Multivariate analysis of fresh-cut carambola slices stored under different temperatures

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Ingredient classification according to the digestible amino acid profile: an exploratory analysis

This study aimed: 1) to classify ingredients according to the digestible amino acid (AA) profile; 2) to determine ingredients with AA profile closer to the ideal for broiler chickens; and 3) to compare digestible AA profiles from simulated diets with the ideal protein profile. The digestible AA levels of 30 ingredients were compiled from the literature and presented as percentages of lysine according to the ideal protein concept. Cluster and principal component analyses (exploratory analyses) were used to compose and describe groups of ingredients according to AA profiles. Four ingredient groups were identified by cluster analysis, and the classification of the ingredients within each of these groups was obtained from a principal component analysis, showing 11 classes of ingredients with similar digestible AA profiles. The ingredients with AA profiles closer to the ideal protein were meat and bone meal 45, fish meal 60 and wheat germ meal, all of them constituting Class 1; the ingredients from the other classes gradually diverged from the ideal protein. Soybean meal, which is the main protein source for poultry, showed good AA balance since it was included in Class 3. on the contrary, corn, which is the main energy source in poultry diets, was classified in Class 8. Dietary AA profiles were improved when corn and/or soybean meal were partially or totally replaced in the simulations by ingredients with better AA balance.

Estimates of genetic parameters, and cluster and principal components analyses of breeding values related to egg production traits in a White Leghorn population

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Comparative studies of the sample decomposition of green and roasted coffee for determination of nutrients and data exploratory analysis

The contents of some nutrients in 35 Brazilian green and roasted coffee samples were determined by flame atomic absorption spectrometry (Ca, Mg, Fe, Cu, Mn, and Zn), flame atomic emission photometry (Na and K) and Kjeldahl (N) after preparing the samples by wet digestion procedures using i) a digester heating block and ii) a conventional microwave oven system with pressure and temperature control. The accuracy of the procedures was checked using three standard reference materials (National Institute of Standards and Technology, SRM 1573a Tomato Leaves, SRM 1547 Peach Leaves, SRM 1570a Trace Elements in Spinach). Analysis of data after application of t-test showed that results obtained by microwave-assisted digestion were more accurate than those obtained by block digester at 95% confidence level. Additionally to better accuracy, other favorable characteristics found were lower analytical blanks, lower reagent consumption, and shorter digestion time. Exploratory analysis of results using Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) showed that Na, K, Ca, Cu, Mg, and Fe were the principal elements to discriminate between green and roasted coffee samples. ©2007 Sociedade Brasileira de Química.

Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph

When searching for prospective novel peptides, it is difficult to determine the biological activity of a peptide based only on its sequence. The trial and error approach is generally laborious, expensive and time consuming due to the large number of different experimental setups required to cover a reasonable number of biological assays. To simulate a virtual model for Hymenoptera insects, 166 peptides were selected from the venoms and hemolymphs of wasps, bees and ants and applied to a mathematical model of multivariate analysis, with nine different chemometric components: GRAVY, aliphaticity index, number of disulfide bonds, total residues, net charge, pI value, Boman index, percentage of alpha helix, and flexibility prediction. Principal component analysis (PCA) with non-linear iterative projections by alternating least-squares (NIPALS) algorithm was performed, without including any information about the biological activity of the peptides. This analysis permitted the grouping of peptides in a way that strongly correlated to the biological function of the peptides. Six different groupings were observed, which seemed to correspond to the following groups: chemotactic peptides, mastoparans, tachykinins, kinins, antibiotic peptides, and a group of long peptides with one or two disulfide bonds and with biological activities that are not yet clearly defined. The partial overlap between the mastoparans group and the chemotactic peptides, tachykinins, kinins and antibiotic peptides in the PCA score plot may be used to explain the frequent reports in the literature about the multifunctionality of some of these peptides. The mathematical model used in the present investigation can be used to predict the biological activities of novel peptides in this system, and it may also be easily applied to other biological systems. © 2011 Elsevier Inc.

