Bioinformatics construction of the human cell surfaceome

Cell surface proteins are excellent targets for diagnostic and therapeutic interventions. By using bioinformatics tools, we generated a catalog of 3,702 transmembrane proteins located at the surface of human cells (human cell surfaceome). We explored the genetic diversity of the human cell surfaceome at different levels, including the distribution of polymorphisms, conservation among eukaryotic species, and patterns of gene expression. By integrating expression information from a variety of sources, we were able to identify surfaceome genes with a restricted expression in normal tissues and/or differential expression in tumors, important characteristics for putative tumor targets. A high-throughput and efficient quantitative real-time PCR approach was used to validate 593 surfaceome genes selected on the basis of their expression pattern in normal and tumor samples. A number of candidates were identified as potential diagnostic and therapeutic targets for colorectal tumors and glioblastoma. Several candidate genes were also identified as coding for cell surface cancer/testis antigens. The human cell surfaceome will serve as a reference for further studies aimed at characterizing tumor targets at the surface of human cells.

Construction of Hamiltonian-Minimal Lagrangian submanifolds in Complex Euclidean Space

We describe several families of Lagrangian submanifolds in complex Euclidean space which are H-minimal, i.e. critical points of the volume functional restricted to Hamiltonian variations. We make use of various constructions involving planar, spherical and hyperbolic curves, as well as Legendrian submanifolds of the odd-dimensional unit sphere.

Optimization of incubation time of protein Tc85 in the construction of biosensor: Is the EIS a good tool?

Electrochemical impedance spectroscopy (EIS) in pH 6.9 phosphate buffer solution was used to investigate each step of the procedure employed to modify a screen-printed electrode (SPE). The SPE was modified with self-assembled monolayers (SAMs) of cystamine (CYS, deposited from 20 mM solution), followed by glutaraldehyde (GA, 0.3 M solution). The Trypanosoma cruzi antigen was immobilized using different deposition times. The influence of incubation time (2-18 h) of protein was also investigated. The topography of modified electrode with this protein was investigated by atomic force microscopy (AFM). Interpretation of impedance data was based on physical and chemical adsorption, and degradation of the layer at high and meddle frequencies, and charge transfer reaction involving mainly the reduction of oxygen at low frequencies. EIS studies on modified electrodes with Tc85 protein immobilized for different incubation times indicated that the optimum incubation time was 6-8 h. It was demonstrated that EIS is a good technique to evaluate the different steps and the integrity of the surface modifications, and to optimize the incubation time of protein in the development of biosensors. (C) 2010 Elsevier B.V. All rights reserved.

Using sentinels to detect intersections of convex and nonconvex polygons

We describe finite sets of points, called sentinels, which allow us to decide if isometric copies of polygons, convex or not, intersect. As an example of the applicability of the concept of sentinel, we explain how they can be used to formulate an algorithm based on the optimization of differentiable models to pack polygons in convex sets. Mathematical subject classification: 90C53, 65K05.

Effects of human trampling on a rocky shore fauna on the Sao Paulo coast, southeastern Brazil

Increased tourist activity in coastal regions demands management strategies to reduce impacts on rocky shores. The highly populated coastal areas in southeastern Brazil are an example of degradation caused by development of industry and tourism. Among different shore impacts, trampling has been intensively studied, and may represent a significant source of stress for intertidal fauna. A randomised blocks design was applied to experimentally study the effects of two different trampling intensities on richness, diversity, density and biomass of the rocky shore fauna of Obuseiro beach, Guarujá, southeastern Brazil. Blocks were distributed in two portions of the intertidal zone, dominated respectively by Chthamalus bisinuatus (Cirripedia) and Isognomon bicolor (Bivalvia). Blocks were trampled over three months, simulating the vacation period in Brazil and were monitored for the following nine months. Results indicate that Chthamalus bisinuatus is vulnerable to trampling impacts. Richness, diversity and turn-over index tended to be higher in trampled plots four months after trampling ceased. In general, results agree with previous trampling studies, suggesting that even low intensities of trampling may cause some impact on intertidal communities. Management strategies should include isolation of sensitive areas, construction of boardwalks, visitor education and monitoring programmes. In Brazil, additional data obtained from experimental studies are necessary in order to achieve a better understanding of trampling impacts on rocky shore communities.

Mechanical strength and thermal conductivity of low-porosity gypsum plates

The thermal conductivity and mechanical strength of gypsum and gypsum-cellulose plates made from commercial plaster by a new process have been measured. The gypsum parts made by the new process, 'novogesso', have high mechanical strength and low porosity. The gypsum strength derives from both the high aspect ratio of the gypsum crystals and the strong adhesion among them by nano-flat layers of confined water, which behaves as supercooled water. Another contribution to the strength comes from the nano-flatness of the lateral surfaces of the gypsum single crystals. The bending and compression strengths, σB and σc, of gypsum plates prepared by this new technique can be as high as 30 and 100 MPa, respectively. The way gypsum plates have been assembled as well as their low thermal conductivity allowed for the construction of a low-cost experimental house with thermal and acoustic comfort.

