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Biomedical subjects

N Altamura

Publications and source records attributed to N Altamura.

At least 19 recordsLinked to original sources
PubMed2000

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status.

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbas e.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.

Animals↗
PubMed2000

Coagulation indicators in patients with paroxysmal atrial fibrillation: effects of electric and pharmacologic cardioversion.

The aim of this study was to determine whether paroxysmal atrial fibrillation (PAF) and/or restoration to sinus rhythm with electric or pharmacologic cardioversion induce modifications to the coagulation system. Thirty-five patients with PAF undergoing either electric (n = 11) or pharmacologic (n = 24) cardioversion were studied. Fibrinopeptide A and D-dimer blood samples were taken immediately before and after cardioversion at different intervals. When compared with the control group (n = 70), the precardioversion fibrinopeptide A plasma values were significantly elevated (11.8 vs 2.5 ng/mL). Fibrinopeptide A plasma values were significantly reduced 5 minutes after cardioversion (11.8 vs 5.3 ng/mL) and remained stable throughout the follow-up sequential measurements. D-dimer plasma values were significantly increased (measured at 12 hours and at day 7) in patients who underwent electrical cardioversions only. A positive correlation (R(2) = 0.76) was found between the energy delivered for cardioversion to sinus rhythm and D-dimer plasma values on day 7. In patients with PAF, levels of fibrinopeptide A, an indicator of coagulation activation, are elevated and soon reduced by the restoration of sinus rhythm. Electric, but not pharmacologic, cardioversion induces an early activation of the fibrinolytic system.

Aged↗
PubMed1999

MitBASE: a comprehensive and integrated mitochondrial DNA database.

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects all available information from different organisms and from intraspecie variants and mutants. Research institutions from different countries are involved, each in charge of developing, collecting and annotating data for the organisms they are specialised in. The design of the actual structure of the database and its implementation in a user-friendly format are the care of the European Bioinformatics Institute. The database can be accessed on the Web at the following address: http://www.ebi.ac. uk/htbin/Mitbase/mitbase.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecie diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.

Animals↗
PubMed1999

MitBASE pilot: a database on nuclear genes involved in mitochondrial biogenesis and its regulation in Saccharomyces cerevisiae.

In the framework of the EU BIOTECH PROGRAM and within the 'MITBASE: a comprehensive and integrated database on mtDNA' project, we have prepared a pilot database (MitBASE Pilot) on nuclear genes involved in mitochondrial biogenesis and its regulation in Saccharomyces cerevisiae. MitBASE Pilot includes nuclear genes encoding mitochondrial proteins as well as nuclear genes encoding products which are localised in other sub-cellular compartments but nevertheless interact with mitochondrial functions. Genes have been classified on the basis of the mitochondrial process in which they participate and the mitochondrial phenotype of the gene knockout. The structure of the MitBASE Pilot database has been conceived for a flexible organisation of the information. An intuitive visual query system has been developed which allows users to select information in different combinations, both in the query and the output format, according to their needs. MitBASE Pilot is a relational database, is maintained at the EMBL-European Bioinformatics Institute (EBI) and is available at the World Wide Web site http://www3.ebi.ac. uk/Research/Mitbase/mitbiog.pl

Cell Nucleus↗
PubMed1997

The transcription of NAM7/UPF1 is enhanced in the absence of Cyp1p/Hap1p concomitant with the appearance of an ISF1-NAM7 cotranscript in Saccharomyces cerevisiae.

The two adjacent nuclear genes ISF1 and NAM7 cooperatively participate in mitochondrial functions. It is well known that Cyp1p(Hap1p) activates a number of genes involved in these same functions. We show in this paper that Cyp1p influences the transcriptional regulation of NAM7. In addition, a significant amount of ISF1-NAM7 cotranscript is observed in a cyp1 mutant context. An extensive analysis of the intergenic region which separates the two genes revealed 5' starts of the NAM7 transcripts, additional to those previously mapped. These new 5' starts overlap the 3' ends of ISF1. We propose that NAM7 is under the control of a negative Cyp1p-dependent regulator and that its absence favours a transcriptional read-through which results in the ISF1-NAM7 cotranscript we have identified.

Amino Acid Sequence↗
PubMed1997

Antibiotic and cholestyramine treatment of chronic diarrhea in HIV-infected children.

