The effect of chronic alcohol consumption on mitochondrial DNA mutagenesis in human blood

The 4977bp deletion of mitochondrial DNA (mtDNA) is known to accumulate with increasing age in post mitotic tissues. Recently, studies came out detecting this specific alteration also in fast replicating cells, e.g. in blood or skin tissue, often in correlation to specific diseases or -- specifically in skin -- external stressors such as UV radiation. In this study, we investigated mitochondrial mutagenesis in 69 patients with a chronic alcoholic disease and 46 age matched controls with a moderate drinking behavior. Two different fragments, specific for total and for deleted mtDNA (dmtDNA) were amplified in a duplex-PCR. A subsequent fragment analysis was performed and for relative quantification, the quotient of the peak areas of amplification products specific for deleted and total mtDNA was determined. Additionally, a real time PCR was performed to quantify mtDNA copy number. The relative amount of 4977bp deleted mtDNA in alcoholics was significantly increased compared to controls. On the other hand, no difference regarding the mtDNA/nuclear DNA ratio in both investigated groups was detected. Additionally, no age dependence could be found nor in alcoholics, neither in the control group. These findings indicate that mtDNA mutagenesis in blood can be influenced by stressors such as alcohol. Ethanol seems to be a significant factor to alter mitochondrial DNA in blood and might be an additional contributor for the cellular aging process.     

Cloning and structural analyses of hepatitis B virus DNAs, subtype adr.

Entire genomes of hepatitis B virus (subtype adr) have been cloned. The nucleotide sequence data were compared with other sequences of HBV genome including: adw [Valenzuela et al. (1981) in Animal Virus Genetics. Fields et al. eds. Academic Press, Inc., NY. pp. 57-70], ayw [Galibert et al. (1979) Nature, 281, 646-650], and adyw [Pasek et al. (1979) Nature 282, 575-579]. Four open coding frames for polypeptides larger than 6,000 dalton were found to be conserved and were highly compressed by overlapping with each other in one strand (L-strand). Sites of initiation of the S gene and termination of the P gene were not conserved. No conserved coding frame was found on the opposite strand (S strand). Amino acid sequences of six surface antigen (HBsAg) peptides, including subtypes adr, adw, and ayw, are deduced from the DNA sequences, and the substitution of amino acid residues which are consistent with the change of subtypes are demonstrated.     

DNA Isolation and Amplification from Cacti

The cacti family is a morphologically heterogeneous group comprising 100 genera and about 1500 species (Hernandez and Barcenas, 1996). With the exception of one genus, all members of this family are native to America (Hernandez and Barcenas, 1996). There are three subfamilies, Opuntioideae, Cactoideae, and Pereskioideae (Gibson and Nobel, 1986). DNA isolation from cacti is notoriously difficult because they contain high amounts of polysaccharides and secondary metabolites which form insoluble complexes with nucleic acids during extraction (Guillemaut and Marechal-Drouard, 1992). Like in other groups of plants, the secondary metabolites and polysaccharides in cacti inhibit enzyme action (Porebski et al., 1997). The polysaccharides are visually evident by their viscous, glue-like texture and they make the DNA unmanageable when pipeting and hard to amplify by the polymerase chain reaction (PCR) (Poresbski et al., 1997). We report an easy and inexpensive protocol to isolate DNA from cacti. We used this method to isolate DNA from 85 species (170 individuals) of 39 genera of the subfamilies Pereskioideae, Opuntioidea, and Cactoideae. This procedure is a modification of a protocol described by De la Cruz et al. (1995) for the Cacti family. It requires only a few grams of tissue and does not require destruction of the whole plant to produce high molecular weight genomic DNA. The DNA from this procedure can be amplified consistently by PCR and used for RAPD analysis.     

