Unilateral NMR study of a XVI century wall painted.

Wall paintings in the XVI century Serra Chapel in the "Chiesa di Nostra Signora del Sacro Cuore" Rome, have been studied using unilateral NMR. In order to map the distribution of moisture content in the wall painted, a large number of Hahn echo measurements, covering large areas of the wall painting were performed. Because the intensity of the Hahn echo is proportional to the amount of moisture in the area under study, the experimental data were transformed into 2D gradient colour maps which allowed an easy visualization of the moisture content of the wall. The state of conservation of the wall painting was monitored using T2 measurements specially with regards to outcropping salt.

The role of water coordination in binary mixtures. A study of two model amphiphilic molecules in aqueous solutions by molecular dynamics and NMR.

Two binary aqueous mixtures which contain the small amphiphilic molecules TMAO (trimethylamine-N-oxide) and TBA (tert-butyl alcohol) have been investigated by molecular dynamics simulations and NMR chemical shift and self-diffusion measurements. TMAO is an osmolyte, while TBA is a monohydrate alcohol. Both possess bulky hydrophobic groups and polar heads, namely, NO in TMAO and OH in TBA. The hydrophilic/hydrophobic content of these isosteric molecules strongly modulates the structure and dynamics of the hydration shell, which is thought to be responsible for the effects observed on proteins and phospholipids. Simulation results, especially on hydrogen-bond networking, spatial correlations, and self-diffusivity, are consistent with NMR data and agree well with previous numerical studies on similar solutions. The methods employed allow the elucidation of the microscopic features of the solutions. For TBA solutions, the hydration shell is found to have a low density and a large spatial spread, and thus, above the molar fraction of 0.03, reduction of hydrophobic hydration drives self-aggregation of the solute. This effect does not take place in TMAO solutions, where the hydration shell is more compact and stable, maintaining its structure over a wider range of solute concentrations.

Fresco paintings studied by unilateral NMR.

Unilateral NMR has been used to monitor the state of conservation of frescoes in the Vasari's house in Florence. The causes of deterioration of ancient frescoes are varied, which result in the detachment and crumbling of the painted film from the supporting plaster and in the outcropping of salts. Unilateral measurements of Hahn echo performed on such frescoes have allowed a perfect identification of the detachment of the painted film from the plaster. The presence of soluble salts on the pictorial film affects the spin-spin relaxation times, T(2). It is then possible using this technique, to characterize the effect of chemical treatments, of cleansing and consolidation procedures using the distribution of T(2) spin-spin relaxation times.

Monitoring degradation in paper: non-invasive analysis by unilateral NMR. Part II.

High quality paper samples have been oxidized with a specific oxidant to reproduce one of the possible causes of the aging of paper. All samples have been characterized by 13C CP-MAS NMR spectroscopy. The artificial aging of paper has been monitored using a standard NMR relaxometer and the results have been compared with the corresponding data obtained using an unilateral NMR relaxometer. Experimental values obtained with both techniques are in agreement, demonstrating that unilateral NMR relaxometric measurements constitute a suitable non-invasive method for assessing the degradation process of cellulose-based materials. The sensitivity of the non-invasive NMR method allows the detection of degradation even at a very early stage. Effects due to the sample volume and to the penetration depth have been investigated.

Analysis of historical porous building materials by the NMR-MOUSE.

Samples of sandstone with and without deposits of silicon oxide stone strengthener as well as samples of historical brick material were analyzed by transverse NMR relaxation and mercury intrusion porosimetry. Relaxation times and relaxation time distributions of the protons from the water saturated samples were measured by low-field NMR using homogeneous and inhomogeneous fields. The measurements in inhomogeneous fields were performed with two different NMR-MOUSE sensors, one with a field gradient of 2 T/m and the other with an average field gradient of about 20 T/m. In the sandstone samples the application of stone strengtheners was shown to result in a confinement of the large pores within the outer layer of a few millimeters depth. Depending on the ferromagnetic contamination of the brick samples, the relaxation time distributions can be affected. The agreement of T2 relaxation time distributions and pore size distributions from mercury intrusion porosimetry was found to be better for the NMR-MOUSE sensors than for the homogeneous field measurements. This is true even for different brick samples, unless the content in ferromagnetic particles is very strong.

Degradation of historical paper: nondestructive analysis by the NMR-MOUSE.

The NMR-MOUSE is a mobile sensor for single-sided NMR inspection of organic materials which takes advantage of the principles of magnetic resonance and inside-out-NMR. Historical books dating from the 17th century were measured at different points by positioning the NMR-MOUSE on the paper. Different degrees of paper degradation can be discriminated from the regularized inverse Laplace transform of the envelope of the acquired echo signals. For the first time the degradation of historical paper was characterized entirely nondestructively by NMR. As a contribution to current preservation efforts, NMR shows great promise for future use in damage assessment of historical documents.

