Soft‐modeling based spectrofluorimetric study of simultaneous equilibria

A two‐way soft resolution method will fail when applied to a simultaneous equilibria system due to rank deficiency in its concentration profiles. Increasing the dimensionality of measurements from two‐way to three‐way data can be used to overcome this problem. Simultaneous dissociation of two weak acids is considered as a model for simultaneous equilibria. Three‐way data obtained from excitation–emission spectrofluorimetric monitoring of a pH‐metric titration is analyzed using a proper combination of well‐known soft‐modeling methods. Multivariate curve resolution‐alternating least squares is used for calculating the excitation and emission spectral profiles of involved species and rank annihilation factor analysis for obtaining the contribution of each species in measured excitation–emission matrices at different pHs. The results of simulated and real simultaneous acids dissociation equilibria showed that the proposed combined method performs well even in situation when the equilibrium constants are close to each other. The applicability of method for study of an acidic dissociation is also shown. Copyright © 2009 John Wiley & Sons, Ltd.     

Acid-base and copper (II) complexation equilibria of poly(inosinic)-poly(cytidylic)

The acid-base and copper (II) complexing properties of the heteropolynucleotide poly(inosinic)-poly(cytidylic) acid were studied by means of potentiometric, spectrophotometric, CD, and molecular fluorescence titrations in a working aqueous medium of 0.15 M ionic strength at 37°C. The study of the acid-base equilibria has proved the existence of four different species in the pH interval 2–11. Two new species are detected in the presence of copper(II) ion, at acidic and neutral pH values. Spectrophotometric, CD, melting, and fluorescence data were treated with a multivariate curve resolution procedure that allowed the determination of the number of species simultaneously present in each system [acid-base equilibria, copper(II) complexation equilibria], and the estimation of their concentration profiles and of the pure spectra for each species. From the concentration profiles an unambiguous assignment of which species are present at any pH conditions can be made. Furthermore, the knowledge of the pure uv-visible, fluorescence, and CD spectra recovered by the proposed resolution method for each species brings important structural information. When this mathematical approach was applied to the thermal denaturation data, the melting profile and the uv pure spectra for all the different species or conformations formed in the melting process, were calculated. © 1997 John Wiley & Sons, Inc. Biopoly 42: 271–283, 1997     

Valorization of onion waste and by-products: MCR-ALS applied to reveal the compositional profiles of alcoholic fermentations of onion juice monitored by near-infrared spectroscopy

The overall purpose of the project, of which this study is a part, was to examine the feasibility of onion waste as a support-substrate for the profitable production of food-grade products. This study focused on the efficient production of ethanol from worthless onions by transforming the onion juice into onion liquor via alcoholic fermentation with the yeast Saccharomyces cerevisiae. The onion bioethanol produced could be later used as a favorable substrate for acetic fermentation to finally obtain onion vinegar. Near-infrared spectroscopy (NIRS), coupled with the multivariate curve resolution-alternating least squares (MCR-ALS) method, has been used to reveal the compositional and spectral profiles for both substrates and products of alcoholic fermentation runs, that is, total sugars, ethanol, and biomass concentration. The ambiguity associated with the ALS calculation was resolved by applying suitable inequality and equality constraints. The quality of the results provided by the NIR-based MCR-ALS methodology adopted was evaluated by several performance indicators, including the variance explained by the model, the lack of fit and the agreement between the MCR-ALS achieved solution and the results computed by applying previously validated PLS reference models. An additional fermentation run was employed to test the actual predictive ability of the ALS model developed. For all the components resolved in the fermentation system studied (i.e., total sugars, ethanol, and biomass), the final model obtained showed a high predictive ability and suitable accuracy and precision, both in calibration and external validation, confirmed by the very good agreement between the ALS responses and the reference values (the coefficient of determination was, in all cases, very close to 1, and the statistics confirmed that no significant difference was found between PLS reference models and the MCR-ALS methodology applied). Thus, the proven reliability of the MCR-ALS model presented in this study, based only on NIR measurements, makes it suitable for monitoring of the key species involved in the alcoholic fermentation of onion juice, allowing the process to be modeled and controlled in real time.     

Analytical characterization of the conformational transitions of polynucleotides by means of different molecular spectroscopies and multivariate curve resolution

A general procedure for the study of conformational transitions of polynucleotides is described. The equilibria between different conformations induced by salt, ethidium bromide, and temperature of poly(dG-dC). poly(dG-dC) and induced by salt and temperature of poly(A). poly(U) are investigated using molecular absorption, circular dichroism, and fluorescence spectroscopies. Spectral data obtained from experiments are analyzed by means of a factor analysis method, namely, multivariate curve resolution, which allows possible intermediate states to be detected and the pure spectra and the concentration profiles of all species present in the system to be estimated. This work shows the application of this procedure for the analysis of data matrices obtained in individual experiments but also for the analysis of several data matrices simultaneously.     

