaged and hydrolysed per cell per day). DNA repair is fundamental to maintain genomic integrity. Base excision repair (BER) is the main mechanism by which cells correct various types of damaged DNA bases generated either by endogenous or exogenous factors. The widely accepted model for BER mechanism involves five sequential reactions: (i) base removal; (ii) incision of the resulting abasic site; (iii) processing of the generated termini at the strand break; (iv) DNA synthesis, and (v) ligation. In this review, we will briefly summarise the biochemistry of each BER step and will concentrate on the biological relevance of BER as inferred from in vitro and in vivo studies. This information will be the basis for speculation on the potential role of malfunction of BER in human pathology.

The mechanism of switching among multiple BER pathways.

To preserve genomic beta DNA from common endogenous and exogenous base and sugar damage, cells are provided with multiple base excision repair (BER) pathways: the DNA polymerase (Pol) beta-dependent single nucleotide BER and the long-patch (2-10 nt) BER that requires PCNA. It is a challenge to identify the factors that govern the mechanism of switching among these pathways. One of these factors is the type of DNA damage induced in DNA. By using different model lesions we have shown that base damages (like hypoxanthine and 1, N6-ethenoadenine) excised by monofunctional DNA glycosylases are repaired via both single-nucleotide and long-patch BER, while lesions repaired by a bifunctional DNA glycosylase (like 7,8-dihydro-8-oxoguanine) are repaired mainly by single-nucleotide BER. The presence of a genuine 5' nucleotide, as in the case of cleavage by a bifunctional DNA glycosylase-beta lyase, would then minimize the strand displacement events. Another key factor in the selection of the BER branch is the relative level of cellular polymerases. While wild-type embryonic mouse fibroblast cell lines repair abasic sites predominantly via single-nucleotide replacement reactions (80% of the repair events), cells homozygous for a deletion in the Pol beta gene repair these lesions exclusively via long-patch BER. Following treatment with methylmethane sulfonate, these mutant cells accumulate DNA single-strand breaks in their genome in keeping with the fact that repair induced by monofunctional alkylating agents goes predominantly via single-nucleotide BER. Since the long-patch BER is strongly stimulated by PCNA, the cellular content of this cell-cycle regulated factor is also extremely effective in driving the repair reaction to either BER branch. These findings raise the interesting possibility that different BER pathways might be acting as a function of the cell cycle stage.

First search for gravitational wave bursts with a network of detectors

We report the initial results from a search for bursts of gravitational radiation by a network of five cryogenic resonant detectors during 1997 and 1998. This is the first significant search with more than two detectors observing simultaneously. No gravitational wave burst was detected. The false alarm rate was lower than 1 per 10(4) yr when three or more detectors were operating simultaneously. The typical threshold was H approximately 4x10(-21) Hz-1 on the Fourier component at approximately 10(3) Hz of the gravitational wave strain amplitude. New upper limits for amplitude and rate of gravitational wave bursts have been set.

DNA polymerase beta is required for efficient DNA strand break repair induced by methyl methanesulfonate but not by hydrogen peroxide.

The most frequent DNA lesions in mammalian genomes are removed by the base excision repair (BER) via multiple pathways that involve the replacement of one or more nucleotides at the lesion site. The biological consequences of a BER defect are at present largely unknown. We report here that mouse cells defective in the main BER DNA polymerase beta (Pol beta) display a decreased rate of DNA single-strand breaks (ssb) rejoining after methyl methanesulfonate damage when compared with wild-type cells. In contrast, Pol beta seems to be dispensable for hydrogen peroxide-induced DNA ssb repair, which is equally efficient in normal and defective cells. By using an in vitro repair assay on single abasic site-containing circular duplex molecules, we show that the long-patch BER is the predominant repair route in Pol beta-null cell extract. Our results strongly suggest that the Pol beta-mediated single nucleotide BER is the favorite pathway for repair of N-methylpurines while oxidation-induced ssb, likely arising from oxidized abasic sites, are the substrate for long-patch BER.

The type of DNA glycosylase determines the base excision repair pathway in mammalian cells.