Multivariate curve resolution analysis applied to time-resolved synchrotron X-ray Absorption Spectroscopy monitoring of the activation of copper alumina catalyst

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Comparative analysis of shell occupation by two southern populations of the hermit crab Loxopagurus loxochelis (Decapoda, Diogenidae)

The present study aimed to comparatively verify the relation between the hermit crabs and the shells they use in two populations of Loxopagurus loxochelis. Samples were collected monthly from July 2002 to June 2003, at Caraguatatuba and Ubatuba Bay, Sao Paulo, Brazil. The animals sampled had their sex identified, were weighed and measured; their shells were identified, measured and weighed, and their internal volume determined. To relate the hermit crab's characteristics and the shells' variables, principal component analysis (PCA) and a regression tree were used. According to the PCA analysis, the three gastropod shells most frequently used by L. loxochelis varied in size. The regression tree successfully explained the relationship between the hermit crab's characteristics and the internal volume of the inhabited shell. It can be inferred that the relationship between the morphometry of an individual hermit crab and its shell is not straightforward and it is impossible to explain only on the basis of direct correlations between the body's and the shell's attributes. Several factors (such as the morphometry and the availability of the shell, environmental conditions and inter- and intraspecific competition) interact and seem to be taken into consideration by the hermit crabs when they choose a shell, resulting in the diversified pattern of shell occupancy shown here and elsewhere.

Study of cerebral gene expression densities using Voronoi analysis

As the available public cerebral gene expression image data increasingly grows, the demand for automated methods to analyze such large amount of data also increases. An important study that can be carried out on these data is related to the spatial relationship between gene expressions. Similar spatial density distribution of expression between genes may indicate they are functionally correlated, thus the identification of these similarities is useful in suggesting directions of investigation to discover gene interactions and their correlated functions. In this paper, we describe the use of a high-throughput methodology based on Voronoi diagrams to automatically analyze and search for possible local spatial density relationships between gene expression images. We tested this method using mouse brain section images from the Allen Mouse Brain Atlas public database. This methodology provided measurements able to characterize the similarity of the density distribution between gene expressions and allowed the visualization of the results through networks and Principal Component Analysis (PCA). These visualizations are useful to analyze the similarity level between gene expression patterns, as well as to compare connection patterns between region networks. Some genes were found to have the same type of function and to be near each other in the PCA visualizations. These results suggest cerebral density correlations between gene expressions that could be further explored. (C) 2011 Elsevier B.V. All rights reserved.

Quantitative Chemical Profile and Multivariate Statistical Analysis of Alembic Distilled Sugarcane Spirit Fractions

Concentrations of 39 organic compounds were determined in three fractions (head, heart and tail) obtained from the pot still distillation of fermented sugarcane juice. The results were evaluated using analysis of variance (ANOVA), Tukey's test, principal component analysis (PCA), hierarchical cluster analysis (HCA) and linear discriminant analysis (LDA). According to PCA and HCA, the experimental data lead to the formation of three clusters. The head fractions give rise to a more defined group. The heart and tail fractions showed some overlap consistent with its acid composition. The predictive ability of calibration and validation of the model generated by LDA for the three fractions classification were 90.5 and 100%, respectively. This model recognized as the heart twelve of the thirteen commercial cachacas (92.3%) with good sensory characteristics, thus showing potential for guiding the process of cuts.

Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli

To understand the regulatory dynamics of transcription factors (TFs) and their interplay with other cellular components we have integrated transcriptional, protein-protein and the allosteric or equivalent interactions which mediate the physiological activity of TFs in Escherichia coli. To study this integrated network we computed a set of network measurements followed by principal component analysis (PCA), investigated the correlations between network structure and dynamics, and carried out a procedure for motif detection. In particular, we show that outliers identified in the integrated network based on their network properties correspond to previously characterized global transcriptional regulators. Furthermore, outliers are highly and widely expressed across conditions, thus supporting their global nature in controlling many genes in the cell. Motifs revealed that TFs not only interact physically with each other but also obtain feedback from signals delivered by signaling proteins supporting the extensive cross-talk between different types of networks. Our analysis can lead to the development of a general framework for detecting and understanding global regulatory factors in regulatory networks and reinforces the importance of integrating multiple types of interactions in underpinning the interrelationships between them.

