miRò: a miRNA knowledge base.

miRò is a web-based knowledge base that provides users with miRNA-phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities. The main goal of miRò is the establishment of a knowledge base which allows non-trivial analysis through sophisticated mining techniques and the introduction of a new layer of associations between genes and phenotypes inferred based on miRNAs annotations. Furthermore, a specificity function applied to validated data highlights the most significant associations. The miRò web site is available at: http://ferrolab.dmi.unict.it/miro.Database URL:http://ferrolab.dmi.unict.it/miro.

DNA fingerprinting analysis by a PCR based method for monitoring the genotoxic effects of heavy metals pollution.

Environmental pollutants can have deleterious effects on living organisms. At high concentrations, or at high activities, they can cause acute toxicity damaging cells, tissues and organs. Chronic toxification, on the other hand, can also cause serious damage from bio-accumulation. Plants, as biological indicators, can measure both the actual and the potential effects of pollutants, when they are used to measure effects of heavy metals. We have applied a system of "molecular fingerprinting" based on PCR (RAPD: Random Amplified Polymorphic DNA) to the evaluation of the genotoxic effects of heavy metals in order to estimate the environmental risk connected with their potential mutagenic effects in the model plant Arabidopsis thaliana, ecotype Columbia. Genomic DNA was utilised for RAPD analysis using random primers (10-mers). DNA from plants exposed to heavy metals solution displayed polymorphic bands which were not detectable in DNA of unexposed plants. The enhanced formation of RAPD polymorphisms was also observed in DNA of plant exposed in situ to an industrial pollution source. The comparison between "unexposed" and "exposed" genomes show that RAPD analysis can be used to evaluate how the environmental pollutants modify the structure of DNA in living organisms.

FOG1 and FOG2 genes, required for the transcriptional activation of glucose-repressible genes of Kluyveromyces lactis, are homologous to GAL83 and SNF1 of saccharomyces cerevisiae.

The fog1 and fog2 mutants of the yeast Kluyveromyces lactis were identified by inability to grow on a number of both fermentable and non-fermentable carbon sources. Genetic and physiological evidences suggest a role for FOG1 and FOG2 in the regulation of glucose-repressible gene expression in response to a glucose limitation. The regulatory effect appears to be at the transcriptional level, at least for beta-galactosidase. Both genes have been cloned by complementation and sequenced. FOG1 is a unique gene homologous to GAL83, SIP1 and SIP2, a family of regulatory genes affecting glucose repression of the GAL system in Saccharomyces cerevisiae. However, major differences exist between fog1 and gal83 mutants. FOG2 is structurally and functionally homologous to SNF1 of S. cerevisiae and shares with SNF1 a role also in sporulation.

Factors related to drug consumption during pregnancy.

A survey on drug intake during pregnancy was carried out in a sample of 3268 women who delivered live-born infants in 11 hospitals located throughout Italy. A large questionnaire on drug use and other aspects of maternal life-style was administered within five days of delivery to 3112 women who consented to the interview. An overall mean consumption of 2.17 drugs per woman was reported. Apart from dietary supplements, the most used drugs were tocolytics, analgesics, and antibiotics. The proportion of women who did not use any drug was 17.3%. The role of some non-medical determinants of drug intake was evaluated as well. Geographic and socio-economic factors were seen to increase drug intake up to 44%, while the presence of anxiety provoked a 60% higher consumption of drugs other than dietary supplements. Other factors influencing drug use during pregnancy were rural vs. urban residence and smoking habits. The need for the recording of these socio-economic factors in surveys on drug use during pregnancy is emphasized.

[Effects of moderate maternal drinking on some neonatal parameters]. / Effetti di un moderato consumo di alcol in gravidanza su alcuni parametri neonatali.

A cross-sectional study was conducted on 2415 mother/newborn pairs, in order to evaluate the relationship between maternal alcohol consumption and birth weight. The results of this study are consistent with previous reports, that pointed out the casual relationship between maternal drinking during pregnancy, and reduction in birth weight. This reduction was evident only on the subset of smokers. A further stratification by the sex of newborn, showed a heavier effect on male newborns, who experienced a significant reduction of 6.2 grams in birth weight for each g of absolute alcohol consumed daily during pregnancy by mother. The findings of this study support the evidence of neonatal functional damages due to alcohol, even at very low doses. A strong increase of early jaundice were found among the outcome of exposed women (OD = 3.30; 95% CI 1.03-10.54).