The base excision repair (BER) of modified nucleotides is initiated by damage-specific DNA glycosylases. The repair of the resulting apurinic/apyrimidinic site involves the replacement of either a single nucleotide (short patch BER) or of several nucleotides (long patch BER). The mechanism that controls the selection of either BER pathway is unknown. We tested the hypothesis that the type of base damage present on DNA, by determining the specific DNA glycosylase in charge of its excision, drives the repair of the resulting abasic site intermediate to either BER branch. In mammalian cells hypoxanthine (HX) and 1,N6-ethenoadenine (epsilonA) are both substrates for the monofunctional 3-methyladenine DNA glycosylase, the ANPG protein, whereas 7,8-dihydro-8-oxoguanine (8-oxoG) is removed by the bifunctional DNA glycosylase/beta-lyase 8-oxoG-DNA gly- cosylase (OGG1). Circular plasmid molecules containing a single HX, epsilonA, or 8-oxoG were constructed. In vitro repair assays with HeLa cell extracts revealed that HX and epsilonA are repaired via both short and long patch BER, whereas 8-oxoG is repaired mainly via the short patch pathway. The preferential repair of 8-oxoG by short patch BER was confirmed by the low efficiency of repair of this lesion by DNA polymerase beta-deficient mouse cells as compared with their wild-type counterpart. These data fit into a model where the intrinsic properties of the DNA glycosylase that recognizes the lesion selects the branch of BER that will restore the intact DNA template.

Mammalian base excision repair by DNA polymerases delta and epsilon.

Two distinct pathways for completion of base excision repair (BER) have been discovered in eukaryotes: the DNA polymerase beta (Pol beta)-dependent short-patch pathway that involves the replacement of a single nucleotide and the long-patch pathway that entails the resynthesis of 2-6 nucleotides and requires PCNA. We have used cell extracts from Pol beta-deleted mouse fibroblasts to separate subfractions containing either Pol delta or Pol epsilon. These fractions were then tested for their ability to perform both short- and long-patch BER in an in vitro repair assay, using a circular DNA template, containing a single abasic site at a defined position. Remarkably, both Pol delta and Pol epsilon were able to replace a single nucleotide at the lesion site, but the repair reaction is delayed compared to single nucleotide replacement by Pol beta. Furthermore, our observations indicated, that either Pol delta and/or Pol epsilon participate in the long-patch BER. PCNA and RF-C, but not RP-A are required for this process. Our data show for the first time that Pol delta and/or Pol epsilon are directly involved in the long-patch BER of abasic sites and might function as back-up system for Pol beta in one-gap filling reactions.

Different DNA polymerases are involved in the short- and long-patch base excision repair in mammalian cells.

Mammalian cells possess two distinct pathways for completion of base excision repair (BER): the DNA polymerase beta (Pol beta)-dependent short-patch pathway (replacement of one nucleotide), which is the main route, and the long-patch pathway (resynthesis of 2-6 nucleotides), which is PCNA-dependent. To address the issue of how these two pathways share their role in BER the ability of Pol beta-defective mammalian cell extracts to repair a single abasic site constructed in a circular duplex plasmid molecule was tested in a standard in vitro repair reaction. Pol beta-deficient extracts were able to perform both BER pathways. However, in the case of the short-patch BER, the repair kinetics was significantly slower than with Pol beta-proficient extracts, while the efficiency of the long-patch synthesis was unaffected by the loss of Pol beta. The repair synthesis was fully dependent on PCNA for the replacement of long patches. These data give the first evidence that in cell extracts DNA polymerases other than Pol beta are specifically involved in the long-patch BER. These DNA polymerases are also able to perform short-patch BER in the absence of PCNA, although less efficiently than Pol beta. These findings lead to a novel model whereby the two BER pathways are characterized by different protein requirements, and a functional redundancy at the level of DNA polymerases provides cells with backup systems.

Two pathways for base excision repair in mammalian cells.