BACKGROUND: Chronic diarrhea is a common feature in children infected with human immunodeficiency virus (HIV), and is associated with an increased risk of death in these patients. To describe the effects of an empiric treatment on diarrhea and body weight on HIV-infected pediatric patients. PATIENTS: Eleven vertically HIV-infected children with chronic diarrhea were treated with oral gentamicin, metronidazole and cholestyramine for 3 to 5 days. RESULTS: In children not infected by Cryptosporidium the treatment resulted in a 50% reduction of stool frequency and a 9% increase in body weight. No statistically significant effect was found in children harbouring this parasite. Diarrhea relapsed within 1-2 months in 3/3 children with Cryptosporidium and in 1/8 children without Cryptosporidium (p < 0.05). No untoward side effects from the treatment were observed. CONCLUSIONS: These results suggest that an empiric treatment of this type should be attempted early in HIV-infected children with chronic diarrhea, particularly in those not infected by Cryptosporidium.

Anti-Bacterial Agents↗
PubMed1996

The Saccharomyces cerevisiae OXA1 gene is required for the correct assembly of cytochrome c oxidase and oligomycin-sensitive ATP synthase.

The nuclear gene OXA1 was first isolated in Saccharomyces cerevisiae and found to be required at a post-translational step in cytochrome c oxidase biogenesis, probably at the level of assembly. Mutations in OXA1 lead to a complete respiratory deficiency. The protein Oxa1p is conserved through evolution and a human homolog has been isolated by functional complementation of a yeast oxa1- mutant. In order to further our understanding of the role of Oxa1p, we have constructed two yeast strains in which the OXA1 open reading frame was almost totally deleted. Cytochrome spectra and enzymatic activity measurements show the absence of heme aa3 and of a cytochrome c oxido-reductase activity and dramatic decrease of the oligomycin sensitive ATPase activity. Analysis of the respiratory complexes in non-denaturing gels reveals that Oxa1p is necessary for the correct assembly of the cytochrome c oxidase and the ATP synthase complex.

Adenosine Triphosphatases↗
PubMed1996

[Challenge for cow's milk protein intolerance diagnosis. Comparison between different modalities].

BACKGROUND: The diagnosis of cow's milk protein intolerance (CMPI) is mainly based on the response to the elimination diet and to the subsequent exposure to these proteins (challenge). METHODS: To find out whether a "formal", strictly scheduled challenge was better than a less formal test in establishing CMPI diagnosis, records were reviewed of 87 children studied in 5 Hospitals in the Milan area during the last 3 years. RESULTS: The study showed that the diagnostic approach (formal vs informal challenge) did not affect the probability of confirming CMPI diagnosis (21% vs 19%). Moreover, this probability was not affected by the source of the first diagnosis (Hospital vs Family Doctor), the time elapsed between first diagnosis and challenge, and the laboratory tests performed during the challenge. CONCLUSIONS: Therefore, a less strictly scheduled approach could be conveniently suggested to confirm CMPI diagnosis, at least in unselected cases.

Animals↗
PubMed1995

The majority of yeast UPF1 co-localizes with polyribosomes in the cytoplasm.

In Saccharomyces cerevisiae the UPF1 protein is required for nonsense-mediated mRNA decay, the accelerated turnover of mRNAs containing a nonsense mutation. Several lines of evidence suggest that translation plays an important role in the mechanism of nonsense mRNA decay, including a previous report that nonsense mRNAs assemble in polyribosomes. In this study we show that UPF1 and ribosomal protein L1 co-localize in the cytoplasm and that UPF1 co-sediments with polyribosomes. To detect UPF1, three copies of the influenza hemagglutinin epitope were placed at the C-terminus. The tagged protein, UPF1-3EP, retains 86% (+/- 5%) of function. Using immunological detection, we found that UPF1-3EP is primarily cytoplasmic and was not detected either in the nucleus or in the mitochondrion. UPF1-3EP and L1 co-distributed with polyribosomes fractionated in a 7-47% sucrose gradient. The sucrose sedimentation profiles for UPF1-3EP and L1 exhibited similar changes using three different sets of conditions that altered the polyribosome profile. When polyribosomes were disaggregated, UPF1-3EP and L1 accumulated in fractions coincident with 80S ribosomal particles. These results suggest that UPF1-3EP associates with polyribosomes. L3 and S3 mRNAs, which code for ribosomal proteins of the 60S and 40S ribosomal subunits, respectively, were on average about 100-fold more abundant than UPF1 mRNA. Assuming that translation rates for L3, S3, and UPF1 mRNA are similar, this result suggests that there are far fewer UPF1 molecules than ribosomes per cell. Constraints imposed by the low UPF1 abundance on the functional relationships between UPF1, polyribosomes, and nonsense mRNA turnover are discussed.