Allelism of IMP1 and GAL2 genes of Saccharomyces cerevisiae.

Cloning and characterization of the previously described Saccharomyces cerevisiae IMP1 gene, which was assumed to be a nuclear determinant involved in the nucleomitochondrial control of the utilization of galactose, demonstrate allelism to the GAL2 gene. Galactose metabolism does not necessarily involve the induction of the specific transport system coded by GAL2/IMP1, because a null mutant takes up galactose and grows on it. Data on galactose uptake are presented, and the dependence on ATP for constitutive and inducible galactose transport is discussed. These results can account for the inability of imp1/gal2 mutants to grow on galactose in a respiration-deficient background. Under these conditions, uptake was affected at the functional level but not at the biosynthetic level.

IMP2, a nuclear gene controlling the mitochondrial dependence of galactose, maltose and raffinose utilization in Saccharomyces cerevisiae.

The IMP2 gene of Saccharomyces cerevisiae is involved in the nucleo-mitochondrial control of maltose, galactose and raffinose utilization as shown by the inability of imp2 mutants to grow on these carbon sources in respiratory-deficient conditions or in the presence of ethidium bromide and erythromycin. The negative phenotype cannot be scored in the presence of inhibitors of respiration and oxidative phosphorylation, indicating that the role of the mitochondria in the utilization of the above-mentioned carbon sources in imp2 mutants is not at the energetical level. Mutations in the IMP2 gene also confer many phenotypic alterations in respiratory-sufficient conditions, e.g. leaky phenotype on oxidizable carbon sources, sensitivity to heat shock and sporulation deficiency. The IMP2 gene has been cloned, sequenced and disrupted. The phenotype of null imp2 mutants is indistinguishable from that of the originally isolated mutant.

Germination of Saccharomyces cerevisiae ascospores without trehalose mobilization as revealed by in vivo 13C nuclear magnetic resonance spectroscopy.

Saccharomyces cerevisiae ascospores germinate in the presence of acetate without any detectable trehalose degradation, as revealed by high-resolution nuclear magnetic resonance spectroscopy and by a standard colorimetric assay. The results presented here substantiate the hypothesis that in S. cerevisiae trehalose supplies energy during dormancy of the spores and not during the germination process.

The respiratory activities of four Hansenula species.

The respiratory activities and the cytochrome spectra from four species belonging to the genus Hansenula have been analysed. The results obtained and described in this paper show that H. glucozyma possesses only the primary, antimycin A-sensitive respiration, H. anomala and H. californica possess primary and secondary (salicylhydroxamate-sensitive) respirations, whereas H. saturnus possesses three respiratory activities (AA-sensitive, SHAM-sensitive, and AA + SHAM-insensitive). The respiratory activity of H. glucozyma is glucose-repressible, whereas the activities of the other species are not. In addition, antimycin A (AA) and erythromycin (ERY) in the culture media differently inhibit the growth of the four species and regulate the respiratory pathways in the species analysed.

Relationship between growth inhibition and mitochondrial function in petite-negative yeasts. I. Effects of antibiotics and dyes upon pathogenic and non-pathogenic Candida species.

Antibiotics and dyes which preclude growth of Saccharomyces cerevisiae in media containing oxidizable carbon sources arrested the growth of Candida albicans, Candida tropicalis and Candida utilis even in glucose medium. The growth in the presence of sub-inhibitory concentrations of the various antibiotics and dyes determined a reduction in the cell survival but with no accumulation of respiratory deficient mutants. Under these culture conditions, the total respiration declined leaving a residual antimycin A-resistant--hydroxamate-sensitive O2 uptake, and the amount of the respiratory cytochromes aa3 and b synthesized was reduced. SDS gel electrophoresis of soluble proteins prepared from the antibiotic-treated cells showed some bands in the MW range 92-100 K, which became faint after the cells were grown in the presence of some mitochondrial inhibitors. The ultrastructural analysis of these cells evidenced disappearance of the mitochondrial cristae and their replacement by unfolded membranes. The data obtained suggest that the petite negative trait of Candida could depend on the non-viability or on the very low viability of those cells which have lost their mitochondrial function.