Three-way multivariate curve resolution applied to speciation of acid-base and thermal unfolding transitions of an alternating polynucleotide.

Analytical speciation of acid-base equilibria and thermal unfolding transitions of an alternating random polynucleotide containing cytosine and hypoxanthine, poly(C, I), is studied. The results are compared with those obtained previously for single-stranded polynucleotides, poly(I) and poly(C), and for the double-stranded poly(I). poly(C), to examine the influence of the secondary structure on the acid-base properties of bases. This study is based on monitoring acid-base titrations and thermal unfolding experiments by molecular absorption, CD, and molecular fluorescence spectroscopies. Experimental data were analyzed by a novel chemometric approach based on a recently developed three-way Multivariate Curve Resolution method, which allowed the simultaneous analysis of data from several spectroscopies. This procedure improves the resolution of the concentration profiles and pure spectra for the species and conformations present in folding-unfolding and acid-base equilibria. The results from acid-base studies showed the existence of only three species in the pH range 2-12 at 37 degrees C and 0.15M ionic strength. No cooperative effects were detected from the resolved concentration profiles, showing that equilibria concerning alternating polynucleotides like poly(C, I) are simpler than those involving poly(I). poly(C). Thermal unfolding experiments at neutral pH confirmed the existence of two transitions and one intermediate conformation. This intermediate conformation could only be detected and resolved without ambiguities when molecular absorption and CD spectral data were analyzed simultaneously.     

Resolution of parallel and antiparallel oligonucleotide triple helices formation and melting processes by multivariate curve resolution

A procedure is described for the complete resolution of concentration profiles of oligonucleotide triplexes as a function of pH and temperature. The pH and temperature ranges at which triplexes are present and the relative concentrations of all the species involved in acid-base and conformational equilibria are successfully estimated from Multivariate Curve Resolution analysis of UV absorbance spectra recorded along acid-base titrations and melting experiments of single stranded, hairpin and their mixtures. The dependence of formation constants upon pH was successfully estimated. The hairpin h26 (5'-GAAGGAGGAGA-TTTT-TCTCCTCCTTC-3'), and the single stranded oligonucleotides s11CT (5'-CTTCCTCCTCT-3'), s11AG (5'-AGAGGAGGAAG-3') and s11TG (5'-TGTGGTGGTTG-3') were synthesized and their protonation and conformational equilibria were studied in detail. The procedure was shown to be especially useful for the study of triplexes with a low hypochromism upon formation.     

Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry

Bronchoalveolar lavage fluid (BALF) contains proteins derived from various pulmonary cell types, secretions and blood. As the characterization of the BALF proteome will be instrumental in establishing potential biomarkers of pathophysiology in the lungs, the objective of this study was to contribute to the comprehensive collection of Mus musculus BALF proteins using high resolution and highly sensitive micro-capillary liquid chromatography (microLC) combined with state-of-the-art high resolution mass spectrometry (MS). BALF was collected from ICR and C57BL/6 male mice exposed to nose-only inhalation to either air or cigarette smoke. The tandem mass spectra were analyzed by SEQUEST for peptide identifications with the subsequent application of accurate mass and time tags resulting in the identification of 1797 peptides with high confidence by high resolution MS. These peptides covered 959 individual proteins constituting the largest collection of BALF proteins to date. High throughput monitoring profiles of this extensive collection of BALF proteins will facilitate the discovery and validation of biomarkers that would elucidate pathogenic or adaptive responses of the lungs upon toxic insults.     

Stability of butterfly assemblages in relation to the level of numerical resolution and altitude

Quick studies on biodiversity are frequently used in conservation assessments. Conclusions from these studies would be consistent if assemblages under consideration are stable over time. The stability of butterfly assemblages in the Picos de Europa in northern Spain was examined at several levels of numerical resolution. The survey was carried out in 1993 and 1995, which allowed at least one complete turnover of all individuals in each locality. Butterfly assemblages were usually stable at the levels of number of species and total number of individuals, species presence and absence, and abundance rankings. But, absolute abundances of individual species changed from 1993 to 1995 out of synchrony with one another. Regional distributions and altitudinal ranges of species were also stable. Assemblages were similar in both study years, judging by similar site ordinations by reciprocal averaging. Overall, these results are in accordance with most studies where stability has been examined at several numerical levels; they also suggest that abundances of individual species do not vary enough to disrupt overall assemblage abundance rankings. Butterfly assemblages at sites at higher altitude tended to be more unstable in terms of abundance rankings and absolute abundances. This agrees with ecological theory predicting less stable assemblages in physically harsh environments. We concluded that monitoring for a relatively short time period can give a clear picture of both local and regional butterfly biodiversity and species composition.     

