Analysis of the protective potential of antigens released by Leishmania (Viannia) shawi promastigotes

Leishmania (Viannia) shawi causes cutaneous lesions in humans. Parasite antigens conferring significant protection against American tegumentar leishmaniosis (ATL) might be important for the development of effective vaccine. Therefore, this work evaluates the protective effect of antigenic fractions released by L. shawi. Antigens released by promastigotes to culture medium were concentrated and isolated by SDS-PAGE. The three main fractions LsPass1 (>75 kDa), LsPass2 (75-50 kDa) and LsPass3 (<50 kDa) were electro-eluted according with their molecular mass. Immunized BALB/c mice were challenged with L. shawi promastigotes and the course of infection monitored during 5 weeks. LsPass1-challenged mice showed no protection, however, a strong degree of protection associated to smaller lesions and high expression of IFN-gamma and TNF-alpha by CD4(+) T, CD8(+) T and double negative CD4CD8 cells was achieved in LsPass3-challenged mice. Furthermore, LsPass2-challenged mice showed an intermediated degree of protection associated to high levels of IFN-gamma, IL-4 and IL-10 mRNA. In spite of increased expression of IFN-gamma and TNF-alpha, high amounts of IL-4 and IL-10 mRNA were also detected in LsPass3-challenged mice indicating a possible contribution of these cytokines for the persistence of a residual number of parasites that may be important in inducing long-lasting immunity. Therefore, LsPass3 seems to be an interesting alternative that should be considered in the development of an effective vaccine against ATL.

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Background: Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Results: Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Conclusions: Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.

Analysis of Vilanova Artigas' unbuilt designs in Sao Paulo

The aim of this article is to examine unbuilt residential projects designed by Vilanova Artigas. The formal and spatial conception of these projects is investigated through physical models. The object of this research project consists of the unbuilt residential projects designed by Vilanova Artigas in Sao Paulo that are available in FAUUSP's digital Library. The results indicate that physical models contribute to a better interpretation of unbuilt architectural design, both from the conceptual and aesthetic and from the functional and technical point of view. The original contribution lies in the object, i.e. the unbuilt projects, in the method, using physical models for analysis, and in the objective, viz. to establish a relationship between Artigas' built works and his unbuilt residential projects in order to better understand the design's spatial conception and its architectural approach.

The contribution of a murine CNS-TB model for the understanding of the host-pathogen interactions in the formation of granulomas

Central nervous system (CNS) tuberculosis (TB) is the most severe form of TB, characterized morphologically by brain granulomas and tuberculous meningitis (TBM). Experimental strategies for the study of the host-pathogen interaction through the analysis of granulomas and its intrinsic molecular mechanisms could provide new insights into the neuropathology of TB. To verify whether cerebellar mycobacterial infection induces the main features of the disease in human CNS and better understand the physiological mechanisms underlying the disease, we injected bacillus Calmette-Guerin (BCG) into the mouse cerebellum. BCG-induced CNS-TB is characterized by the formation of granulomas and TBM, a build up of bacterial loads in these lesions, and microglial recruitment into the lesion sites. In addition, there is an enhanced expression of signaling molecules such as nuclear factor-kappa B (NF-kappa B) and there is a presence of inducible nitric oxide synthase (iNOS) in the lesions and surrounding areas. This murine model of cerebellar CNS-TB was characterized by cellular and biochemical immune responses typically found in the human disease. This model could expand our knowledge about granulomas in TB infection of the cerebellum, and help characterize the physiological mechanisms involved with the progression of this serious illness that is responsible for killing millions people every year. (C) 2012 Elsevier B.V. All rights reserved.