Relationship between growth inhibition and mitochondrial function in petite-negative yeasts. II. Effects of central nervous system drugs upon pathogenic and non-pathogenic Candida species.

Six nervous system drugs which inhibited vegetative reproduction of S. cerevisiae arrested also mitotic division of C. utilis, C. albicans and C. tropicalis. Chlorpromazine and chlorpheniramine which proved to be the most effective, affected respiration and cytochrome biosynthesis. Electrophoretic bands with MW congruent to 100 K were faint in silver-stained electrophoregrams of proteins from cells grown in the presence of a sub-inhibitory concentration of chlorpromazine.

ALG/alg: a single gene controlling the utilization of lactate in the presence of antimycin in the yeast Saccharomyces cerevisiae.

A strain dependent growth on lactate in the presence of antimycin A (AA) has been observed - the strain D261 can grow on lactate and AA, whereas in the strain K8/6C antimycin A prevents the utilization of lactate and the induction of LDH.Genetic analysis demonstrates that growth on lactate in the presence of AA segregates from D261 as a single nuclear factor which we indicate by ALG1 and alg1 in its dominant and recessive states. alg1 complements the gene(s) which give(s) rise to the same phenotype in K8/6C.The analysis of the regulation by lactate of LDH in the absence and presence of AA and in rho (-) cells shows that growth on lactate and antimycin A is not corretated with the induction by lactate of LDH.

Involvement of mitochondrial protein synthesis in sporulation: effects of erythromycin on macromolecular synthesis, meiosis, and ascospore formation in Saccharomyces cerevisiae.

Cells of strain Z270 (MAT alpha/MAT alpha) of Saccharomyces cerevisiae did not undergo ascospore formation in buffered or unbuffered acetate sporulation medium in the presence of erythromycin. The drug inhibited sporulation when added within the first 6 to 8 h and affected to different extents some of the metabolic and sporulation-specific events that normally occur during this period. In sporulation medium, protein synthesis was highly sensitive to erythromycin, whereas RNA synthesis was unaffected and premeiotic DNA synthesis was partially inhibited. Intragenic recombination occurred at normal rates for the various heteroallelic loci tested, but rates of intergenic recombination were markedly reduced, and commitment to haploidization did not occur; hence, development was evidently arrested between intragenic and intergenic recombination. Cells kept for 8 h in acetate sporulation medium that were ready for sporulation in water without erythromycin failed to sporulate in water containing the drug, indicating that erythromycin can inhibit sporulation independent of acetate utilization.

The role of the nuclear gene "mitochondrial mutability control" (MMC1) in the process of mutability of the mitochondrial genome by different mutagens in Saccharomyces cerevisiae.

The accumulation of respiratory deficient (RD) mutants in Saccharomyces cerevisiae depended upon the mutagens used and upon the presence of the nuclear gene previously identified as MMC1 (one) which we showed to control the spontaneous and the erythromycin-induced RD mutability. In this paper data are reported about the accumulation of RD mutants in the presence of manganous ions (Mn++) and UV which was higher in the mmc1 (one) than in MMC1 strains. We found that the characters 'low spontaneous' and 'low induced' RD mutability by erythromycin, manganous ions and UV, were controlled by the same genetic determinant. In the presence of manganous ions, also the frequency of antibiotic resistant mutants capR and eryR was higher in the mmc1 strains. Moreover, the accumulation of RD mutants in the presence of berenil, 5-fluorouracil and basic fuchsin was higher in the mmc1 than in MMC1 strains. In contrast, RD mutants accumulation by acriflavine and ethidium bromide treatments did not appear affected by the MMC1 genetic constitution.

Computer-assisted karyotyping system of banded chromosomes.