Global DNA promoter methylation in frontal cortex of alcoholics and controls

To determine if ethanol consumption and alcoholism cause global DNA methylation disturbances, we examined alcoholics and controls using methylation specific microarrays to detect all annotated gene and non-coding microRNA promoters and their CpG islands. DNA was isolated and immunoprecipitated from the frontal cortex of 10 alcoholics and 10 age and gender-matched controls then labeled prior to co-hybridization. A modified Kolmogorov–Smirnov test was used to predict differentially enriched regions (peaks) from log-ratio estimates of amplified vs input DNA. More than 180,000 targets were identified for each subject which correlated with > 30,000 distinct, integrated peaks or high probability methylation loci. Peaks were mapped to regions near 17,810 separate annotated genes per subject representing hypothetical methylation targets. No global methylation differences were observed between the two subject groups with 80% genetic overlap, but extreme methylation was observed in both groups at specific loci corresponding with known methylated genes (e.g., H19) and potentially other genes of unknown methylation status. Methylation density patterns targeting CpG islands visually correlated with recognized chromosome banding. Our study provides insight into global epigenetic regulation in the human brain in relationship to controls and potentially novel targets for hypothesis generation and follow-up studies of alcoholism.     

四种绒螯蟹分子分类与系统发育

利用PCR技术,扩增了中华绒螯解、狭额绒螯蟹线粒体16SrDNA片段,经测序,与GenBank数据库中的日本绒螯解16SrDNA同源序列进行比较。结果显示,在长为376bp的16SrDNA同源序列中有33个多态性核革酸位点（8．78％）,其中种间多态性核苷酸位点28个（7．45％）,种间差异远大于种内差异。引入方蟹科其它近缘种类厚纹蟹、相手蟹和张口蟹的16SrDNA同源序列与上述4种绒螯蟹比较分析,MP法和NJ法构建的分子系统树表明：中华绒螯蟹与日本绒螯蟹亲缘关系最近,首先聚在一起,然后与台湾绒螯蟹聚为一支,狭额绒螯蟹则为相对独立的一支,且进化速度大于前3种绒螯蟹,但最后与前者仍聚在同一组,狭额绒螯蟹只是绒螯蟹属系统进化中的一个侧支,故本研究结果不支持Sakai（1983）和Guo等（1997）把狭额绒螯蟹和台湾绒螯蟹各自立为新属的观点。     

Sequence analysis of exon 8 of MAO-A gene in alcoholics with antisocial personality and normal controls

Brunner et al. (1993, Science 262, 578-580) reported a family in which several males were affected by a syndrome of borderline mental retardation and abnormal behavior. Sequencing of exon 8 of the MAO-A gene revealed a mutation that results in a termination codon and was associated with the syndrome in the family. To determine the possible role of any mutation in exon 8 of the MAO-A gene in susceptibility to alcoholism associated with antisocial personality (ASP), we sequenced genomic DNA from 50 alcoholics and 50 normal controls. We detected only the point mutation at the position 941 (T --> G). Additional samples of alcoholics and normal controls were also screened for this mutation and the mutation in exon 14 by PCR assays. Comparison of alcoholics with ASP to normal controls for both mutation frequencies in exons 8 and 14 was positive. However, the haplotype frequency differences in the above groups were borderline significant. The most common haplotype between these mutations and a (CA)n repeat marker in the gene was F1E,C6. The frequency differences between alcoholics with ASP and normal controls for this haplotype were significant (P = 0.033). In TDT analysis, comparison of the overall haplotypes, transmitted to nontransmitted, was borderline significant. These data indicate that mutations in the MAO-A gene may play a role in the development of alcoholism associated with ASP.     

An IS4 transposition causes a 13-bp duplication of phage lambda DNA and results in the constitutive expression of the cI and cro gene products

We have examined the nature of the additional DNA present in lambda hyp- mutants (Eisen et al., 1982). This DNA is an IS4 element in orientation I, in the y region of bacteriophage lambda at nucleotide position 39,139 (see Moore et al., 1979). Our assignment is based on (i) the similarity in size derived from the PstI, AvaI, and HindII restriction pattern and (ii) the DNA sequence of both the left and right lambda-IS4 DNA junctions in phage lambda hyp15rev4. The IS4 integration event resulted in the duplication of 13 bp of lambda DNA in contrast to the 11- and 12-bp duplications previously observed at the sites of IS4 integrations elsewhere (Klaer et al., 1981).     

