Biomedical subjects

A Viari

Publications and source records attributed to A Viari.

10 recordsLinked to original sources

PubMed1992

Saponins from Steganotaenia araliacea.

Six saponins have been isolated and identified from the leaves of Steganotaenia araliacea. They were identified as 3-O-[beta-D-galactopyranosyl(1----2)-(beta-D-galactopyranosyl (1----3))-beta-D-glucuronopyranosyl]-21-O-tigloyl and -21-O-angeloyl-R1-barrigenol, 3-O-[beta-D-glucopyranosyl(1----2)-(beta-D-xylopyranosyl (1----3))-beta-D-glucuronopyranosyl]-21-O-tigloyl and -21-O-angeloyl-R1-barrigenol, 3-O-[beta-D-glucopyranosyl(1----2)-(beta-D-glucopyranosyl-(1----3))-(alp ha-L- rhamnopyranosyl(1----4))-beta-D-glucopyranosyl] steganogenin and 3-O-[(beta-D-galactopyranosyl(1----2)-beta-D-glucuronopyranosyl]-2 8-O- beta-D-glucopyranosyl olean-12-ene-28-oic acid. Steganogenin is a new 17,22-seco-oleanolic acid derivative. The structures of the saponins were established by analysis of their 1H and 13C NMR spectra with the help of 2D-experiments and by Californium Plasma Desorption Mass Spectrometry.

Carbohydrate Sequence↗

PubMed1992

Saponins from stem bark of Petersianthus macrocarpus.

Two bioactive saponins were isolated from the stem bark of Petersianthus macrocarpus. Their structures were elucidated by chemical degradations and by a combination of 2D NMR techniques and by Californium plasma desorption mass spectrometry. They are 3-O-([beta-D-galactopyranosyl (1-->2)][beta-D-galactopyranosyl (1-->3)]- beta-D-glucuronopyranosyl)-21-O-[3-(3-tigloyloxynilic acid)-4-tigloyloxy- alpha-L-arabinopyranosyl] barringtogenol C and 3-O-([beta-D-galactopyranosyl (1-->2)][beta-D-galactopyranosyl (1-->3)]-beta-D-glucuronopyranosyl)-28-O-alpha-L-rhamnopyranosyl barringtogenol C-21-O-benzoate. The absolute configuration of nilic acid was determined by partial synthesis. 3,3'-Dimethoxy ellagic acid and 3,3'-dimethoxy-4-O-beta-D- glucopyranosyl ellagic acid were also isolated.

Carbohydrate Sequence↗

PubMed1991

Formation of cyclobutane thymine dimers photosensitized by pyridopsoralens: quantitative and qualitative distribution within DNA.

As after irradiation with 254-nm UV light, exposure of thymidine and three isomeric pyridopsoralen derivatives to UVA radiation, in the dry state, leads to the formation of the six diastereomers of cyclobutadithymidine as the predominant reaction. This unexpected photosensitized reaction, which also gives rise to both 5R* and 5S* diastereomers of 5,6-dihydro-5-(alpha-thymidylyl)thymidine (or "spore" photoproduct), is selective since [2 + 2] dimerization of 2'-deoxycytidine was not detected under the same experimental conditions. The cis-syn isomer of cyclobutadithymine was also found to be produced within isolated DNA following UVA irradiation in aqueous solutions containing 7-methylpyrido[3,4-c]psoralen. Quantitatively, this photoproduct represents about one-fifth of the overall yield of the furan-side pyridopsoralen [2 + 2] photocycloadducts to thymine. DNA sequencing methodology was used to demonstrate that pyridopsoralen-photosensitized DNA is a substrate for T4 endonuclease V and Escherichia coli photoreactivating enzyme, two enzymes acting specifically on cyclobutane pyrimidine dimers. Furthermore, the dimerization reaction of thymine is sequence dependent, with a different specificity from that mediated by far-UV irradiation as inferred from gel sequencing experiments. Interestingly, adjacent thymine residues are excellent targets for 7-methylpyrido[3,4-c]psoralen-mediated formation of cyclobutadithymine in TTTTA and TTAAT sites, which are also the strongest sites for photoaddition. The formation of cyclobutane thymine dimers concomitant to that of thymine-furocoumarin photoadducts and their eventual implication in the photobiological effects of the pyridopsoralens are discussed.

Autoradiography↗

PubMed1991

'Multifrequency' location and clustering of sequence patterns from proteins.

In previous work, we have shown that a set of characteristics, defined as (code frequency) pairs, can be derived from a protein family by the use of a signal-processing method. This method enables the location and extraction of sequence patterns by taking into account each (code frequency) pair individually. In the present paper, we propose to extend this method in order to detect and visualize patterns by taking into account several pairs simultaneously. Two 'multifrequency' methods are described. The first one is based on a rewriting of the sequences with new symbols which summarize the frequency information. The second method is based on a clustering of the patterns associated with each pair. Both methods lead to the definition of significant consensus sequences. Some results obtained with calcium-binding proteins and serine proteases are also discussed.

Amino Acid Sequence↗

PubMed1991

Escherichia coli molecular genetic map (1500 kbp): update II.

