Sperm head morphometry in ejaculates of adult marmosets (Callithrix jacchus): a model for studying sperm subpopulations and among-donor variations

In humans and other mammals, sperm morphology has been considered one of the most important predictive parameters of fertility. The objective was to determine the presence and distribution of sperm head morphometric subpopulations in a nonhuman primate model (Callithrix jacchus), using an objective computer analysis system and principal component analysis (PCA) methods to establish the relationship between the subpopulation distribution observed and among-donor variation. The PCA method revealed a stable number of principal components in all donors studied, that represented more than 85% of the cumulative variance in all cases. After cluster analysis, a variable number (from three to seven) sperm morphometric subpopulations were identified with defined sperm dimensions and shapes. There were differences in the distribution of the sperm morphometric subpopulations (P < 0.001) in all ejaculates among the four donors analyzed. In conclusion, in this study, computerized sperm analysis methods combined with PCA cluster analyses were useful to identify, classify, and characterize various head sperm morphometric subpopulations in nonhuman primates, yielding considerable biological information. In addition, because all individuals were kept in the same conditions, differences in the distribution of these subpopulations were not attributed to external or management factors. Finally, the substantial information derived from subpopulation analyses provided new and relevant biological knowledge which may have a practical use for future studies in human and nonhuman primate ejaculates, including identifying individuals more suitable for assisted reproductive technologies. (c) 2012 Elsevier Inc. All rights reserved.

Use of a gold microelectrode for discrimination of gunshot residues

Gunshot residues (GSR) can be used in forensic evaluations to obtain information about the type of gun and ammunition used in a crime. In this work, we present our efforts to develop a promising new method to discriminate the type of gun [four different guns were used: two handguns (0.38 revolver and 0.380 pistol) and two long-barrelled guns (12-calibre pump-action shotgun and 0.38 repeating rifle)] and ammunition (five different types: normal, semi-jacketed, full-jacketed, green, and 3T) used by a suspect. The proposed approach is based on information obtained from cyclic voltammograms recorded in solutions containing GSR collected from the hands of the shooters, using a gold microelectrode; the information was further analysed by non-supervised pattern-recognition methods [(Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA)]. In all cases (gun and ammunition discrimination), good separation among different samples in the score plots and dendrograms was achieved. (C) 2012 Elsevier B.V. All rights reserved.

Expression profiling and cross-species RNA interference (RNAi) of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae

Abstract Background Some organisms can survive extreme desiccation by entering a state of suspended animation known as anhydrobiosis. The free-living mycophagous nematode Aphelenchus avenae can be induced to enter anhydrobiosis by pre-exposure to moderate reductions in relative humidity (RH) prior to extreme desiccation. This preconditioning phase is thought to allow modification of the transcriptome by activation of genes required for desiccation tolerance. Results To identify such genes, a panel of expressed sequence tags (ESTs) enriched for sequences upregulated in A. avenae during preconditioning was created. A subset of 30 genes with significant matches in databases, together with a number of apparently novel sequences, were chosen for further study. Several of the recognisable genes are associated with water stress, encoding, for example, two new hydrophilic proteins related to the late embryogenesis abundant (LEA) protein family. Expression studies confirmed EST panel members to be upregulated by evaporative water loss, and the majority of genes was also induced by osmotic stress and cold, but rather fewer by heat. We attempted to use RNA interference (RNAi) to demonstrate the importance of this gene set for anhydrobiosis, but found A. avenae to be recalcitrant with the techniques used. Instead, therefore, we developed a cross-species RNAi procedure using A. avenae sequences in another anhydrobiotic nematode, Panagrolaimus superbus, which is amenable to gene silencing. Of 20 A. avenae ESTs screened, a significant reduction in survival of desiccation in treated P. superbus populations was observed with two sequences, one of which was novel, while the other encoded a glutathione peroxidase. To confirm a role for glutathione peroxidases in anhydrobiosis, RNAi with cognate sequences from P. superbus was performed and was also shown to reduce desiccation tolerance in this species. Conclusions This study has identified and characterised the expression profiles of members of the anhydrobiotic gene set in A. avenae. It also demonstrates the potential of RNAi for the analysis of anhydrobiosis and provides the first genetic data to underline the importance of effective antioxidant systems in metazoan desiccation tolerance.

Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

The Compositional Aesthetic of Rodolfo Coelho de Souza in Paradise Station: an analysis

This article focuses on the compositional aesthetics of Rodolfo Coelho de Souza (1952-), a Brazilian fine art composer and active researcher, whose concerns surpasses the musical composition isolated from the social communication aspect. This is particularly evident in his piece Paradise Station, which, when analyzed, features the structural depth of its compositional process without disregarding the dialog with the listener and the Brazilian character, according to pitch, rhythm, texture, timbre and dynamics. The present analysis reveals a modular structure based on set classes, worked through a transformation network, which follows the David Lewin model.

Modeling the exergy behavior of human body

Exergy analysis is applied to assess the energy conversion processes that take place in the human body, aiming at developing indicators of health and performance based on the concepts of exergy destroyed rate and exergy efficiency. The thermal behavior of the human body is simulated by a model composed of 15 cylinders with elliptical cross section representing: head, neck, trunk, arms, forearms, hands, thighs, legs, and feet. For each, a combination of tissues is considered. The energy equation is solved for each cylinder, being possible to obtain transitory response from the body due to a variation in environmental conditions. With this model, it is possible to obtain heat and mass flow rates to the environment due to radiation, convection, evaporation and respiration. The exergy balances provide the exergy variation due to heat and mass exchange over the body, and the exergy variation over time for each compartments tissue and blood, the sum of which leads to the total variation of the body. Results indicate that exergy destroyed and exergy efficiency decrease over lifespan and the human body is more efficient and destroys less exergy in lower relative humidities and higher temperatures. (C) 2012 Elsevier Ltd. All rights reserved.

Genotype x location x feeding interactions in Nellore cattle calculated through three-mode principal component analysis

The main objective of this study was to apply three-mode principal component analysis to assess the triple interaction (genotype x location x feeding) on direct genetic value for weight at 205 days of age. We used 60 sires with offspring in three regions of northeastern Brazil (Maranhao, Mata and Agreste, and Reconcavo Baiano) and raised on a pasture regime or with supplementation. There was no interaction between genotype and location, but there was a correlation between genotype and direct effect of feeding. The use of sires should be dictated according to the system of rearing of their offspring.

Description of Rhodnius montenegrensis n. sp (Hemiptera: Reduviidae: Triatominae) from the state of Rondonia, Brazil

We present here a multisource approach that takes advantage of several disciplines to address a taxonomic issue. A triatomine related to Rhodnius robustus Larrousse, 1927 was recently found in the state of Rondonia, Brazil. The name Rhodnius montenegrensis n. sp. is suggested because it was found in the municipality of Monte Negro. The main differences between these two species can be detected in the female and male genitalia, but there are also noticeable differences in their eggs. Molecular analysis using PCR-RFLP technique and Bayesian inferences based on a fragment of the Cytochrome b (Cyt b) gene corroborated the morphological findings. We used this integrative approach to address the taxonomic decision for a new Rhodnius species and its relationship with others of this genus. Results obtained herein stress that morphology must be used as the major approach for obtaining phenotypic information, and molecular data should be taken as a complementary tool.

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.

PXRF and multivariate statistics analysis of pre-colonial pottery from northeast of Brazil

Portable system of energy dispersive X-ray fluorescence was used to determine the elemental composition of 68 pottery fragments from Sambaqui do Bacanga, an archeological site in Sao Luis, Maranhao, Brazil. This site was occupied from 6600 BP until 900 BP. By determining the element chemical composition of those fragments, it was possible to verify the existence of engobe in 43 pottery fragments. Obtained from two-dimensional graphs and hierarchical cluster analysis performed in fragments of stratigraphies from surface and 113-cm level, and 10 to 20, 132 and 144-cm level, it was possible to group these fragments in five distinct groups, according to their stratigraphies. The results of data grouping (two-dimensional graphics) are in agreement with hierarchical cluster analysis by Ward method. Copyright (C) 2011 John Wiley & Sons, Ltd.