Base Sequence↗
PubMed1994

Two adjacent nuclear genes, ISF1 and NAM7/UPF1, cooperatively participate in mitochondrial functions in Saccharomyces cerevisiae.

We previously isolated a nuclear 5.7 kb genomic fragment carrying the NAM7/UPF1 gene, which is able to suppress mitochondrial splicing deficiency when present in multiple copies. We show here that an immediately adjacent gene ISF1 (Increasing Suppression Factor) increases the efficiency of the NAM7/UPF1 suppressor activity. The ISF1 gene has been independently isolated as the MBR3 gene and comparison of the ISF1 predicted protein sequence with data libraries revealed a significant similarity with the MBR1 yeast protein. The ISF1 and NAM7 genes are transcribed in the same direction, and RNase mapping allowed the precise location of their termini within the intergenic region to be determined. The ISF1 gene is not essential for cell viability or respiratory growth. However as for many mitochondrial genes, ISF1 expression is sensitive to fermentative repression; in contrast expression of the NAM7 gene is unaffected by glucose. We propose that ISF1 could influence the NAM7/UPF1 function, possibly at the level of mRNA turnover, thus modulating the expression of nuclear genes involved in mitochondrial biogenesis.

Amino Acid Sequence↗
PubMed1992

NAM7 nuclear gene encodes a novel member of a family of helicases with a Zn-ligand motif and is involved in mitochondrial functions in Saccharomyces cerevisiae.

The yeast nuclear gene NAM7 was previously isolated within a genomic fragment of 7.7 kb (1 kb = 10(3) bases or base-pairs), having the ability to suppress mitochondrial intronic mutations defective in RNA splicing. We have identified and sequenced the region on the insert corresponding to the NAM7 gene. A long open reading frame has been revealed which could code for a protein of 971 amino acids. Comparison of the NAM7 putative protein with data libraries did not reveal any strong similarity with known proteins. However, the NAM7 protein contains several motifs typical for proteins interacting with nucleic acids: (1) five motifs diagnostic for a superfamily of helicases appear in the same order and with similar distances; (2) the N-terminal portion possesses potential Zn-ligand structures belonging to the C chi superfamily. Deletion of the chromosomal copy of NAM7 gene leads to a partial impairment in respiratory growth that is particularly striking at low temperature. Southern blot analysis of DNA extracted from a nam7 :: URA3 deleted strain revealed the presence of a second gene whose sequence is related to that of the NAM7 gene and which could participate in the same process.

Amino Acid Sequence↗
PubMed1989

Novel class of nuclear genes involved in both mRNA splicing and protein synthesis in Saccharomyces cerevisiae mitochondria.

We have cloned three distinct nuclear genes, NAM1, NAM7, and NAM8, which alleviate mitochondrial intron mutations of the cytochrome b and COXI (subunit I of cytochrome oxidase) genes when present on multicopy plasmids. These nuclear genes show no sequence homology to each other and are localized on different chromosomes: NAM1 on chromosome IV, NAM7 on chromosome XIII and NAM8 on chromosome VIII. Sequence analysis of the NAM1 gene shows that it encodes a protein of 440 amino acids with a typical presequence that would target the protein to the mitochondrial matrix. Inactivation of the NAM1 gene by gene transplacement leads to a dramatic reduction of the overall synthesis of mitochondrial protein, and a complete absence of the COXI protein which is the result of a specific block in COXI pre-mRNA splicing. The possible mechanisms by which the NAM1 gene product may function are discussed.

Amino Acid Sequence↗
PubMed1988

Ketone-body metabolism in hyperthyroid rats: reduced activity of D-3-hydroxybutyrate dehydrogenase in both liver and heart and of succinyl-coenzyme A: 3-oxoacid coenzyme A-transferase in heart.

