Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.

     

A multi-technique surface study of the mercury(II) chalcogenide ion-selective electrode in saline media

X-ray photoelectron spectroscopy (XPS), secondary ion mass spectrometry (SIMS), rotating disc electrode-electrochemical impedance spectroscopy (RDE-EIS) and synchrotron radiation-grazing incidence X-ray diffraction (SR-GIXRD) have been used to study the response mechanism of the mercury(II) chalcogenide ion-selective electrode (ISE) in saline media. XPS and SIMS have shown that the chalcogenide surface is poisoned by silver chloride, or a mixture of silver halides, on continuous exposure to synthetic and real seawater. Significantly, the in-situ SR-GIXRD study demonstrated that electrode fouling in synthetic seawater is linked to the formation of poorly crystalline or amorphous silver chloride, and that the low level of free mercury(II) in a calibration buffer (i.e., 10(-14) M) is able to undergo metathesis with silver(II) sulfide in the membrane generating mercury(II) sulfide. Significantly, the results of this detailed surface study have shown that silver chloride fouling of the electrode is ameliorated in real seawater comprising natural organic ligands, and this has been attributed to the peptization of silver chloride by the surfactant-like nature of seawater ligands at pH 8. RDE-EIS aging studies have revealed that the chalcogenide membrane experiences a sluggish charge transfer reaction in seawater, and contrary to a previous report for a static electrode, the seawater matrix does not passivate the RDE. The results of this XPS, SIMS, RDE-EIS and SR-GIXRD study have elucidated the response mechanism of the mercury(II) ISE in saline media.     

Vilsmeier formylation of 5,10,15-triphenylcorrole: expected and unusual products

5,10,15-Triphenylcorrole (1) reacts with the Vilsmeier reagent (POCl(3)/DMF) to give the corresponding 3-formyl derivative 3 as the major product. The regioselectivity of the reaction was proven by X-ray crystallography and only traces of the 2-formyl isomer were observed. A more polar product is also observed and this compound becomes the major product when an excess of DMF is used for the preparation of the Vilsmeier reagent, while the formation of the 3-formyl isomer is almost completely suppressed. X-ray crystallography allowed us to identify this compound as the fully substituted N-ethane bridged derivative 4, formed from the attack of the Vilsmeier reagent at the inner core of the macrocycle. This compound is unique among porphyrinoid macrocycles, and further confirms the peculiarity of corrole chemistry.     

Determination of hydroxycarbamates in aqueous matrices by direct derivatization and GC-MS analysis in chemical ionization mode

A rapid and effective procedure, developed for the determination of polar compounds in water, has been applied to hydroxycarbamates. In few minutes, it is possible to perform a catalyzed derivatization of such compounds directly in the aqueous medium, using n-hexyl chloroformate. Extraction with n-hexane and injection into a benchtop GC-MS system are the only two further steps to complete the analysis. Chemical ionization proved to be more effective than electron impact to produce valuable mass spectra in terms of selectivity and sensitivity. Linear quantitative responses were demonstrated over a two-order-of-magnitude range. The minimum detectable concentration was 3 ppb for acetohydroxamic acid and 10 ppb for hydroxyurethane, obtained from Po river water samples spiked with the two hydroxycarbamate standards.     

Use of modified rice husks as a natural solid adsorbent of trace metals: characterisation and development of an on-line preconcentration system for cadmium and lead determination by FAAS

The use of rice husks as an alternative adsorbent in an on-line preconcentration system for Cd (II) and Pb (II) determination by flame atomic absorption spectrometry (FAAS) is described. The potential of rice husks as a natural adsorbent was evaluated as a material modified with 0.75 mol l⁻¹ NaOH solution and in the unmodified form. For this task, several techniques such as spectroscopy and thermogravimetry were used for elucidation of possible functional groups responsible for the uptake of Cd (II) and Pb (II). Furthermore, based on adsorption studies and adsorption isotherms applied to the Langmüir model, it was possible to verify that modified rice husks present a higher adsorption capacity for both metals. After establishing this material as a promising natural adsorbent, it was used for on-line preconcentration of Cd (II) and Pb (II) metals. The multivariate optimisation of chemical and flow variables was performed by using a full factorial design (2⁴) including the following factors: preconcentration time, preconcentration flow rate, concentration and volume of eluent. The optimum pH values used for on-line preconcentration were taken from prior univariate experiments. Under optimised conditions for Cd (II) determination (4 min of preconcentration at a 6 ml min⁻¹ preconcentration flow rate, in which comprises 24 ml of preconcentration volume, 200 μl elution volume and 1.0 mol l⁻¹ HNO₃ solution as eluent), the system achieved a detection limit of 1.14 μg l⁻¹ and an enrichment factor of 72.4. Similar conditions were used for Pb (II) determination (4 min of preconcentration, 6 ml min⁻¹ preconcentration flow rate, 300 μl elution volume and 1.0 mol l⁻¹ HNO₃ solution as eluent) from which a detection limit of 14.1 μg l⁻¹ and enrichment factor of 46.0 were achieved. Also, rice husks have been shown to be a homogeneous and stable adsorbent in which more than 100 preconcentration/elution cycles provide a relative standard deviation (RSD) of less than 6.0% on the analytical signal. The satisfactory accuracy of the method developed was obtained by using spiked water samples (mineral water and lake water) and spiked red wine samples. These values were confirmed by electrothermal atomic absorption spectrometry (ETAAS). The certified reference material [pig kidney (CRM 186)] and the reference material [beech leaves (CRM 100)] were also used.     