Records of sedimentary dynamics in the continental shelf and upper slope between Aveiro-Espinho (N Portugal)

The sedimentary unconsolidated cover of the Aveiro-Espinho continental shelf and upper slope (NW Portugal) records a complex interplay of processes including wave energy and currents, fluvial input, sediment transport alongshore and cross-shelf, geological and oceanographic processes and sediment sources and sinks. In order to study this record, a set of surface sediment samples was studied. Sediment grain size and composition, as well as the mineralogical composition (by XRD) of the fine (<63 mu m) and clay (<2 mu m) fractions and benthic microfaunal (foraminifera) data were analysed. Cluster analysis applied to the sedimentological data (grain size, sediment composition and mineralogy) allowed the establishment of three main zones corresponding to the: inner-, mid- and outer-shelf/upper slope. On the inner-shelf, the sedimentary coverture is composed of siliciclastic fine to very fine sand, essentially comprising modern (immature) terrigenous particles. The sediment grain size, as well as mineralogical and microfaunal composition, denote the high energetic conditions of this sector in which the alongshore transport of sand is predominantly southward and occurs mostly during the spring-summer oceanographic regime, when the main river providing sediments to this area, the River Douro, undergoes periods of drought. This effect may emphasize the erosive character of this coastal sector at present, since the Ria de Aveiro provides the shelf with few sediments. On the mid-shelf, an alongshore siliciclastic band of coarse sand and gravel can be found between the 40 m and 60 m isobaths. This gravelly deposit includes relic sediments deposited during lower sea-level stands. This structure stays on the surface due to the high bottom energy, which promotes the remobilization of the fine-grained sediments, and/or events of sediments bypassing. Benthic foraminifera density and "Benthic Foraminifera High Productivity" (BFHP) proxy values are in general low, which is consistent with the overall small supply of organic matter to the oceanic bottom in the inner- and mid-shelf. However, the Ria de Aveiro outflow, which delivers organic matter to the shelf, leaves its imprint mainly on the mid-shelf, identifiable by the increase in foraminifera density and BFHP values in front of the lagoon mouth. The higher values of BFHP along the 100 m isobath trace the present position of an oceanic thermal front whose situation may have changed in the last 3/5 ka BP. This zone marks a clear difference in the density, diversity and composition of benthic foraminifera assemblages. Here, in addition, sediment composition changes significantly, giving rise to carbonate-rich fine to medium sand in the deeper sector. The low bottom energy and the small sedimentation rate of the outer-shelf contributed to the preservation of a discontinuous carbonate-rich gravel band, between the 100 m and 140 m isobaths, also related to paleo-littorals, following the transgression that has occurred since the Last Glacial Maximum. The winter oceanographic regime favours the transport of fine grained sediments to the outer-shelf and upper slope. The inner- and mid-shelf, however, have low amounts of this kind of sediment and the Cretacic carbonated complexes Pontal da Galega and Pontal da Cartola, rocky outcrops located at the mid- and outer-shelf, act as morphological barriers to the cross-shelf transport of sediments. Thus a reduced sedimentation rate occurs in these deeper sectors, as indicated by the lower abundance of detrital minerals, which is compensated for the high sedimentary content of biogenic carbonates. The relatively high BFHP and Shannon Index values indicate water column stratification, high supply of organic matter and environmental stability, which provide favourable conditions for a diversified benthic fauna to flourish. These conditions also encourage authigenic chemical changes, favourable to glauconite formation, as well as illite and kaolinite degradation. Benthic foraminifera and clay mineral assemblages also reveal the effect of the internal waves pushing upward, and downslope losses of the sediments on the outer-shelf and upper slope.