Characterization of wound responses of stems of paper birch (Betula papyrifera) and European white birch (Betula pendula)

Plants respond to feeding injury by chewing insects by inducing both a general response to mechanical wounding and a specific response to herbivore-associated elicitors. In both cases, plant response involves complex biochemical and physiological changes. We compared chemical and physical responses of paper birch (B. papyrifera) and European white birch (B. pendula) stems to mechanical injury to determine if aspects of their wound response correspond with the much higher resistance of paper birch to bronze birch borer (Agrilus anxius). We also characterized stem responses to mechanical wounding plus bronze birch borer larval homogenate to determine if larval cues elicited a more specific response than mechanical wounding alone. In both species, wounding decreased concentrations of individual phenolics, total phenolics, and condensed tannins, perhaps because they were diverted to lignin biosynthesis, the concentration of which increased. Nitrogen concentration increased in both species while free amino acid concentrations declined, perhaps because they were utilized to synthesize proteins. Application of larval homogenate did not elicit a response different from that induced by mechanical injury. When comparing wound responses of the two birch species, phenolic profiles differed most conspicuously. However, multivariate analyses revealed no differences between constitutive and wound-induced phenolic profiles within each species, and the rate of wound periderm growth was equivalent between species. These results suggest that components of the wound response we measured may not contribute to interspecific variation in bronze birch borer resistance of paper birch and European white birch.     

Binding properties of food colorant allura red with human serum albumin in vitro

Allura red (AR) is a widely used colorant in food industry, but may have a potential security risk. In this study, the properties of interaction between AR and human serum albumin (HSA) in vitro were determined by fluorescence, UV–Vis absorption and circular dichroism (CD) spectroscopy combining with multivariate curve resolution–alternating least squares (MCR–ALS) chemometrics and molecular modeling approaches. An expanded UV–Vis data matrix was resolved by MCR–ALS method, and the concentration profiles and pure spectra for the three reaction components (AR, HSA, and AR–HSA complex) of the system were then successfully obtained to evaluate the progress interaction of AR with HSA. The calculated thermodynamic parameters indicated that hydrogen binding and hydrophobic interactions played major roles in the binding process, and the interaction induced a decrease in the protein surface hydrophobicity. The competitive experiments revealed that AR mainly located in Sudlow’s site I of HSA, and this result was further supported by molecular modeling studies. Analysis of CD spectra found that the addition of AR induced the conformational changes of HSA. This study have provided new insight into the mechanism of interaction between AR and HSA.     

Niche shifts in Greater Antillean Anolis communities: effects of niche metric and biological resolution on null model tests

Summary Using published data, a Monte Carlo approach was used to determine if niche shifts in communities of Anolis lizards have occurred within two islands in the Greater Antilles. Communities at 4 sites on Puerto Rico and 4 sites on Jamaica were randomly assembled using resource-use data from any of the 4 sites with the constraint that the species list of the random community was identical to that observed for each site. The observed niche structure and that of the randomly assembled community were compared at each site. The null hypothesis tested was that one of several functions of niche overlap did not produce lower values in the observed communities compared to those randomly assembled. The sensitivity of this method to details of the analysis was investigated by using 5 variations on the procedure for quantifying the niche structure of the communities. I investigated the effects of (1) using Pianka's versus Levins' metric of niche overlap, (2) using complete resource-use data versus the marginals of the distributions, (3) asymmetric responses to overlap due to size differences between overlapping species, (4) using estimated electivities versus the observed proportional use of resource states, and (5) methods of niche analysis based on different degrees of biological resolution (e.g., community-wide statistics versus individual species responses). The results of the simulations and statistical comparisons did not provide a clear, unambiguous answer to the question of the occurrence of niche shifts. Statistical evidence for niche shifts was more frequently detected using Levins' metric compared to Pianka's, and shifts were easier to detect using high biological resolution (examination of individual species) compared to community-wide measures of niche structure response.     