Abasic sites (apurinic/apyrimidinic, AP sites) are the most common DNA lesions generated by both spontaneous and induced base loss. In a previous study we have shown that circular plasmid molecules containing multiple AP sites are efficiently repaired by Chinese hamster extracts in an in vitro repair assay. An average patch size of 6.6 nucleotides for a single AP site was calculated. To define the exact repair patch, a circular DNA duplex with a single AP site was constructed. The repair synthesis carried out by hamster and human cell extracts was characterized by restriction endonuclease analysis of the area containing the lesion. The results indicate that, besides the repair events involving the incorporation of a single nucleotide at the lesion site, repair synthesis occurred also 3' to the AP site and involved a repair patch of approximately 7 nucleotides. This alternative repair pathway was completely inhibited by the presence in the repair reaction of a polyclonal antibody raised against human proliferating cell nuclear antigen. These data give the first evidence that mammalian cell extracts repair natural AP sites by two distinct pathways: a single nucleotide gap filling reaction targeted at the AP site and a proliferating cell nuclear antigen-dependent pathway that removes a short oligonucleotide containing the abasic site and 3'-flanking nucleotides.

Analysis of DNA alkylation damage and repair in mammalian cells by the comet assay.

The single cell gel electrophoresis (SCGE) or comet assay, which measures DNA strand breaks in individual cells, was used to analyse DNA damage and repair induced by the SN1-type alkylating carcinogens N-ethyl-N'-nitro-N-nitrosoguanidine and N-ethyl-N-nitrosourea in CHO cells. The comet assay was comparable in sensitivity to the alkaline elution assay. The alkyl-adducts detected as DNA single-strand breaks (ssb) by this technique were completely repaired within 24 h after treatment. These data indicate that long-lived lesions, such as alkylphosphotriesters, are not converted into ssb under the standard SCGE alkaline conditions (pH 13.5). The lesions revealed by the comet assay are mainly apurinic/apyrimidinic (AP) sites and breaks formed as intermediates in the base excision repair process of N-alkylpurines. When SCGE was performed at pH 12.5 instead of pH 13.5 a lower level of ssb was detected and these breaks were completely resealed within 2 h after treatment. These data suggest that different subsets of lesions are detected under different pH conditions. The SCGE combined with inclusion within the cells of endonuclease III revealed that a high portion of AP sites induced by alkylation damage were not converted into ssb by alkali. The level of endonuclease III-sensitive sites decreased as a function of the repair time and by 24 h after treatment no sites were left on the DNA. The use of this modified SCGE assay allows the estimation of the total amount of unrepaired AP sites present on DNA. Alkylation-induced ssb as detected by the comet assay should be regarded as an indicator of repair rate and balance more than a measure of actual DNA damage.

Repair of abasic sites by mammalian cell extracts.

Hamster cell extracts that perform repair synthesis on covalently closed circular DNA containing pyrimidine dimers, were used to study the repair of apurinic/apyrimidinic (AP) sites and methoxyamine (MX)-modified AP sites. Plasmid molecules were heat-treated at pH 5 and incubated with MX when required. The amount of damage introduced ranged from 0.2 to 0.9 AP sites/kb. Extracts were prepared from the Chinese hamster ovary CHO-9 cell line and from its derivative, 43-3B clone which is mutated in the nucleotide excision repair (NER) ERCC1 gene. AP and MX-AP sites stimulated repair synthesis by CHO-9 cell extracts. The level of synthesis correlated with the number of lesions and was of similar magnitude to the repair stimulated by 4.3 u.v. photoproducts/kb. Repair of AP and MX-AP sites was faster than the repair of u.v. damage and was independent of ERCC1 gene product. The high level of repair replication was due to a very efficient and rapid incision of plasmids carrying AP or MX-AP sites, performed by abundant AP endonucleases present in the extract. The calculated average repair patch sizes were: 7 nucleotides per AP site; 10 nucleotides per MX-AP site; 28 nucleotides per (6-4) u.v. photoproduct or cyclobutane pyrimidine dimer. The data indicate that AP and MX-AP sites are very efficiently repaired by base-excision repair in mammalian cells and suggest that MX-AP sites may also be processed via alternative repair mechanisms.

Molecular analysis of mutations induced by chemical carcinogens in mammalian cells. I. The use of selectable gene loci.

Several lines of evidence indicate the important role of mutation in the process of carcinogenesis, however our understanding of the factors that influence the formation of mutation is still limited. Recent developments in the analysis of gene mutations at selectable loci in cultured mammalian cells has allowed to accumulate a significant amount of information on the type and distribution of mutations induced by a variety of chemical and physical agents. The purpose of this review is to summarize the data relative to chemical carcinogens and to discuss how their mechanism of interaction with DNA and the repair processes active on the induced lesions affect mutational spectra.