Multivariate analysis of fresh-cut carambola slices stored under different temperatures

Quality of fresh-cut carambola (Averrhoa carambola L) is related to many chemical and biochemical variables especially those involved with softening and browning, both influenced by storage temperature. To study these effects, a multivariate analysis was used to evaluate slices packaged in vacuum-sealed polyolefin bags, and stored at 2.5 degrees C, 5 degrees C and 10 degrees C, for up to 16 d. The quality of slices at each temperature was correlated with the duration of storage, O(2) and CO(2) concentration in the package, physical chemical constituents, and activity of enzymes involved in softening (PG) and browning (PPO) metabolism. Three quality groups were identified by hierarchical cluster analysis, and the classification of the components within each of these groups was obtained from a principal component analysis (PCA). The characterization of samples by PCA clearly distinguished acceptable and non-acceptable slices. According to PCA, acceptable slices presented higher ascorbic acid content, greater hue angles ((o)h) and final lightness (L-5) in the first principal component (PC1). On the other hand, non-acceptable slices presented higher total pectin content. PPO activity in the PC1. Non-acceptable slices also presented higher soluble pectin content, increased pectin solubilisation and higher CO(2) concentration in the second principal component (PC2) whereas acceptable slices showed lower total sugar content. The hierarchical cluster and PCA analyses were useful for discriminating the quality of slices stored at different temperatures. (C) 2011 Elsevier B.V. All rights reserved.

Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates

Abstract Background Prostate cancer is a leading cause of death in the male population, therefore, a comprehensive study about the genes and the molecular networks involved in the tumoral prostate process becomes necessary. In order to understand the biological process behind potential biomarkers, we have analyzed a set of 57 cDNA microarrays containing ~25,000 genes. Results Principal Component Analysis (PCA) combined with the Maximum-entropy Linear Discriminant Analysis (MLDA) were applied in order to identify genes with the most discriminative information between normal and tumoral prostatic tissues. Data analysis was carried out using three different approaches, namely: (i) differences in gene expression levels between normal and tumoral conditions from an univariate point of view; (ii) in a multivariate fashion using MLDA; and (iii) with a dependence network approach. Our results show that malignant transformation in the prostatic tissue is more related to functional connectivity changes in their dependence networks than to differential gene expression. The MYLK, KLK2, KLK3, HAN11, LTF, CSRP1 and TGM4 genes presented significant changes in their functional connectivity between normal and tumoral conditions and were also classified as the top seven most informative genes for the prostate cancer genesis process by our discriminant analysis. Moreover, among the identified genes we found classically known biomarkers and genes which are closely related to tumoral prostate, such as KLK3 and KLK2 and several other potential ones. Conclusion We have demonstrated that changes in functional connectivity may be implicit in the biological process which renders some genes more informative to discriminate between normal and tumoral conditions. Using the proposed method, namely, MLDA, in order to analyze the multivariate characteristic of genes, it was possible to capture the changes in dependence networks which are related to cell transformation.

Comparative analysis of shell occupation by two southern populations of the hermit crab Loxopagurus loxochelis (Decapoda, Diogenidae)

The present study aimed to comparatively verify the relation between the hermit crabs and the shells they use in two populations of Loxopagurus loxochelis. Samples were collected monthly from July 2002 to June 2003, at Caraguatatuba and Ubatuba Bay, São Paulo, Brazil. The animals sampled had their sex identified, were weighed and measured; their shells were identified, measured and weighed, and their internal volume determined. To relate the hermit crab's characteristics and the shells' variables, principal component analysis (PCA) and a regression tree were used. According to the PCA analysis, the three gastropod shells most frequently used by L. loxochelis varied in size. The regression tree successfully explained the relationship between the hermit crab's characteristics and the internal volume of the inhabited shell. It can be inferred that the relationship between the morphometry of an individual hermit crab and its shell is not straightforward and it is impossible to explain only on the basis of direct correlations between the body's and the shell's attributes. Several factors (such as the morphometry and the availability of the shell, environmental conditions and inter- and intraspecific competition) interact and seem to be taken into consideration by the hermit crabs when they choose a shell, resulting in the diversified pattern of shell occupancy shown here and elsewhere.