Geographical characterization of italian extra virgin olive oils using high-field (1)H NMR spectroscopy.

1H high-field nuclear magnetic resonance (NMR) was used to analyze 216 extra virgin olive oils collected in three years (1996, 1997, and 1998) in different Italian areas in order to evaluate the potential contribution of this technique to the geographical characterization of olive oils. A statistical procedure performed on the intensity of selected NMR peaks has been proposed. Tree clustering analysis of NMR data performed without any a priori hypothesis showed the existence of reliable parameters able to group the olive oils according to the location of olive oil production. Linear discriminant analysis applied to selected NMR parameters of olive oils of the same year of production allowed the grouping of samples according to their geographical origin with only very few errors. Moreover, a satisfactory grouping is reached by combining the NMR data of olive oils from two different years (1996 and 1997). Operating on appropriate sampling, a careful analysis of data yielded the conclusion that the place of olive production could be singled out as a discriminating factor regardless of the cultivars from which the olive oils are derived.

The structure of gellan in dilute aqueous solution.

A full assignment of high-field nmr spectra of gellan was obtained in dilute aqueous solution by performing a series of selective one-dimensional nmr experiments. The observed nuclear Overhauser effects (NOEs) cannot be interpreted assuming that each sugar residue is intrinsically rigid and in a chair conformation. In fact, the rhamnose residue gives strong NOE contacts coherent only with an equilibrium involving both a chair as well as a boat (or a hemiboat) conformation. Molecular dynamic calculations performed on a heptamer with a central rhamnose support the above finding, and show a structure based on a very stiff single chain in which it is present a flipping of the rhamnose residue. At low temperatures (5-20 degrees C) in very dilute solutions (0.018 mg/mL) nmr spectra show a splitting of the resonance due to the methyl group of rhamnose residue, thus confirming the presence of a slow equilibrium among different conformers.

Conformations in solution of the fuscopeptins. Phytotoxic metabolites of Pseudomonas fuscovaginae.

Fuscopeptins are phytotoxic amphiphilic lipodepsipeptides containing 19 amino acid residues. They are produced by the plant pathogenic bacterium Pseudomonas fuscovaginae in two forms, A and B, which differ only in the number of methylene groups in the fatty acid chain. Their covalent structure and biological properties have been reported previously. CD and NMR spectroscopy investigations in solution revealed the absence of identifiable elements of secondary and tertiary structure for these molecules. Fuscopeptin B appears to be completely unstructured in aqueous solution, and has a large molecular flexibility. A dramatic conformational change was observed upon addition of trifluoroethanol. This study reports the complete interpretation of the two-dimensional NMR spectra and the NOE results obtained for fuscopeptin B in water/trifluoroethanol solutions; the signals relative to the peptidic moiety are identical to those observed for fuscopeptin A. The results of this investigation were used to determine the solution structure of fuscopeptin B by computer simulations applying distance geometry and simulated annealing procedures. In water/trifluoroethanol solutions the peptidic region appears to have a partly helical structure. The lactonic ring assumes defined conformations very similar to those already reported for other lipodepsipeptides. The structure for fuscopeptin B in solution is also valid for fuscopeptin A because of the negligible structural difference between the two metabolites.

LC/MS analysis and antioxidative efficiency of Maillard reaction products from a lactose-lysine model system.

Aqueous solutions of lactose and lysine were refluxed for up to 4 h without pH control. Samples were collected every hour, and the reaction was monitored by measuring the pH, the optical density at 420 nm, and the relative antioxidative efficiency (RAE). The greatest change in optical density and antioxidative efficiency occurred for the mixture heated for 4 h. The 4 h solution was separated into three fractions according to the molecular weights of the components and tested for RAE. The high molecular weight fraction was more colored, and it had the highest antioxidative activity. The low molecular weight fraction was separated by high-performance liquid chromatography (HPLC). RAE values were measured for each purified compound. HPLC coupled with diode array and electrospray mass spectrometry allowed a rapid screening of the solutions and a tentative identification of several peaks. Nuclear magnetic resonance analysis allowed the identification of galactosylisomaltol and pyrraline. The resonance assignments for these compounds were revised.

AMASS: a structured pattern matching approach to shotgun sequence assembly.