Effect of pulse repetition rate and number of pulses in the analysis of polypropylene and high density polyethylene by nanosecond infrared laser induced breakdown spectroscopy

Pulse repetition rates and the number of laser pulses are among the most important parameters that do affect the analysis of solid materials by laser induced breakdown spectroscopy, and the knowledge of their effects is of fundamental importance for suggesting analytical strategies when dealing with laser ablation processes of polymers. In this contribution, the influence of these parameters in the ablated mass and in the features of craters was evaluated in polypropylene and high density polyethylene plates containing pigment-based PbCrO4. Surface characterization and craters profile were carried out by perfilometry and scanning electron microscopy. Area, volume and profile of craters were obtained using Taylor Map software. A laser induced breakdown spectroscopy system consisted of a Q-Switched Nd:YAG laser (1064 nm, 5 ns) and an Echelle spectrometer equipped with ICCD detector were used. The evaluated operating conditions consisted of 10, 25 and 50 laser pulses at 1, 5 and 10 Hz, 250 mJ/pulse (85 J cm(-2)), 2 mu s delay time and 6 mu s integration time gate. Differences in the topographical features among craters of both polymers were observed. The decrease in the repetition rate resulted in irregular craters and formation of edges, especially in polypropylene sample. The differences in the topographical features and ablated masses were attributed to the influence of the degree of crystallinity, crystalline melting temperature and glass transition temperature in the ablation process of the high density polyethylene and polypropylene. It was also observed that the intensities of chromium and lead emission signals obtained at 10 Hz were two times higher than at 5 Hz by keeping the number of laser pulses constant. (C) 2011 Elsevier B. V. All rights reserved.

Molecular Analysis of the Differentiation Potential of Murine Mesenchymal Stem Cells from Tissues of Endodermal or Mesodermal Origin

Mesenchymal stem cells (MSCs) have received great attention due to their remarkable regenerative, angiogenic, antiapoptotic, and immunosuppressive properties. Although conventionally isolated from the bone marrow, they are known to exist in all tissues and organs, raising the question on whether they are identical cell populations or have important differences at the molecular level. To better understand the relationship between MSCs residing in different tissues, we analyzed the expression of genes related to pluripotency (SOX2 and OCT-4) and to adipogenic (C/EBP and ADIPOR1), osteogenic (OMD and ALP), and chondrogenic (COL10A1 and TRPV4) differentiation in cultures derived from murine endodermal (lung) and mesodermal (adipose) tissue maintained in different conditions. MSCs were isolated from lungs (L-MSCs) and inguinal adipose tissue (A-MSCs) and cultured in normal conditions, in overconfluence or in inductive medium for osteogenic, adipogenic, or chondrogenic differentiation. Cultures were characterized for morphology, immunophenotype, and by quantitative real-time reverse transcription-polymerase chain reaction for expression of pluripotency genes or markers of differentiation. Bone marrow-derived MSCs were also analyzed for comparison of these parameters. L-MSCs and A-MSCs exhibited the typical morphology, immunophenotype, and proliferation and differentiation pattern of MSCs. The analysis of gene expression showed a higher potential of adipose tissue-derived MSCs toward the osteogenic pathway and of lung-derived MSCs to chondrogenic differentiation, representing an important contribution for the definition of the type of cell to be used in clinical trials of cell therapy and tissue engineering.

The contribution of HGAL/GCET2 in immunohistological algorithms: a comparative study in 424 cases of nodal diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma can be subclassified into at least two molecular subgroups by gene expression profiling: germinal center B-cell like and activated B-cell like diffuse large B-cell lymphoma. Several immunohistological algorithms have been proposed as surrogates to gene expression profiling at the level of protein expression, but their reliability has been an issue of controversy. Furthermore, the proportion of misclassified cases of germinal center B-cell subgroup by immunohistochemistry, in all reported algorithms, is higher compared with germinal center B-cell cases defined by gene expression profiling. We analyzed 424 cases of nodal diffuse large B-cell lymphoma with the panel of markers included in the three previously described algorithms: Hans, Choi, and Tally. To test whether the sensitivity of detecting germinal center B-cell cases could be improved, the germinal center B-cell marker HGAL/GCET2 was also added to all three algorithms. Our results show that the inclusion of HGAL/GCET2 significantly increased the detection of germinal center B-cell cases in all three algorithms (P<0.001). The proportions of germinal center B-cell cases in the original algorithms were 27%, 34%, and 19% for Hans, Choi, and Tally, respectively. In the modified algorithms, with the inclusion of HGAL/GCET2, the frequencies of germinal center B-cell cases were increased to 38%, 48%, and 35%, respectively. Therefore, HGAL/GCET2 protein expression may function as a marker for germinal center B-cell type diffuse large B-cell lymphoma. Consideration should be given to the inclusion of HGAL/GCET2 analysis in algorithms to better predict the cell of origin. These findings bear further validation, from comparison to gene expression profiles and from clinical/therapeutic data. Modern Pathology (2012) 25, 1439-1445; doi: 10.1038/modpathol.2012.119; published online 29 June 2012