Physical mapping of the factor VIII gene proximal to two polymorphic DNA probes in human chromosome band Xq28: implications for factor VIII gene segregation analysis

Genomic DNA segments for the coagulation factor VIIIc gene (F8C), which exhibits only limited restriction length polymorphism, map to the proximal region of band Xq28 by somatic cell hybridization analysis and in situ hybridization. Using somatic cell hybrids, we have obtained data which place probes DX13 (used to detect locus DXS15) and St14 (used to detect DXS52) distal to F8C, within band Xq28. Previous studies have mapped the factor IX gene (F9) and probe 52A (used to detect DXS51) proximal to F8C, in Xq26----q27 and Xq27, respectively (Camerino et al., 1984; Drayna et al., 1984; Mattei et al., 1985). Thus, the relative order of genetic marker loci in the Xq27----qter region is most likely cen-F9-DXS51-F8C-(DXS15, DXS52)-Xqter. The collection of these molecular probes is thus potentially useful in three-factor crosses of factor VIII gene segregation.     

Modulation of calcium-mediated inactivation of ionic currents by Ca2+/calmodulin-dependent protein kinase II.

Iontophoretic injection of Ca2+ causes reduction of I0A (an early rapidly activating and inactivating K+ current) and I0C (a late Ca2+-dependent K+ current) measured across the isolated type B soma membrane (Alkon et al., 1984, 1985; Alkon and Sakakibara, 1984, 1985). Similarly, voltage-clamp conditions which cause elevation of [Ca2+]i are followed by reduction of I0A and I0C lasting 1-3 min. Iontophoretic injection of highly purified Ca2+/CaM-dependent protein kinase II (CaM kinase II) isolated from brain tissue (Goldenring et al., 1983) enhanced and prolonged this Ca2+-mediated reduction of I0A and I0C. ICa2+, a voltage-dependent Ca2+ current, also showed some persistent reduction under these conditions. Iontophoretic injection of heat-inactivated enzyme had no effect. Agents that inhibit or block Ca2+/CaM-dependent phosphorylation produced increased I0A and I0C amplitudes and prevented the effects of CaM kinase II injection. The results reported here and in other studies implicate Ca2+-stimulated phosphorylation in the regulation of type B soma ionic currents.     

Mechanic stimulation of the soles support zones as a countermeasure of the contractile properties decline under microgravity conditions

Decrease in muscle contractility is an inevitable consequence of exposure in microgravity. A wealth of currently accumulated facts is indicative of profound modifications in structure and function of the skeletal muscles in the absence of gravity. Investigations with humans during space flights of varying duration (L.I. Kakurin et al., 1971; I.B. Kozlovskaya et al., 1984, 1987, 1991;.), ground-based simulation studies (A.M. Genin et al., 1969; L.S. Grigorieva et al., 1983), and numerous experiments with animals (E.I. IIyina-Kakueva et al., 1979; O.M. Edgerton et al 1991; B.S. Shenkman et al., 1994) made it evident that removal of gravitational loading is fraught with significant reductions in the contractile properties of muscular fibers, especially noticeable in muscles-extensors. Results of ground-based simulation studies led to the hypothesis that changes in muscle contractility developing already after few days in microgravity conditions are consequent to reduction in support afferentation that plays an important role in initiation and maintenance of the activity of tonic motor units (A.V. Kirenskaya et al., 1986). In view of the above, an idea has been proposed to prevent losses in tonic muscles contractility by application of artificial support. Testing of this hypothesis was the theme of the present investigation.     