In this paper, we propose an efficient, reliable shotgun sequence assembly algorithm based on a fingerprinting scheme that is robust to both noise and repetitive sequences in the data, two primary roadblocks to effective whole-genome shotgun sequencing. Our algorithm uses exact matches of short patterns randomly selected from fragment data to identify fragment overlaps, construct an overlap map, and deliver a consensus sequence. We show how statistical clues made explicit in our approach can easily be exploited to correctly assemble results even in the presence of extensive repetitive sequences. Our approach is both accurate and exceptionally fast in practice: e.g., we have correctly assembled the whole Mycoplasma genitalium genome (approximately 580 kbp) is roughly 8 minutes of 64MB 200MHz Pentium Pro CPU time from real shotgun data, where most existing algorithms can be expected to run for several hours to a day on the same data. Moreover, experiments with artificially-shotgunned data prepared from real DNA sequences from a wide range of organisms (including human DNA) and containing complex repeating regions demonstrate our algorithm's robustness to input noise and the presence of repetitive sequences. For example, we have correctly assembled a 238-kbp human DNA sequence in less than 3 min of 64-MB 200-MHz Pentium Pro CPU time.

Solution conformation of the Pseudomonas syringae MSU 16H phytotoxic lipodepsipeptide Pseudomycin A determined by computer simulations using distance geometry and molecular dynamics from NMR data.

Pseudomycin A is a cyclic lipodepsinonapeptide phytotoxin produced by a strain of the plant pathogenic bacterium Pseudomonas syringae. Like other members of this family of bacterial metabolites, it is characterised by a fatty acylated cyclic peptide with mixed chirality and lactonic closure. Several biological activities of Pseudomycin A are lower than those found for some of its congeners, a difference which might depend on the diverse number and distribution of charged residues in the peptide moiety. Hence, it was of interest to investigate its conformation in solution. After the complete interpretation of the two-dimensional NMR spectra, NOE data were obtained and the structure was determined by computer simulations, applying distance geometry and molecular dynamics procedures. The conformation of the large ring of Pseudomycin A in solution includes three rigid structural regions interrupted by three short flexible regions that act as hinges. The overall three-dimensional structure of the cyclic moiety is similar to that of previously studied bioactive lipodepsinonapeptides produced by other pseudomonads.

Corpeptins, new bioactive lipodepsipeptides from cultures of Pseudomonas corrugata.

The structure of the corpeptins, bioactive lipodepsipeptides produced in culture by Pseudomonas corrugata, the causal agent of tomato pith necrosis, has been determined. The combined use of FAB-mass spectrometry, NMR spectroscopy and chemical procedures has allowed us to assign the following primary structure to the peptide moiety: Dhb-Pro-Ala-Ala-Ala-Val-Val-Dhb-Hse-Val-alle-Dhp-Ala-Ala-Ala-Val-D hb-aThr-Ala-Dab-Ser-Ile with the terminal carboxy group closing a macrocyclic ring on the hydroxy group of the allo-threonine residue. The N-terminus is in turn acylated by 3-hydroxydecanoate in corpeptin A and by cis-3-hydroxy-5-dodecenoate in corpeptin B. Some preliminary data on the biological activity of corpeptins are included.

Solution conformation of the Pseudomonas syringae pv. syringae phytotoxic lipodepsipeptide syringopeptin 25-A. Two-dimensional NMR, distance geometry and molecular dynamics.

Syringopeptin 25-A is a phytotoxic amphiphilic lipodepsipeptide containing 25 amino acid residues, produced by some isolates of the plant pathogenic bacterium Pseudomonas syringae pv. syringae. Previous papers have reported its covalent structure and some of its biological properties. Attention has now been directed to define its conformation in solution, a structural feature regarded as important for understanding its possible role in the bacterial colonization of host plants, and its toxic action on the plant cell. Here we report the stereochemistry of its amino acid components, the complete interpretation of the two-dimensional NMR spectra and NOE data, and finally the structure obtained by computer simulations applying distance geometry and molecular dynamics procedures. The conformation of syringopeptin 25-A in aqueous solution includes three different structural regions interrupted by rigid 2,3-dehydro-2-aminobutyric acid residues: a loop from residue 2 to 6, a helicoidal zone from 8 to 15, and the lactone ring from 18 to 25. The three-dimensional structure of the lactone moiety is very similar to that of two previously studied bioactive lipodepsinonapeptides. Preliminary circular dichroism evidence of conformational variations in solution of trifluoroethanol, which stimulates a membrane-like environment, are also reported.

Structure-activity relationships in open ansa-chain rifamycin S derivatives as inhibitors of HIV-1 reverse transcriptase.