Trends in Preconcentration Procedures for Metal Determination Using Atomic Spectrometry Techniques

 Methods for metal preconcentration are often described in the literature. However, purposes are often different, depending on whether the methods are applied in environmental, clinical or technological fields. The respective method needs to be efficient, give high sensitivity, and ideally also is selective which is useful when used in combination with atomic spectroscopy. This review presents the actual tendencies in metal preconcentration using techniques such as Flame Atomic Absorption Spectrometry (FAAS), Electrothermal Atomic Absorption Spectrometry (ETAAS), Hydride Generation Atomic Absorption Spectrometry (HGAAS), Inductively Coupled Plasma Optical Emission Spectrometry (ICP OES) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Procedures based on related to electrochemical, coprecipitation/precipitation, liquid–liquid and solid–liquid extraction and atom trapping mechanisms are presented. Correspondence: Department of Analytical Chemistry, Universidade Estadual de Campinas – UNICAMP, P.O. Box 6154, 13083-970 Campinas, Brazil. e-mail: zezzi@iqm.unicamp.br Received December 20, 2001; accepted October 11, 2002     

Heavy metals content in rain water collected in three different locations in Italy during 1999

Rain water samples collected at three different locations in Italy during 1999 were analysed for heavy metals determination. Results for V, Cr, Mn, Co, Cu, Cd, Sb, Pb, Al and Ni are reported in this paper. For most of the elements higher concentration values have been measured in the samples from Alpe Gera (rural site): only for Cd and V were the concentrations higher at Pisa. The total annual deposition (microg m(-2) y(-1)) shows a similar behaviour, with Alpe Gera being the location with highest total annual input for Cr, Mn, Co, and in particular for Cu, Sb, Pb and Al. The reason of the higher deposition at a rural site in comparison to a urban one (Milan) is not known: further experimental work and investigations are needed. Generally, no evident seasonal trends have been observed for the measured concentrations, while few correlations have been found among elements within the same station. Crustal contribution to total concentration varies from about 20% for V to less than 1% for Cu, Cd, Sb, Pb and Ni.     

Adsorption kinetics, orientation, and self-assembling of N-acetyl-L-cysteine on gold: a combined ATR-IR, PM-IRRAS, and QCM study

The adsorption of N-acetyl-L-cysteine from ethanol solution on gold has been studied by in situ attenuated total reflection infrared (ATR-IR) spectroscopy, polarization modulation infrared reflection absorption spectroscopy, and a quartz crystal microbalance. After an initial fast adsorption, in situ ATR-IR revealed two considerably slower processes, besides further adsorption. The appearance of carboxylate bands and the partial disappearance of the carboxylic acid bands demonstrated that part of the molecules on the surface underwent deprotonation. In addition, the C=O stretching vibration of the carboxylic acid group shifted to lower and the amide II band to higher wavenumbers, indicating hydrogen-bonding interactions within the adsorbate layer. Based on the initial ATR-IR spectrum, which did not reveal deprotonation, the orientation of the molecule within the adsorbate layer was determined. For this, density functional theory was used to calculate the transition dipole moment vectors of the vibrational modes of N-acetyl-l-cysteine. The projections of the latter onto the z-axis of the fixed surface coordinate system were used to determine relative band intensities for different orientations of the molecule. The analysis revealed that the amide group is tilted with respect to and points away from the surface, whereas the carboxylic acid is in proximity to the surface, which is also supported by a shift of the C-O-H bending mode. This position of the acid group favors its deprotonation assisted by the gold surface and easily enables intermolecular interactions. Periodic acid stimuli revealed reversible protonation/deprotonation of part of the adsorbed molecules. However, only non-hydrogen-bonded carboxylic acid groups showed a response toward the acid stimuli.     

Oriented thin films from soluble polythiophenes

The degree of orientation of thin films of eight different polymeric structures, belonging to the class of soluble polyalkylthiophenes (PATs) has been studied. Thin films of the polymers, obtained by spin coating onto glass substrates, were oriented by means of the rubbing technique. The degree of orientation is related to the regioregularity of the system: highly regioregular polymers can be oriented, while regiorandom materials are not oriented. The degree of orientation can be improved by thermal annealing of the oriented films. As a result of annealing, which was performed at different temperatures according to the thermal behavior of the polymers, it was possible to increase the polarization ratio for poly(3-decylthiophene) up to 12–13 as detected from the UV-vis spectra in polarized light. Moreover in the investigated PATs, both the key role of molecular weight and its distribution for achieving a high orientation degree has been assessed. Copyright © 2003 John Wiley & Sons, Ltd.