Fuzzy Connectedness Image Segmentation in Graph Cut Formulation: A Linear-Time Algorithm and a Comparative Analysis

A deep theoretical analysis of the graph cut image segmentation framework presented in this paper simultaneously translates into important contributions in several directions. The most important practical contribution of this work is a full theoretical description, and implementation, of a novel powerful segmentation algorithm, GC(max). The output of GC(max) coincides with a version of a segmentation algorithm known as Iterative Relative Fuzzy Connectedness, IRFC. However, GC(max) is considerably faster than the classic IRFC algorithm, which we prove theoretically and show experimentally. Specifically, we prove that, in the worst case scenario, the GC(max) algorithm runs in linear time with respect to the variable M=|C|+|Z|, where |C| is the image scene size and |Z| is the size of the allowable range, Z, of the associated weight/affinity function. For most implementations, Z is identical to the set of allowable image intensity values, and its size can be treated as small with respect to |C|, meaning that O(M)=O(|C|). In such a situation, GC(max) runs in linear time with respect to the image size |C|. We show that the output of GC(max) constitutes a solution of a graph cut energy minimization problem, in which the energy is defined as the a"" (a) norm ayenF (P) ayen(a) of the map F (P) that associates, with every element e from the boundary of an object P, its weight w(e). This formulation brings IRFC algorithms to the realm of the graph cut energy minimizers, with energy functions ayenF (P) ayen (q) for qa[1,a]. Of these, the best known minimization problem is for the energy ayenF (P) ayen(1), which is solved by the classic min-cut/max-flow algorithm, referred to often as the Graph Cut algorithm. We notice that a minimization problem for ayenF (P) ayen (q) , qa[1,a), is identical to that for ayenF (P) ayen(1), when the original weight function w is replaced by w (q) . Thus, any algorithm GC(sum) solving the ayenF (P) ayen(1) minimization problem, solves also one for ayenF (P) ayen (q) with qa[1,a), so just two algorithms, GC(sum) and GC(max), are enough to solve all ayenF (P) ayen (q) -minimization problems. We also show that, for any fixed weight assignment, the solutions of the ayenF (P) ayen (q) -minimization problems converge to a solution of the ayenF (P) ayen(a)-minimization problem (ayenF (P) ayen(a)=lim (q -> a)ayenF (P) ayen (q) is not enough to deduce that). An experimental comparison of the performance of GC(max) and GC(sum) algorithms is included. This concentrates on comparing the actual (as opposed to provable worst scenario) algorithms' running time, as well as the influence of the choice of the seeds on the output.

Aerosol and precipitation chemistry measurements in a remote site in Central Amazonia: the role of biogenic contribution