Epidemiological and ecological aspects related to malaria in the area of influence of the lake at Porto Primavera dam, in western São Paulo State, Brazil

A study was carried out in the area of influence of the Porto Primavera Hydroelectric Power Station, in western São Paulo State, to investigate ecological and epidemiological aspects of malaria in the area and monitor the profile of the anopheline populations following the environmental changes brought about by the construction of the lake. Mosquitoes captured were analyzed by standardized indicator species analysis (ISA) before and during different flooding phases (253 m and 257 m elevations). The local human population was studied by means of parasitological (thin/thick blood smears), molecular (PCR) and serological tests. Serological tests consisted of Enzyme Linked Immunosorbent Assay (ELISA) with synthetic peptides of the circumsporozoite protein (CSP) from classic Plasmodium vivax, P. vivax variants (VK247 and "vivax-like"), P. malariae and P. falciparum and Indirect Immunofluorescence Assay (IFA) with asexual forms of P. vivax, P. malariae and P. falciparum. The results of the entomological survey indicated that, although the Anopheles darlingi population increased after the flooding, the population density remained very low. No malaria, parasite infection or DNA was detected in the inhabitants of the study area. However, there was a low frequency of antibodies against asexual forms and a significant prevalence of antibodies against P. vivax, P. vivax variants, P. falciparum and P. malariae; the presence of these antibodies may result from recent or less recent contact with human or simian Plasmodium (a parallel study in the same area revealed the existence of a sylvatic cycle). Nevertheless, these results suggest that, as in other places where malaria is present and potential vectors circulate, the local epidemiological conditions observed could potentially support the transmission of malaria in Porto Primavera Lake if infected individuals are introduced in sufficient numbers. Further studies are required to elucidate the phenomena described in this paper.

A reliable measure of similarity based on dependency for short time series: an application to gene expression networks

Background: Microarray techniques have become an important tool to the investigation of genetic relationships and the assignment of different phenotypes. Since microarrays are still very expensive, most of the experiments are performed with small samples. This paper introduces a method to quantify dependency between data series composed of few sample points. The method is used to construct gene co-expression subnetworks of highly significant edges. Results: The results shown here are for an adapted subset of a Saccharomyces cerevisiae gene expression data set with low temporal resolution and poor statistics. The method reveals common transcription factors with a high confidence level and allows the construction of subnetworks with high biological relevance that reveals characteristic features of the processes driving the organism adaptations to specific environmental conditions. Conclusion: Our method allows a reliable and sophisticated analysis of microarray data even under severe constraints. The utilization of systems biology improves the biologists ability to elucidate the mechanisms underlying celular processes and to formulate new hypotheses.

From ""Geography of Accumulation"" to ""Geography of Reproduction"": a dialogue with Harvey

This article aims to discuss the space, revealing its powerful in the comprehension of modem world, from the thesis which the geographic space consists itself as condition, medium and product of society reproduction in its totality, evolving several temporal-spatial scales and several levels of reality, that should prolong Marx's work, having in view the construction of a ""social theory of space"" in the sense of a radical critical geography. This argumentation allows to understand, in the limits of geography, the passage of the notion ""production of space"" as condition of the accumulation of capital to the notion ""production of space"" as condition of present reproduction in front of the accumulation crisis. As a starting point, a discussion about some David Harvey's works, who supports the thesis that accumulation crisis of capital would be solved, in the modem world, through the spatial fix.

In vitro development of cloned bovine embryos produced by handmade cloning using somatic cells from distinct levels of cell culture confluence

The relationship between the level of cell confluence near the plateau phase of growth and blastocyst yield following somatic cell cloning is not well understood. We examined the effect of distinct cell culture confluence levels on in vitro development of cloned bovine embryos. In vitro-matured bovine oocytes were manually bisected and selected by DNA staining. One or two enucleated hemi-cytoplasts were paired and fused with an adult skin somatic cell. Cultured skin cells from an adult Nellore cow harvested at three distinct culture confluence levels (70-80, 80-90, and > 95%) were used for construction of embryos and hemi-embryos. After activation, structures were cultured in vitro as one embryo (1 x 100%) or as aggregates of two hemi-embryos (2 x 50%) per microwell. Fusion, cleavage and blastocyst rates were compared using the chi(2) test. The fusion rate for hemi-embryos (51.4%) was lower than for embryos (67.6%), with no influence of degree of cell confluence. However, blastocyst rates improved linearly (7.0, 17.5, and 29.4%) with increases in cell confluence. We conclude that degree of cell culture confluence significantly influences subsequent embryo development; use of a cell population in high confluence (> 90%) for nuclear transfer significantly improved blastocyst yield after cloning.