Incidence of Leptospirosis infection in the East Zone of Sao Paulo City, Brazil

Abstract Background Leptospirosis is a zoonosis which is spread through contamined running water. This contaminations is seriously affected by the flooding which occurs in the area surrounding the Aricanduva river. The transmission of the disease results mainly from the contact of water with soil contaminated by the urine of infected animals. We aimed to conduct an epidemiological survey on Leptospirosis cases in Sao Paulo East Zone area. Method The analysis conducted in this study was based on data collected from the health authorities of that region close the Aricanduva river between 2007 and 2008 years, which give the rates of confirmed cases, mortality and death from human Leptospirosis. Other information concerned with the relationships among rainfall index, points of flooding and incidence of Leptospirosis. Results We observed a direct and important water contamination. Records of flooding points and dates of the reported cases in the region showed a direct relationship from which the period of higher rainfall also recorded an increase in cases. The annual record of the city and the region and rainfall regions also presented correlation. Conclusion The association between the indices of flooding and Leptospirosis cases indicates that preventive measures are necessary to avoid exposing the community.

cDNA-AFLP analysis of Psidium guajava L. cultivars under water stress and mechanical injury: methodological implications

Studies involving amplified fragment length polymorphism (cDNA-AFLP) have often used polyacrylamide gels with radiolabeled primers in order to establish best primer combinations, to analyze, and to recover transcript-derived fragments. Use of automatic sequencer to establish best primer combinations is convenient, because it saves time, reduces costs and risks of contamination with radioactive material and acrylamide, and allows objective band-matching and more precise evaluation of transcript-derived fragments intensities. This study aimed at examining the gene expression of commercial cultivars of P. guajava subjected to water and mechanical injury stresses, combining analyses by automatic sequencer and fluorescent kits for polyacrylamide gel electrophoresis. Firstly, 64 combinations of EcoRI and MseI primers were tested. Ten combinations with higher number of polymorphic fragments were then selected for transcript-derived fragments recovering and cluster analysis, involving 45 saplings of P. guajava. Two groups were obtained, one composed by the control samplings, and another formed by samplings undergoing stress, with no clear distinction between stress treatments. The results revealed the convenience of using a combination of automatic sequencer and fluorescent kits for polyacrylamide gel electrophoreses to examine gene expression profiles. The Unweighted Pair Group Method with Arithmetic Mean analysis using Euclidean distances points out a similar induced response mechanism of P. guajava undergoing water stress and mechanical injury.

Microbial Translocation Is Associated with Extensive Immune Activation in Dengue Virus Infected Patients with Severe Disease

Background: Severe dengue virus (DENV) disease is associated with extensive immune activation, characterized by a cytokine storm. Previously, elevated lipopolysaccharide (LPS) levels in dengue were found to correlate with clinical disease severity. In the present cross-sectional study we identified markers of microbial translocation and immune activation, which are associated with severe manifestations of DENV infection. Methods: Serum samples from DENV-infected patients were collected during the outbreak in 2010 in the State of Sa˜o Paulo, Brazil. Levels of LPS, lipopolysaccharide binding protein (LBP), soluble CD14 (sCD14) and IgM and IgG endotoxin core antibodies were determined by ELISA. Thirty cytokines were quantified using a multiplex luminex system. Patients were classified according to the 2009 WHO classification and the occurrence of plasma leakage/shock and hemorrhage. Moreover, a (non-supervised) cluster analysis based on the expression of the quantified cytokines was applied to identify groups of patients with similar cytokine profiles. Markers of microbial translocation were linked to groups with similar clinical disease severity and clusters with similar cytokine profiles. Results: Cluster analysis indicated that LPS levels were significantly increased in patients with a profound pro-inflammatory cytokine profile. LBP and sCD14 showed significantly increased levels in patients with severe disease in the clinical classification and in patients with severe inflammation in the cluster analysis. With both the clinical classification and the cluster analysis, levels of IL-6, IL-8, sIL-2R, MCP-1, RANTES, HGF, G-CSF and EGF were associated with severe disease. Conclusions: The present study provides evidence that both microbial translocation and extensive immune activation occur during severe DENV infection and may play an important role in the pathogenesis.