Inhibition of homoserine dehydrogenase I by L-serine in Escherichia coli

We have reported that a major cause of growth inhibition of Escherichia coli by L-serine is its inhibition of homoserine dehydrogenase I (HDH I), which is involved in the biosyntheses of threonine and isoleucine [Hama, H., Sumita, Y., Kakutani, Y., Tsuda, M., & Tsuchiya, T. (1990) Biochem. Biophys. Res. Commun. 168, 1211-1216]. However, Patte et al. reported that L-serine does not inhibit HDH I [Patte, J.-C., Truffa-Bachi, P., & Cohen, G.N. (1966) Biochim. Biophys. Acta 128, 426-439]. In studies on the reason for these discrepant results, we found that the concentration of K+ and the pH in the assay mixture strongly influenced the inhibitory effect of L-serine. L-Serine strongly inhibited the HDH I activities in both the forward and reverse reactions between aspartate semialdehyde and homoserine at a physiological K+ concentration (100 to 200 mM) and physiological pH (7.5) for E. coli cells. On the other hand, two well-known inhibitors of HDH I, L-threonine and L-cysteine, strongly inhibited the activity regardless of the K+ concentration and pH.     

World distribution of the T833C/844INS68 CBS in cis double mutation: a reliable anthropological marker

Mild hyperhomocysteinemia is associated to mutations either in cystathionine beta-synthase (CBS) or in 5,10-methylenetetrahydrofolate reductase (MTHFR) genes. In 1995, Sebastio et al. characterized a 68 bp insertion in cis with the most common CBS mutation (T833C) detected in homocystinuric patients. Recently, this double mutation has been detected in Italian and North-American controls. Compared to a group of patients affected by coronary artery disease, North-American controls showed not statistically significant difference. Moreover, Italian controls displayed a microheterogeneity in the mutant allele frequency distribution depending on their geographical origin (North or South of Italy). Aim of our study was to evaluate the prevalence of the double in cis mutation in different populations. We studied 377 healthy subjects belonging to various human groups. Genomic DNA, extracted from peripheral blood samples, was amplified using specific primers; PCR fragments were digested with Bsr I restriction enzyme to detect the double mutation. Our data show a significant heterogeneity among the populations studied, therefore this mutation turned out to be a reliable anthropogenetic marker. The distribution of the double mutation will contribute, with other DNA polymorphisms, to evaluate the genetic admixture of mixed populations such as Afro-Americans.     

Polymorphism in the 5'-flanking region of the human insulin gene and the incidence of diabetes.

DNA length polymorphism in the 5'-flanking region of the human insulin gene has been reported by Bell et al. (1981), Rotwein et al. (1981), and Owerbach and Nerup (1982). Bgl I digestions of human DNA that have been hybridized to an insulin probe using the Southern technique shows that there are two distinct groups of 5'-flanking lengths: one being shorter than 3.6 kilobases (kb) and the other being longer than 4.3 kb. The insulin genes with the former length are denoted as A1, and those with the latter as A2. Using these data and demographic data of diabetes, it is estimated that, when the fitness of A1 A2 individual was taken as unity, the amounts of fitness reduction for A1 A1 was 6.5 X 10(-6) and that for A2 A2 was -5.6 X 10(-6). Because of these small magnitudes of selection, the changes in population incidences of insulin-dependent diabetes and noninsulin-dependent diabetes are not affected much by the polymorphism in the 5'-flanking region of the insulin gene.     

Molecular analysis of the histone gene cluster of Psammechinus miliaris: II. The arrangement of the five histone-coding and spacer sequences

Histone DNA of Psammechinus miliaris was obtained in an enriched form by buoyant density gradient centrifugation and was cleaved into 6 kb repeat units (Birnstiel et al., 1975a) by the action of the specific endonucleases EcoRI and HindIII. Since it was suspected that the 6 kb unit harbored all five histone-coding sequences, the histone DNA unit was subdivided into five segments with the aim of providing five fragments carrying just one coding sequence each. This was achieved by the combined use of EcoRI HindII, HindIII, and Hpa I. A physical map was constructed from the overlaps arising in these restriction experiments. Each of the five segments was shown to hybridize uniquely with just one of the five highly purified histone mRNAs (Gross et al., 1976a). By this procedure, the order of the mRNA sequences on the histone DNA was found to be a, c, d, b, e (Gross et al., 1976a), and hence of the protein coding sequences H4, H2B, H3, H2A, and H1. Further evidence is presented that the 6 kb repeat unit, amplified by means of a Murray λ vector phage, contains AT-rich DNA sequences which would be expected not to code for histone proteins.     

