Allometric analysis of the ontogenetic variation and evolution of the skull in Caiman spix, 1825 (Crocodylia: Alligatoridae)

We studied ontogenetic variation in the shape of the skull among species of Caiman using principal component analysis. Comparison of multivariate allometric coefficients and ontogenetic trends between size and shape reveals that C. sclerops and C. yacare have similar ontogenetic processes, and they are more related to each other than either is to C. latirostris. Allometric relationships of the characters measured are similar in all species studied. The greater differences were in the width measurements, with higher coefficients in shape (second principal component) for C. latirostris, and length measurements with higher coefficients in shape for C. yacare and C. sclerops. The ontogenetic process leading to change in skull shape in the group seems to be plesiomorphic for elongation and derived for broadening. Statistical comparison of the ontogenetic trends with models of allometric heterochrony suggests that C. latirostris has diverged from the other species by a neotenic process, and that C. sclerops is separated from C. yacare by ontogenetic scaling (progenesis).

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.

Avaliação dos fatores abióticos e bióticos de uma área petroquímica da região de Paulínia, SP, e fotodocumentação dos fungos transientes isolados

Pós-graduação em Ciências Biológicas (Microbiologia Aplicada) - IBRC

Variação geográfica de Osteocephalus taurinus Steindachner, 1862 (Amphibia : Anura : Hylidae)

Osteocephalus taurinus é uma espécie nominal de ampla distribuição na Amazônia e nos llanos do Orinoco. Sua grande variação morfológica indica que se trata de um complexo de espécies. O presente estudo examina a variação geográfica de vários caracteres morfológicos e morfométricos da espécie nominal, avalia a hipótese de tratar-se de fato um complexo de espécies; e testa a teoria da atual distribuição das formas, através de padrões biogeográficos, ecológicos e de regímen de precipitação já definidos. A partir de 431 espécimes estudados foram selecionadas 16 populações, nas quais foram analisados 20 caracteres anatômicos internos, 14 caracteres morfométricos e seis caracteres morfológicos externos. Através de análises estatística e mapas de isolinhas evidenciou-se que O. taurinus não se trata de um complexo de espécies e sim possui uma grande variação intra e interpopulacional das caraterísticas morfométricas e morfológicas. Simultaneamente, foram observados caracteres anatômicos internos polimórficos. O primeiro componente obtido através de uma análise de componentes principais mostra uma variação clinal do tamanho corporal ao longo da distribuição geográfica total, mais evidente nos machos. Em outros caracteres analisados, a variação fico independente do cline. O padrão espacial do tamanho indicou que as formas maiores ocorrem nas terras baixas da Amazônia, onde a vegetação de floresta ombrofila divide as áreas de cerrado ao norte e ao sul do continente sul americano. Nestas últimas áreas, ocorrem com maior intensidade as formas menores. Esta distribuição espacial não se explicou através das divisões propostas por outros autores para Amazônia, o que pode ser devido a um mascaramento gerado pela grande variação intrapopulacional. O modelo espacial do tamanho corporal de O. taurinus não corresponde a um padrão de isolamento por distância, o que pode sugerir que a colonização da espécie em algumas áreas seja recente. Este estudo confirma a hipótese da origem do gênero no início do Plioceno, o que indica que O. taurinus teria tido tempo suficiente para se dispersar antes do surgimento dos Andes como barreira geográfica.

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)

Singular Value Decomposition and Ligand Binding Analysis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Design e semântica: investigação de técnicas estatísticas para auxílio no projeto de produto

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Spatial analysis of egg distribution and geographic changes in the spawning habitat of the Brazilian sardine Sardinella brasiliensis

This paper establishes the spawning habitat of the Brazilian sardine Sardinella brasiliensis and investigates the spatial variability of egg density and its relation with oceanographic conditions in the shelf of the south-east Brazil Bight (SBB). The spawning habitats of S. brasiliensis have been defined in terms of spatial models of egg density, temperature-salinity plots, quotient (Q) analysis and remote sensing data. Quotient curves (Q(C)) were constructed using the geographic distribution of egg density, temperature and salinity from samples collected during nine survey cruises between 1976 and 1993. The interannual sea surface temperature (SST) variability was determined using principal component analysis on the SST anomalies (SSTA) estimated from remote sensing data over the period between 1985 and 2007. The spatial pattern of egg occurrences in the SBB indicated that the largest concentration occurred between Paranagua and Sao Sebastiao. Spawning habitat expanded and contracted during the years, fluctuating around Paranagua. In January 1978 and January 1993, eggs were found nearly everywhere along the inner shelf of the SBB, while in January 1988 and 1991 spawning had contracted to their southernmost position. The SSTA maps for the spawning periods showed that in the case of habitat expansion (1993 only) anomalies over the SBB were zero or slightly negative, whereas for the contraction period anomalies were all positive. Sardinella brasiliensis is capable of exploring suitable spawning sites provided by the entrainment of the colder and less-saline South Atlantic Central Water onto the shelf by means of both coastal wind-driven (to the north-east of the SBB) and meander-induced (to the south-west of the SBB) upwelling.

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.

Theoretical models for the antitrypanosomal activity of thiosemicarbazone derivatives

Thiosemicarbazones are cruzain inhibitors which have been identified as potential antitrypanosomal agents. In this work, several molecular properties were calculated at the density functional theory (DFT)/B3LYP/6-311G* level for a set of 44 thiosemicarbazones. Unsupervised and supervised pattern recognition techniques (hierarchical cluster analysis, principal component analysis, kth-nearest neighbors, and soft independent modeling by class analogy) were used to obtain structureactivity relationship models, which are able to classify unknown compounds according to their activities. The chemometric analyses performed here revealed that 12 descriptors can be considered responsible for the discrimination between high and low activity compounds. Classification models were validated with an external test set, showing that predictive classifications were achieved with the selected variable set. The results obtained here are in good agreement with previous findings from the literature, suggesting that our models can be useful on further investigations on the molecular determinants for the antichagasic activity. (C) 2012 Wiley Periodicals, Inc.

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.

EVAPORATIVE LIGHT-SCATTERING DETECTOR FOR ANALYSIS OF NATURAL PRODUCTS

EVAPORATIVE LIGHT-SCATTERING DETECTOR FOR ANALYSIS OF NATURAL PRODUCTS. The interest in the use of evaporative light scattering detector (ELSD) for the analysis of different classes of natural products has grown over the years. This is because this detector has become an excellent alternative compared to other types of detectors, such as the refractive index detector and the ultraviolet (UV) detector. This review describes the basic principles of ELSD functioning and discusses the advantages and disadvantages in using an ELSD for the analysis of organic compounds. Additionally, an overview, covering the last 23 years, of ELSD applications in natural products analysis (saponins, terpenes, carbohydrates, glycosides, alkaloids, steroids, flavonoids, peptides, polyketides, coumarins and iridoids) is presented and discussed.

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.