Multivariate spectroscopic methods for the analysis of solutions

In this thesis some multivariate spectroscopic methods for the analysis of solutions are proposed. Spectroscopy and multivariate data analysis form a powerful combination for obtaining both quantitative and qualitative information and it is shown how spectroscopic techniques in combination with chemometric data evaluation can be used to obtain rapid, simple and efficient analytical methods. These spectroscopic methods consisting of spectroscopic analysis, a high level of automation and chemometric data evaluation can lead to analytical methods with a high analytical capacity, and for these methods, the term high-capacity analysis (HCA) is suggested. It is further shown how chemometric evaluation of the multivariate data in chromatographic analyses decreases the need for baseline separation. The thesis is based on six papers and the chemometric tools used are experimental design, principal component analysis (PCA), soft independent modelling of class analogy (SIMCA), partial least squares regression (PLS) and parallel factor analysis (PARAFAC). The analytical techniques utilised are scanning ultraviolet-visible (UV-Vis) spectroscopy, diode array detection (DAD) used in non-column chromatographic diode array UV spectroscopy, high-performance liquid chromatography with diode array detection (HPLC-DAD) and fluorescence spectroscopy. The methods proposed are exemplified in the analysis of pharmaceutical solutions and serum proteins. In Paper I a method is proposed for the determination of the content and identity of the active compound in pharmaceutical solutions by means of UV-Vis spectroscopy, orthogonal signal correction and multivariate calibration with PLS and SIMCA classification. Paper II proposes a new method for the rapid determination of pharmaceutical solutions by the use of non-column chromatographic diode array UV spectroscopy, i.e. a conventional HPLC-DAD system without any chromatographic column connected. In Paper III an investigation is made of the ability of a control sample, of known content and identity to diagnose and correct errors in multivariate predictions something that together with use of multivariate residuals can make it possible to use the same calibration model over time. In Paper IV a method is proposed for simultaneous determination of serum proteins with fluorescence spectroscopy and multivariate calibration. Paper V proposes a method for the determination of chromatographic peak purity by means of PCA of HPLC-DAD data. In Paper VI PARAFAC is applied for the decomposition of DAD data of some partially separated peaks into the pure chromatographic, spectral and concentration profiles.

Pyrolysis-Gas Chromatography-Mass Spectometry and Chemometric Analysis for the Characterization of Complex Matrices

The present PhD thesis was focused on the development and application of chemical methodology (Py-GC-MS) and data-processing method by multivariate data analysis (chemometrics). The chromatographic and mass spectrometric data obtained with this technique are particularly suitable to be interpreted by chemometric methods such as PCA (Principal Component Analysis) as regards data exploration and SIMCA (Soft Independent Models of Class Analogy) for the classification. As a first approach, some issues related to the field of cultural heritage were discussed with a particular attention to the differentiation of binders used in pictorial field. A marker of egg tempera the phosphoric acid esterified, a pyrolysis product of lecithin, was determined using HMDS (hexamethyldisilazane) rather than the TMAH (tetramethylammonium hydroxide) as a derivatizing reagent. The validity of analytical pyrolysis as tool to characterize and classify different types of bacteria was verified. The FAMEs chromatographic profiles represent an important tool for the bacterial identification. Because of the complexity of the chromatograms, it was possible to characterize the bacteria only according to their genus, while the differentiation at the species level has been achieved by means of chemometric analysis. To perform this study, normalized areas peaks relevant to fatty acids were taken into account. Chemometric methods were applied to experimental datasets. The obtained results demonstrate the effectiveness of analytical pyrolysis and chemometric analysis for the rapid characterization of bacterial species. Application to a samples of bacterial (Pseudomonas Mendocina), fungal (Pleorotus ostreatus) and mixed- biofilms was also performed. A comparison with the chromatographic profiles established the possibility to: • Differentiate the bacterial and fungal biofilms according to the (FAMEs) profile. • Characterize the fungal biofilm by means the typical pattern of pyrolytic fragments derived from saccharides present in the cell wall. • Individuate the markers of bacterial and fungal biofilm in the same mixed-biofilm sample.