Effect of quercetin on the amiloride–bovine serum albumin interaction using spectroscopic methods,molecular docking and chemometric approaches

The effect of quercetin flavonoid (QUE), on the binding interaction of antihypertensive drug, amiloride (AMI) with bovine serum albumin (BSA) was investigated in this study. Spectroscopic methods such as steady‐state, synchronous, three‐dimensional fluorescence, and circular dichroism spectroscopy were employed to study the interaction. Fluorescence data were analyzed using the Stern–Volmer equation and a static quenching process was found to be involved in the formation of AMI–BSA and QUE–BSA complexes and were in good agreement with the thermodynamic study. The thermodynamic parameters illustrated that the process is spontaneous and enthalpy driven. Hydrophobicity is acting as the primary force in the binding interaction. Fluorescence spectral data were resolved using a multivariate curve resolution‐alternating least squares method (MCR–ALS). Site marker and molecular docking studies confirmed the binding site of AMI on BSA, i.e. site II. The binding distance between amino acid of BSA and AMI was calculated and found to be 2.18 nm which indicated that energy transfer has occurred from an amino acid of BSA to AMI. The binding affinity of AMI to BSA was found to be reduced in the presence of QUE, which may lead to the poor distribution of AMI at the desired site.     

Protonation studies and multivariate curve resolution on oligodeoxynucleotides carrying the mutagenic base 2-aminopurine

2-Aminopurine (P) is a mutagen causing A.T to G.C transitions in prokaryotic systems. To study the base-pairing schemes between P and cytosine (C) or thymine (T), two self-complementary dodecamers containing P paired with either C or T were synthesized, and their protonation equilibria were studied by acid-base titrations and melting experiments. The mismatches were incorporated into the self-complementary sequence d(CGCPCCGGXGCG), where X was C or T. Spectroscopic data obtained from molecular absorption, circular dichroism (CD), and molecular fluorescence spectroscopy were analyzed by a factor-analysis-based method, multivariate curve resolution based on the alternating least squares optimization procedure (MCR-ALS). This procedure allows determination of the number of acid-base species or conformations present in an acid-base or melting experiment and the resolution of the concentration profiles and pure spectra for each of them. Acid-base experiments have shown that at pH 7, 150 mM ionic strength, and 37 degrees C, both C and P are deprotonated. At pH near 4, the majority of species shows C protonated and P deprotonated. Finally, at pH values near 3, the majority of species shows both protonated C and P. These results are in agreement with NMR studies showing a wobble geometry for the P x C base pair and a Watson-Crick geometry for the P x T base pair at neutral pH. Melting experiments were carried out to confirm the proposed acid-base distribution profile. For the sequence including the P x T mismatch, only one transition was observed at neutral pH. However, for the sequence including the P x C mismatch, two transitions were detected by CD but only one by molecular absorption. This behavior agrees with that observed by other authors for oligonucleotides of similar sequence and suggests the following sequence of conformational changes during melting: duplex --> hairpin --> random coil.     

van't Hoff and calorimetric enthalpies II: effects of linked equilibria

The complexity of binding reactions, including the linkage with other equilibria, is becoming increasingly apparent in biological processes such as signal transduction. Understanding these interactions requires obtaining thermodynamic profiles for each of the equilibria that occur in a binding event. Concern has been raised as to whether linked equilibria contribute differently to thermodynamics, such as DeltaH degrees and DeltaC(p), obtained from calorimetric and van't Hoff methods. We have previously shown that linked equilibria do not contribute differently to the van't Hoff and calorimetrically determined DeltaH degrees for processes such as linked folding or hydration. Here, examples of proton and ion linkage are examined. We show that there is no reason to expect the calorimetric and van't Hoff DeltaH degrees to be different, even without prior knowledge of the presence or absence of linked equilibria, as long as the system is permitted to equilibrate. However, it is possible to create experimental scenarios that result in and discrepancies. Furthermore, it is found that the presence of linked equilibria in all cases can result in "nonconventional" DeltaH degrees and DeltaC(p) profiles, making data analysis nontrivial.     

Study of the influence of metal ions on tRNA(Phe) thermal unfolding equilibria by UV spectroscopy and multivariate curve resolution

The influence of metal ions (Na(+), Mg(2+) and Cd(2+)) on the thermal unfolding of phenylalanine transfer ribonucleic acid (tRNA(Phe)) was studied by UV spectroscopy-monitored melting experiments. Absorbance data were obtained during the unfolding process in the range 220-340 nm and later analyzed by a multivariate curve resolution approach (MCR-ALS) based on factor analysis. This procedure determines the number of spectroscopically distinct conformations present during the unfolding process and reveals their concentration profiles and pure spectra, without any initial assumption having to be made about the number of steps in the unfolding pathway. From the concentration profiles and pure spectra, information such as T(m) values can be recovered. The results were compared with those obtained previously in spectroscopic and calorimetric unfolding experiments, showing that the multivariate approach recovers information that complements that obtained in traditional spectroscopic melting experiments.     