In this analysis a 3.5 years data set of aerosol and precipitation chemistry, obtained in a remote site in Central Amazonia (Balbina, (1A degrees 55' S, 59A degrees 29' W, 174 m a.s.l.), about 200 km north of Manaus) is discussed. Aerosols were sampled using stacked filter units (SFU), which separate fine (d < 2.5 mu m) and coarse mode (2.5 mu m < d < 10.0 mu m) aerosol particles. Filters were analyzed for particulate mass (PM), Equivalent Black Carbon (BCE) and elemental composition by Particle Induced X-Ray Emission (PIXE). Rainwater samples were collected using a wet-only sampler and samples were analyzed for pH and ionic composition, which was determined using ionic chromatography (IC). Natural sources dominated the aerosol mass during the wet season, when it was predominantly of natural biogenic origin mostly in the coarse mode, which comprised up to 81% of PM10. Biogenic aerosol from both primary emissions and secondary organic aerosol dominates the fine mode in the wet season, with very low concentrations (average 2.2 mu g m(-3)). Soil dust was responsible for a minor fraction of the aerosol mass (less than 17%). Sudden increases in the concentration of elements as Al, Ti and Fe were also observed, both in fine and coarse mode (mostly during the April-may months), which we attribute to episodes of Saharan dust transport. During the dry periods, a significant contribution to the fine aerosols loading was observed, due to the large-scale transport of smoke from biomass burning in other portions of the Amazon basin. This contribution is associated with the enhancement of the concentration of S, K, Zn and BCE. Chlorine, which is commonly associated to sea salt and also to biomass burning emissions, presented higher concentration not only during the dry season but also for the April-June months, due to the establishment of more favorable meteorological conditions to the transport of Atlantic air masses to Central Amazonia. The chemical composition of rainwater was similar to those ones observed in other remote sites in tropical forests. The volume-weighted mean (VWM) pH was 4.90. The most important contribution to acidity was from weak organic acids. The organic acidity was predominantly associated with the presence of acetic acid instead of formic acid, which is more often observed in pristine tropical areas. Wet deposition rates for major species did not differ significantly between dry and wet season, except for NH4+, citrate and acetate, which had smaller deposition rates during dry season. While biomass burning emissions were clearly identified in the aerosol component, it did not present a clear signature in rainwater. The biogenic component and the long-range transport of sea salt were observed both in aerosols and rainwater composition. The results shown here indicate that in Central Amazonia it is still possible to observe quite pristine atmospheric conditions, relatively free of anthropogenic influences.

A simple analysis of the influence of the solvent-induced electronic polarization on the N-15 magnetic shielding of pyridine in water

Electronic polarization induced by the interaction of a reference molecule with a liquid environment is expected to affect the magnetic shielding constants. Understanding this effect using realistic theoretical models is important for proper use of nuclear magnetic resonance in molecular characterization. In this work, we consider the pyridine molecule in water as a model system to briefly investigate this aspect. Thus, Monte Carlo simulations and quantum mechanics calculations based on the B3LYP/6-311++G (d,p) are used to analyze different aspects of the solvent effects on the N-15 magnetic shielding constant of pyridine in water. This includes in special the geometry relaxation and the electronic polarization of the solute by the solvent. The polarization effect is found to be very important, but, as expected for pyridine, the geometry relaxation contribution is essentially negligible. Using an average electrostatic model of the solvent, the magnetic shielding constant is calculated as -58.7 ppm, in good agreement with the experimental value of -56.3 ppm. The explicit inclusion of hydrogen-bonded water molecules embedded in the electrostatic field of the remaining solvent molecules gives the value of -61.8 ppm.

Identification of protein expression signatures in gastric carcinomas using clustering analysis

Background and Aim: The identification of gastric carcinomas (GC) has traditionally been based on histomorphology. Recently, DNA microarrays have successfully been used to identify tumors through clustering of the expression profiles. Random forest clustering is widely used for tissue microarrays and other immunohistochemical data, because it handles highly-skewed tumor marker expressions well, and weighs the contribution of each marker according to its relatedness with other tumor markers. In the present study, we e identified biologically- and clinically-meaningful groups of GC by hierarchical clustering analysis of immunohistochemical protein expression. Methods: We selected 28 proteins (p16, p27, p21, cyclin D1, cyclin A, cyclin B1, pRb, p53, c-met, c-erbB-2, vascular endothelial growth factor, transforming growth factor [TGF]-beta I, TGF-beta II, MutS homolog-2, bcl-2, bax, bak, bcl-x, adenomatous polyposis coli, clathrin, E-cadherin, beta-catenin, mucin (MUC) 1, MUC2, MUC5AC, MUC6, matrix metalloproteinase [ MMP]-2, and MMP-9) to be investigated by immunohistochemistry in 482 GC. The analyses of the data were done using a random forest-clustering method. Results: Proteins related to cell cycle, growth factor, cell motility, cell adhesion, apoptosis, and matrix remodeling were highly expressed in GC. We identified protein expressions associated with poor survival in diffuse-type GC. Conclusions: Based on the expression analysis of 28 proteins, we identified two groups of GC that could not be explained by any clinicopathological variables, and a subgroup of long-surviving diffuse-type GC patients with a distinct molecular profile. These results provide not only a new molecular basis for understanding the biological properties of GC, but also better prediction of survival than the classic pathological grouping.