The banding automatic system (BAS) we describe in this paper is a computer-assisted karyotyping system suitable for the analysis of both normal and abnormal karyotypes in banded chromosome specimens. In the BAS system recognition of the various features and constituents of the chromosomes is performed by an operator, whereas chromosome identification and classification are entrusted to a computer. The connection between operator and computer is the CYGEN1 program, which is tailored to distinguish chromosome morphology on the basis of the operator input band patterns alone. The karyotyping operation is therefore significantly speeded up: the operator simply has to read through a certain number of banded metaphases, encoding band-pattern data to the computer. The machine signals when the operation has gone through the whole karyotype or, for instance, when chromosomes are missing or present in extra number above the significance level from the analyzed metaphases. Chromosome identification and classification are then carried out by the computer, which performs as a real-time recognizing key. Moreover, the data being accumulated in the computer will provide a file of cytogenetic records accessible to the operator, as well as to the computer, for further diagnostic operations. The efficacy of the BAS system is demonstrated for the diagnosis of various structural aberrations, including a complex translocation. The processing of 20 metaphases by the method described takes 40-45 min, and a cytogenetic technician can make effective use of the system after 25-30 h of intensive training.

Effect of chloramphenicol, antimycin A and hydroxamate on the morphogenetic development of the dimorphic ascomycete Endomycopsis capsularis.

Mitochondrial protein synthesis, primary (antimycin-sensitive) respiration and secondary (antimycin-insensitive, salicyl-hydroxamate-sensitive) respiration, have been characterized in the dimorphic yeast Endomycopsis capsularis. The inhibition by chloramphenicol (CAP) of the morphogenetic development from the yeast-like form to the mycelial structure in this yeast could represent the intervention in the morphogenetic process of mitochondrial protein synthesis, since chloramphenicol blocks in vivo and in vitro mitochondrial protein synthesis. In fact, other functions such as primary and secondary respiration, do not seem to play a role in the morphogenetic development since their inhibition by antimycin A (AA) or by salicyl-hydroxamic acid (SHAM) does not affect the process. In addition, mitochondrial protein synthesis has been shown to be uninhibited by the two respiratory inhibitors.

IMP1/imp1: a gene involved in the nucleo-mitochondrial control of galactose fermentation in Saccharomyces cerevisiae.

In some strains of Saccharomyces cerevisiae, the induction of enzymes of the Leloir pathway, galactose fermentation and growth on galactose depend on mitochondrial function; mitochondrial dependence is elicited through the recessive allele imp1 of the nuclear gene IMP1. The genetic element IMP1 is not allelic to any of the known GAL genes; IMP1 strains can grow on and ferment galactose in respiratory-deficient (RD) condition or in the presence of the mitochondrial inhibitors ethidium bromide and erythromycin; whereas, imp1 strains can grow on and ferment galactose only in respiratory-sufficient (RS) condition. The imp1 elicited mitochondrial dependence apparently involves regulation of the synthesis of the galactose catabolizing enzymes and synthesis of the galactose specific permease. IMP1 is not the only genetic determinant that elicits an interaction of the mitochondrion and the expression of the Gal system; the GAL3 gene, whose role in galactose utilization is demonstrated by the long-term adaptation phenotype of gal3 rS mutants, gives rise to a noninducible phenotype in RD condition or in the presence of mitochondrial inhibitors.

Erythromycin and cycloheximide sensitivities of protein and RNA Synthesis in sporulating cells of Saccharomyces cerevisiae: Environmentally induced modifications controlled by chromosomal and mitochondrial genes.

The purpose of the experiments reported below was to examine the response in sporulation medium of the three diploid cell types MATα MATα, MATα MATα (asporogenic diploids) and MATα MATα (sporogenic diploid) to erythromycin, a specific inhibitor of mitochondrial protein synthesis (MPS) in vegetative cultures, and cycloheximide, a specific inhibitor of cytosol protein synthesis (CPS) in vegetative cultures. When MATα MATα diploids are transferred to sporulation medium a significant fraction of total protein synthesis (CPS + MPS) becomes sensitive to erythromycin in contrast to the behavior of MATa MATa and MATα MATα diploids in which the resistance of CPS to erythromycin is maintained. The decompartmentalization of erythromycin sensitivity is thus cell type specific. Erythromycin stimulates total RNA synthesis of MATα MATα cells in sporulation medium but not of MATα MATα and MATα MATα cells. Cycloheximide inhibits protein synthesis and stimulates RNA synthesis in all three diploid cell types. An erythromycin resistant mutant, shown to be due to a mutation of the mitochondrial genome, exhibited only partial resistance of CPS to erythromycin in sporulation medium in the background of the MATα MATα mating type genotype. Total RNA synthesis in this mutant was not stimulated. The results reported indicate that mitochondrial functions during sporulation are not restricted to those involving respiratory metabolism.