The DNA sequence data for Escherichia coli deposited in the EMBL library (release 27), together with miscellaneous data obtained from several laboratories, have been localized on an updated and corrected version of the restriction map of the chromosome generated by Kohara et al. (1987) and modified by others. This second update adds a further 500 kbp, increasing the amount of the E. coli chromosome sequenced to about one third of the total: 1510 kbp of sequenced DNA is included in the present data base. The accuracy of the map is assessed, and allows us to propose a precise genetic map position for every sequenced gene. The location of rare-cutting sites such as AvrII, NotI and SfiI have also been included in the update in order to combine the data obtained from different sources into one single file. The distribution of palindromic sequences (to which most restriction sites belong) has been studied in coding sequences. There appears to be a significant counter-selection against several such sequences in E. coli coding sequences (but not in other organisms such as Saccharomyces cerevisiae), suggesting the existence of constraints on DNA structure in E. coli, perhaps indicative of a functional role for horizontal gene transfer, preserving coding sequences, in this type of bacteria.

Base Sequence↗

PubMed1990

Identification of the two cis-syn [2 + 2] cycloadducts resulting from the photoreaction of 3-carbethoxypsoralen with 2'-deoxycytidine and 2'-deoxyuridine.

Near-ultraviolet photolysis of 2'-deoxycytidine (dCyd) and 3-carbethoxypsoralen (3-CPs) in the dry state was found to generate two main stable photoadducts which were separated by thin-layer and high-performance liquid chromatography. Fast atom bombardment and plasma desorption mass spectrometry analyses suggested that the bound molecule to 3-CPs is dCyd. These two compounds were found to produce the corresponding 2'-deoxyuridine (dUrd) derivatives through a deamination process when left in aqueous solutions with a lifetime close to 24 h at 20 degrees C. The chemical structure of the deaminated photoadducts was confirmed by photochemical synthesis using dUrd as the substrate. UV and fluorescent measurements indicated that the furan moiety of 3-CPs is involved in the photobinding reaction. The cyclobutane type structure of the modified dUrd derivatives was established on the basis of its photoreversibility and detailed 1H NMR analysis. The cis-syn stereoconfiguration of the two photocycloadducts was inferred from coupling constant considerations and on the basis of the complete assignment of the cyclobutyl protons, requiring the synthesis of deuterated nucleosides at pyrimidine carbon C(6). Further confirmation of the diastereoisomeric relationship between the two cis-syn dUrd <54' 65'> 3-CPs was provided by circular dichroism measurements.

Deoxycytidine↗

PubMed1990

A scale-independent signal processing method for sequence analysis.

In this paper, we present methods to detect and localize patterns in biologically related protein sequences (family). The patterns common to the sequences of the family are detected by using Fourier analysis. No previous scales (codes) are needed, they are actually produced as a result of the analysis procedure, together with the frequencies of the Fourier decompositions. Characteristic features of the family are thus expressed as (code-frequency) pairs. Various tools are proposed in order to localize the patterns, to compare the codes, and to evaluate the proximity of an arbitrary sequence to the investigated family. The general strategy is illustrated on a family composed of calcium-binding proteins.

Amino Acid Sequence↗

PubMed1989

Plasma desorption mass spectrometric study of UV-induced lesions within DNA model compounds.

Positive and negative plasma desorption (PD) mass spectra of the di-deoxyribonucleoside monophosphate d(TpT) and of its biologically relevant ultraviolet-induced intramolecular photodimers are examined and discussed. The photodimers which were analysed by PD mass spectrometry include the cis-syn and trans-syn cyclobutyl isomers d(T[p]T), the pyrimidine-pyrimidone photoadduct (6-4)d(TpT) and its Dewar valence isomer. Molecular ions, quasi-molecular ions and several fragment ions are observed in all cases. It is shown that, despite the absence of mass differences between these dinucleoside monophosphates, the fragmentation pattern differs significantly between the two main classes: cyclobutane dimers and (6-4) adducts. PD mass spectrometry can therefore be envisaged for characterizing their formation within short DNA fragments.

DNA↗

PubMed1988

Characterization and sequencing of normal and modified oligonucleotides by 252Cf plasma desorption mass spectrometry.

Plasma desorption (PD) mass spectra of normal deoxyribo-oligonucleotides and of neutral methylphosphonate deoxyribo-oligonucleosides are examined and discussed. Molecular ions of oligonucleotides up to nonamer have been observed for neutral species. It is also shown that PD mass spectra can be used to monitor chemical modifications of oligonucleotides, such as the covalent binding of an organic fluorescent probe, along the synthesis process.

Californium↗

PubMed1988

A new class of psoralen photoadducts to DNA components: isolation and characterization of 8-MOP adducts to the osidic moiety of 2'-deoxyadenosine.

The near-UV-induced photoreaction of the bifunctional 8-methoxypsoralen (8-MOP) with 2'-deoxyadenosine (dAdo) was investigated in the dry state. Four main monoadducts of 8-MOP to 2'-deoxyadenosine were separated by high performance liquid chromatography and subsequently characterized by soft ionization mass spectrometry (fast atom bombardment and plasma desorption mass spectrometries) and extensive 1H NMR analysis including nuclear Overhauser effect (NOE) measurements. These new types of furocoumarin-nucleic acid component which appear to be specific to 2'-deoxyadenosine were shown to result from recombination of the 3,4-dihydropyron-4-yl radical of 8-MOP with 2'-deoxyadenosyl radical either at the 1' or the 5' position.

Chromatography, High Pressure Liquid↗