A strategy for modelling dynamic responses in metabolic samples characterized by GC/MS

A multivariate strategy for studying the metabolic response over time in urinary GC/MS data is presented and exemplified by a study of drug-induced liver toxicity in the rat. The strategy includes the generation of representative data through hierarchical multivariate curve resolution (H-MCR), highlighting the importance of obtaining resolved metabolite profiles for quantification and identification of exogenous (drug related) and endogenous compounds (potential biomarkers) and for allowing reliable comparisons of multiple samples through multivariate projections. Batch modelling was used to monitor and characterize the normal (control) metabolic variation over time as well as to map the dynamic response of the drug treated animals in relation to the control. In this way treatment related metabolic responses over time could be detected and classified as being drug related or being potential biomarkers. In summary the proposed strategy uses the relatively high sensitivity and reproducibility of GC/MS in combination with efficient multivariate curve resolution and data analysis to discover individual markers of drug metabolism and drug toxicity. The presented results imply that the strategy can be of great value in drug toxicity studies for classifying metabolic markers in relation to their dynamic responses as well as for biomarker identification.     

Application of multivariate curve resolution alternating least squares method for determination of caffeic acid in the presence of catechin interference

In the current article, preparation and application of a graphene oxide nanosheets-based sensor for electrochemical determination of caffeic acid (CA) in the presence of catechin is described. This measurement was performed using the differential pulse voltammetry (DPV) technique and chemometric methods such as multivariate curve resolution–alternating least squares (MCR–ALS). The modified sensor was characterized by various techniques such as Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, ultraviolet–visible, X-ray diffraction (XRD), and scanning electron microscopy (SEM). Operating conditions and influencing variables (involving several chemical and instrumental variables) were optimized with central composite rotatable design and response surface methodology. The second-order electrochemical data were generated by changing the pulse height in DPV, and after potential shift correction MCR–ALS was applied. Under the optimized conditions, the dynamic range for CA was from 0.5 to 100.0 μM and the detection limit was found to be 1.1 × 10^–9 M. The results revealed that the modified electrode shows an improvement in anodic oxidation activity of CA due to a marked enhancement in the current response compared with the bare carbon paste electrode. The modified electrode demonstrated good sensitivity, selectivity, and stability. The proposed method was successfully applied in determination of caffeic acid in the presence of unexpected electroactive interferences with a very high degree of overlapping such as catechin in real samples.     

Characterization of Cu2+-binding modes in the prion protein by visible circular dichroism and multivariate curve resolution

Visible circular dichroism (CD) spectra from the copper(II) titration of the metal-binding region of the prion protein, residues 57-98, were analyzed using the self-modeling curve resolution method multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS is a set of mathematical tools for estimating pure component spectra and composition profiles from mixture spectra. Model-free solutions (e.g., soft models) are produced under the assumption that pure component profiles should be nonnegative and unimodal. Optionally, equality constraints can be used when the concentration or spectrum of one or more species is known. MCR-ALS is well suited to complex biochemical systems such as the prion protein which binds multiple copper ions and thus gives rise to titration data consisting of several pure component spectra with overlapped or superimposed absorption bands. Our study reveals the number of binding modes used in the uptake of Cu²⁺ by the full metal-binding region of the prion protein and their relative concentration profiles throughout the titration. The presence of a non-CD active binding mode can also be inferred. We show that MCR-ALS analysis can be initialized using empirically generated or mathematically generated pure component spectra. The use of small model peptides allows us to correlate specific Cu²⁺-binding structures to the pure component spectra.     

The system VO2+ +oxidized glutathione: a potentiometric and spectroscopic study

The equilibria in the system VO2+ +oxidized glutathione in aqueous solution have been studied in the pH range 2-11 by a combination of pH potentiometry and spectroscopy (EPR, visible absorption and circular dichroism). The results of the various methods are self-consistent and the equilibrium model includes the species MLH4, MLH3, MLH2, MLH, ML, MLH(-1), MLH(-2) and several hydrolysis products (where H4L denotes oxidized glutathione); individual formation constants and spectra are given. Plausible structures for each stoichiometry are discussed.