The specific activity of D-3-hydroxybutyrate dehydrogenase is reduced by about a third in liver and heart mitochondria of hyperthyroid rats. State 3 respiration is also reduced in isolated mitochondria from the same animals when DL-3-hydroxybutyrate is the substrate. Determination of the kinetic parameters of the membrane-bound D-3-hydroxybutyrate dehydrogenase in liver of hyperthyroid rats reveals a decreased in maximal velocity (Vmax). The Michaelis and dissociation constants of NAD+ and D-3-hydroxybutyrate are also significantly influenced, thus indicating that both the affinity and the binding of this enzyme toward its substrates are affected. In hyperthyroid rats a significant ketone-body increase is found in both liver and heart: in blood, an almost doubled concentration can be measured. At the same time, in heart mitochondria of these animals the activity of succinyl-coenzyme A: 3-oxoacid coenzyme A-transferase is significantly reduced. The decrease in both D-3-hydroxybutyrate dehydrogenase and 3-oxoacid coenzyme A-transferase associated with the increase in ketone bodies supports the suggestion that there is a lower utilization of these compounds by peripheral tissues. In the blood of hyperthyroid rats a higher D-3-hydroxybutyrate/acteoacetate ratio is also found, probably resulting from a selective utilization of the two compounds in this pathological state.

Acyl Coenzyme A↗
PubMed1986

Effect of N-ethylmaleimide on rat liver phosphatidylcholine-specific and non-specific transfer protein activities: its dependence on donor liposome composition.

Phosphatidylcholine exchange between liposomes and mitochondria catalyzed by rat liver phosphatidylcholine transfer protein is strongly stimulated by N-ethylmaleimide (NEM) when PC/PI (molar ratio, 4:1) donor liposomes are used. In the presence of PC/PE or PC liposomes the exchange activity by this protein is unaffected. In the same experimental conditions, the activity of rat liver non-specific transfer protein is always stimulated by N-ethylmaleimide with all the types of liposomes tested in the order PC/PI greater than PC/PE greater than PC. Since the effect of NEM depends on the type of liposomes used and appears to be similar for both phospholipid transfer proteins, the possibility that their mode of action implies the formation of a ternary complex should be considered. As far as non-specific transfer protein is concerned, its interaction could vary depending on the nature of the exchanging membranes. Data are also presented indicating that when the two transfer proteins are together their activity is additive, therefore suggesting a specific role in phospholipid biomembrane assembly for each of them.

Androgen-Binding Protein↗
PubMed1980

The H+/e- stoicheiometry of respiration-linked proton translocation in the cytochrome system of mitochondria.

1. The -->H(+)/e(-) quotients for proton release from mitochondria associated with electron flow from succinate and duroquinol to O(2), ferricyanide or ferricytochrome c, and from NNN'N'-tetramethyl-p-phenylenediamine+ascorbate to O(2), were determined from rate measurements of electron flow and proton translocation. 2. Care was taken to avoid, or to take into account, unrelated electron flow and proton translocation, which might take place in addition to the oxido-reductions that were the subject of our analysis. Spectrophotometric techniques were chosen to provide accurate measurement of the rate of consumption of oxidants and reductants. The rate of proton translocation was measured with fast pH meters with a precision of 10(-3) pH unit. 3. The -->H(+)/O quotient for succinate or duroquinol oxidation was, at neutral pH, 4, when computed on the basis of spectrophotometric determinations of the rate of O(2) consumption or duroquinol oxidation. Higher -->H(+)/O quotients for succinate oxidation, obtained from polarographic measurements of O(2) consumption, resulted from underestimation of the respiratory rate. 4. The -->H(+)/2e(-) quotient for electron flow from succinate and duroquinol to ferricyanide or ferricytochrome c ranged from 3.9 to 3.6. 5. Respiration elicited by NNN'N'-tetramethyl-p-phenylenediamine+ascorbate by antimycin-inhibited mitochondria resulted in extra proton release in addition to that produced for oxidation of ascorbate to dehydroascorbate. Accurate spectrophotometric measurement of respiration showed that the -->H(+)/e(-) ratio was only 0.25 and not 0.7-1.0 as obtained with the inadequate polarographic assay of respiration. Proton release was practically suppressed when mitochondria were preincubated aerobically in the absence of antimycin. Furthermore, the rate of scalar proton consumption for water production was lower than that expected from the stoicheiometry. Thus the extra proton release observed during respiration elicited by NNN'N'-tetramethyl-p-phenylenediamine+ascorbate is caused by oxidation of endogenous hydrogenated reductants. 6. It is concluded that (i) the -->H(+)/O quotient for the cytochrome system is, at neutral pH, 4 and not 6 or 8 as reported by others; (ii) all the four protons are released during electron flow from quinol to cytochrome c; (iii) the oxidase transfers electrons from cytochrome c to protons from the matrix aqueous phase and does not pump protons from the matrix to the outer aqueous phase.

Animals↗