Risk factors for hepatitis C virus infection in Inland Brazil: An analysis of pooled epidemiological sectional studies

In order to assess the contribution of different parenteral routes as risk exposure to the hepatitis C virus (HCV), samples from nine surveys or cross-sectional studies conducted in two Brazilian inland regions were pooled, including a total of 3,910 subjects. Heterogeneity among the study results for different risk factors was tested and the results were shown to be homogeneous. Anti-HCV antibodies were observed in 241 individuals, of which 146 (3.7%, 95% CI?=?3.24.4) had HCV exposure confirmed by immunoblot analysis or PCR test. After adjustment for relevant variables, a correlation between confirmed HCV exposure and injection drug use, tattooing, and advance age was observed. In a second logistic model that included exposures not searched in all nine studies, a smaller sample was analyzed, revealing an independent HCV association with past history of surgery and males who have sex with other males, in addition to repeated injection drug use. Overall, these analyses corroborate the finding that injection drug use is the main risk factor for HCV exposure and spread, in addition to other parenteral routes. J. Med. Virol. 84:756762, 2012. (C) 2012 Wiley Periodicals, Inc.

Hydrodynamic analysis of particle collection efficiency: comparing downflow and upflow filtration

Models of the filtration phenomenon describe the mass balance in bed filtration in terms of particle removal mechanisms, and allow for the determination of global particle removal efficiencies. These models are defined in terms of the geometry and characteristic elements of granule collectors, particles and fluid, and also the composition of the balance of forces that act in the particle collector system. This work analyzes particles collection efficiency comparing downflow and upflow direct filtration, taking into account the contribution of the gravitational factor of the settling removal efficiency in future proposal of initial collection efficiency models for upflow filtration. A qualitative analysis is also made of the proposal for the collection efficiency models for particle removal in direct downflow and upflow filtration using a Computational Fluid Dynamics (CFD) tool. This analysis showed a strong influence of gravitational factor in initial collection efficiency (t = 0) of particles, as well as the reasons of their values to be smaller for upflow filtration in comparison with the downflow filtration.

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

Abstract Background Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Conclusions Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.

Contribution to the stratigraphy of the onshore Paraíba Basin, Brazil

Several publications have contributed to improve the stratigraphy of the Paraíba Basin in northeastern Brazil. However, the characterization and distribution of sedimentary units in onshore areas of this basin are still incomplete, despite their significance for reconstructing the tectono-sedimentary evolution of the South American passive margin. This work provides new information to differentiate among lithologically similar strata, otherwise entirely unrelated in time. This approach included morphological, sedimentological and stratigraphic descriptions based on surface and sub-surface data integrated with remote sensing, optically stimulated luminescence dating, U+Th/He dating of weathered goethite, and heavy mineral analysis. Based on this study, it was possible to show that Cretaceous units are constrained to the eastern part of the onshore Paraíba Basin. Except for a few outcrops of carbonatic rocks nearby the modern coastline, deposits of this age are not exposed to the surface in the study area. Instead, the sedimentary cover throughout the basin is constituted by mineralogically and chronologically distinctive deposits, inserted in the Barreiras Formation and mostly in the Post-Barreiras Sediments, of early/middle Miocene and Late Pleistocene-Holocene ages, respectively. The data presented in this work support tectonic deformation as a factor of great relevance to the distribution of the sedimentary units of the Paraíba Basin.