The city of Maringa, PR. The initial plan and the "urban requalifications"

The city of Maringa, located in the Northwest of Parana State, Brazil, was part of an extensive area colonized by the Companhia de Terras Norte do Parana replaced by the Companhia Melhoramentos Norte do Parana. Starting from a modem project elaborated in midlles of 1940's, Maringa emerged quickly amid the forest. We analyzed the initial plan, the projects for the reformulation of the central area and the tendencies of the public actions in the urban area that turn for real estate promotion and disrespect the popular participation. In its regional scale, Maringa follows the same orientation of cities that are used by the The obsession for the modernity takes to the systematic construction of new spaces that substitute the memory and the urban history in projects that reconduct to the aestheticization and the spectacularization of the urban landscape of Maringa.

Complete Genome Sequence of Mycoplasma suis and Insights into Its Biology and Adaption to an Erythrocyte Niche

Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454) and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS). The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD(+) kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems.

Comparison of (120)Sn((6)He, (6)He)(120)Sn and (120)Sn(alpha,alpha)(120)Sn elastic scattering and signatures of the (6)He neutron halo in the optical potential

Cross sections of (120)Sn(alpha,alpha)(120)Sn elastic scattering have been extracted from the alpha-particle-beam contamination of a recent (120)Sn((6)He,(6)He)(120)Sn experiment. Both reactions are analyzed using systematic double-folding potentials in the real part and smoothly varying Woods-Saxon potentials in the imaginary part. The potential extracted from the (120)Sn((6)He,(6)He)(120)Sn data may be used as the basis for the construction of a simple global (6)He optical potential. The comparison of the (6)He and alpha data shows that the halo nature of the (6)He nucleus leads to a clear signature in the reflexion coefficients eta(L) : The relevant angular momenta L with eta(L) >> 0 and eta(L) << 1 are shifted to larger L with a broader distribution. This signature is not present in the alpha-scattering data and can thus be used as a new criterion for the definition of a halo nucleus.

On quantum integrability of the Landau-Lifshitz model

We investigate the quantum integrability of the Landau-Lifshitz (LL) model and solve the long-standing problem of finding the local quantum Hamiltonian for the arbitrary n-particle sector. The particular difficulty of the LL model quantization, which arises due to the ill-defined operator product, is dealt with by simultaneously regularizing the operator product and constructing the self-adjoint extensions of a very particular structure. The diagonalizibility difficulties of the Hamiltonian of the LL model, due to the highly singular nature of the quantum-mechanical Hamiltonian, are also resolved in our method for the arbitrary n-particle sector. We explicitly demonstrate the consistency of our construction with the quantum inverse scattering method due to Sklyanin [Lett. Math. Phys. 15, 357 (1988)] and give a prescription to systematically construct the general solution, which explains and generalizes the puzzling results of Sklyanin for the particular two-particle sector case. Moreover, we demonstrate the S-matrix factorization and show that it is a consequence of the discontinuity conditions on the functions involved in the construction of the self-adjoint extensions.

PLANT ACCUMULATIONS ALONG THE ITANHAEM RIVER BASIN, SOUTHERN COAST OF SAO PAULO STATE, BRAZIL

Examination of the mechanisms involved in the construction of present-day vegetative deposits along coastal waterways has made it possible to establish depositional patterns that can be compared with those found in similar environments in geologic time. These patterns include not only the composition and transport of the debris but also an estimation of the time involved in its deposition. Six sites with active deposits of plant macrodebris in the coastal basin of the Itanhaem River, Sao Paulo State, Brazil, were used in the study. In the central portion of the basin, the interior coastal plain is covered with restinga forest (dense, wet tropical forest of low altitudes), while the lower portion consists of mangrove swamps. The coast reflects anthropogenic intervention, and only a few scattered remnants of precolonization dune vegetation remain. The results after three years of study suggest that the accumulation of plant macrodebris in the middle and lower portions of the basin is parautochthonous, since only the leaves of genera typical of the restinga forest and mangrove swamp, respectively, were found. Along the coast the accumulations involved a mixture of parautochthonous and allochthonous elements. On the levee of the Branco River and within the mangrove swamp, deposition was slow, and many of the elements decayed quickly; such accumulations show little potential for preservation and eventual fossilization. A different site, however, reveals the rapid deposition of thick layers of plant debris, presumably associated with storms, and these accumulations are preserved for long periods, constituting good candidates for possible fossilization.