Comparison of the nucleotide sequences at the 3′-terminal region of RNAs from RNA coliphages

In order to study the genealogical relationships among four groups (I to IV) of RNA coliphages, we sequenced 200 to 260 nucleotides from the 3′ termini of 14 phage RNAs according to the method of Sanger et al. (1977), and compared the results. It was found that the sequences of phage RNAs in the same group were extremely homologous (about 90%). On the other hand, when the sequences were compared with those from other groups, they were seen to be only about 50 to 60% homologous between group I and group II, and about 50% homologous between group III and group IV. In other combinations, such as groups I (or II) and III, and groups I (or II) and IV, however, the extent of homology was small. Furthermore, the sequences up to 30 residues from the 3′ end were found to be about 90% homologous between groups I and II, and between groups III and IV.These results confirm our previous findings, that the sequences located in the proximity of the 3′ end of phage RNA in the same group were well-conserved (Inokuchi et al., 1979), and that close relationships exist between groups I and II, and between groups III and IV (Furuse et al., 1979).     

Purification and DNA-binding properties of the cro-type regulatory repressor protein cng encoded by the Lactobacillus plantarum phage phi g1e

The putative repressor protein Cng (10kDa on an SDS gel) for the lytic pathway of Lactobacillus plantarum phage φg1e was purified using the Escherichia coli Pt7 system, and its DNA-binding ability for the seven operator-like sequences, the GATAC-boxes (Gb1 to Gb7), was investigated in vitro. In gel-shift assays, Cng selectively bound to the DNA fragments containing the GATAC-box(es). In addition, DNase I footprinting analysis with supercoiled DNA demonstrated that Cng can specifically cover about a 25bp region centered around each of the GATAC-boxes, although two boxes, Gb4 and Gb6, were only partially protected. Moreover, protein crosslinking experiments using glutaraldehyde suggested that Cng most likely functions as a dimer. On the other hand, the binding ability of Cpg for the GATAC-boxes in supercoiled DNA was also examined under the same conditions as in Cng; unlike Cng, Cpg covered Gb4 and Gb6 completely sufficiently as well as the other five boxes. Thus, the present and previous [Kakikawa et al., Gene 215 (1998) 371-379; 242 (2000) 155-166] results indicate a possibility that the two proteins Cng and Cpg selectively bind to the GATAC-boxes that act as operators, and can decide between the lytic or lysogenic pathways through repression of the promoter activity of P(R) as well as P(L).     

Analysis of the junctions between human immunodeficiency virus type 1 proviral DNA and human DNA.

Integrated retroviral DNA is flanked by short direct repeats of the target DNA. The length of these repeats is specific for the provirus that is integrated (H.E. Varmus, in J.A. Shapiro, ed., Mobile Genetic Elements, 1983). For the human immunodeficiency virus type I (HIV-1), the length of the direct repeats in the target DNA was shown to be 5 bp in one case (Muesing et al., Nature [London] 313:450-458, 1985) and 7 bp in another (Starcich et al., Science 227:538-540, 1985). One possible explanation for this discrepancy is that the direct repeats flanking HIV-1 proviruses are variable. To investigate this, we analyzed the junctions between HIV-1 proviral DNA and human DNA from nine individual clones. In each clone the provirus was flanked by a 5-bp direct repeat of human DNA. Analysis of the proviral clone previously described as being flanked by a 7-bp direct repeat of target DNA (Starcich et al., op. cit.) revealed that this clone was flanked by a 5-bp repeat instead. Therefore, we conclude that HIV-1 proviruses are flanked by 5-bp direct repeats of human DNA. The sequences of the 5-bp duplications from the different proviral clones do not have any apparent similarity to each other or to HIV-1 DNA.