Three types of open ansa-chain rifamycin S derivatives have been prepared: derivatives with the ansa-chain open at C(29) and the original dihydrofuranone ring; derivatives with the ansa-chain open at C(29) and a furane ring; derivatives with the ansa-chain at open NH-C(15). Only derivatives of the first type are weak inhibitors of HIV-1 reverse transcriptase (IC50 ca.300 microM) while derivatives of the two other types are inactive. It has been hypothesized that the active derivatives inhibit the viral enzyme interacting through the groups C(14)H3, C(13)H3, and C(1)O at the same site as the well-known inhibitors TIBO and Nevirapine. In particular C(13)H3 must be unhindered and in an appropriate position out of the plane containing the chromophore-rings. The open ansa-chain seems to play the role of a lipophylic substituent.

Novel bioactive lipodepsipeptides from Pseudomonas syringae: the pseudomycins.

The covalent structure and most of the stereochemistry of the pseudomycins, bioactive metabolites of a transposon-generated mutant of a Pseudomonas syringae wild-type strain proposed for the biological control of Dutch elm disease, have been determined. While two pseudomycins are identical to the known syringopeptins 25-A and 25-B, pseudomycins A, B, C, C' are new lipodepsinonapeptides. For all of these the peptide moiety corresponds to L-Ser-D-Dab-L-Asp-L-Lys-L-Dab-L-aThr-Z-Dhb-L-Asp(3-OH) -L-Thr (4-Cl) with the terminal carboxyl group closing a macrocyclic ring on the OH group of the N-terminal Ser. This is in turn N-acylated by 3,4-dihydroxytetradecanoate in pseudomycin A, by 3-hydroxytetradecanoate in pseudomycin B, by 3,4-dihydroxyhexadecanoate in pseudomycin C, and by 3-hydroxyhexadecanoate in pseudomycin C'. Some preliminary data on the biological activity of pseudomycin A are reported.

Solution conformation of a pectic acid fragment by 1H-NMR and molecular dynamics.

1H-NMR and molecular dynamics simulations in vacuo and in water of (1-->4)-alpha-D-galacturono-disaccharide were performed. The results of the molecular dynamics simulations showed that the molecule fluctuates between two conformations characterized by different values of torsion angles around the glycosidic linkage and two different intramolecular hydrogen bonds. When these conformations are extrapolated to a regular polymeric structure, they generate pectic acid compatible with a 2(1)- or a right-handed 3(1)-helix.

Fusapyrone and deoxyfusapyrone, two antifungal alpha-pyrones from Fusarium semitectum.

A strain of Fusarium semitectum Berk. & Rav. from maize stalk rot in southern Italy produced bioactive metabolites when cultured on autoclaved rice kernels at room temperature for 4 weeks. The organic extracts of fungal culture showed a strong antibiotic activity towards Geotrichum candidum in disk diffusion assays, but they were not toxic to Artemia salina larvae. Two antifungal metabolites were isolated and characterized by chemical and spectroscopic methods as two 3-substituted-4-hydroxy-6-alkyl-2-pyrones, in particular, the 3-(4-deoxy-beta-xylo-hexopyranosyl)-4-hydroxy-6-[2-hydroxy-7-hydroxymeth yl- 1,1,5,9,11-pentamethyl-3,5,8-heptadecatrienyl]-2H-pyran-2-one and its 6-[2-hydroxy-1,1,5,7,9,11-hexamethyl] analog, which were named fusapyrone and deoxyfusapyrone, respectively.

Episodic changes of serum procollagen type I carboxy-terminal propeptide levels in fertile and postmenopausal women.

The aim of the present study was to optimize the use of serum procollagen type I carboxy-terminal propeptide (PICP) as a possible marker of postmenopausal-376lted changes of bone metabolism. Postmenopausal (n = 20) and healthy fertile young (n = 4) women were studied after informed consent. The postmenopausal women were subdivided in 4 groups: (1) nontreated; (2) treated with estrogen-progestogen replacement therapy; (3) treated with calcitonin, or (4) with kidney or liver diseases. Blood samples were collected at 15-min time intervals for 4, 6 or 8 h. Serum concentration of PICP was measured by radioimmunoassay, in duplicate at two different dilutions. In postmenopausal women mean +/- SEM serum PICP levels were slightly but nonsignificantly higher than in fertile women. Serum PICP levels in estrogen-progestogen or calcitonin-treated women were significantly lower than in non-treated postmenopausal women. Episodic changes of circulating PICP level were observed in fertile and postmenopausal women. The pulses of serum PICP levels did not show significant differences among the groups of women studied. The present study showed that the measurement of serum PICP levels is a useful marker for investigating the changes of bone metabolism. In particular, low PICP levels in postmenopausal women under steroid hormone or calcitonin treatment in part reflect the changes of bone turnover. The pulses of serum PICP levels during a time interval suggest that collagen metabolism in women undergoes a rapid turnover.