Random X Inactivation and Extensive Mosaicism in Human Placenta Revealed by Analysis of Allele-Specific Gene Expression along the X Chromosome

Imprinted inactivation of the paternal X chromosome in marsupials is the primordial mechanism of dosage compensation for X-linked genes between females and males in Therians. In Eutherian mammals, X chromosome inactivation (XCI) evolved into a random process in cells from the embryo proper, where either the maternal or paternal X can be inactivated. However, species like mouse and bovine maintained imprinted XCI exclusively in extraembryonic tissues. The existence of imprinted XCI in humans remains controversial, with studies based on the analyses of only one or two X-linked genes in different extraembryonic tissues. Here we readdress this issue in human term placenta by performing a robust analysis of allele-specific expression of 22 X-linked genes, including XIST, using 27 SNPs in transcribed regions. We show that XCI is random in human placenta, and that this organ is arranged in relatively large patches of cells with either maternal or paternal inactive X. In addition, this analysis indicated heterogeneous maintenance of gene silencing along the inactive X, which combined with the extensive mosaicism found in placenta, can explain the lack of agreement among previous studies. Our results illustrate the differences of XCI mechanism between humans and mice, and highlight the importance of addressing the issue of imprinted XCI in other species in order to understand the evolution of dosage compensation in placental mammals.

Identification and Phylogenetic Analysis of Heme Synthesis Genes in Trypanosomatids and Their Bacterial Endosymbionts

It has been known for decades that some insect-infecting trypanosomatids can survive in culture without heme supplementation while others cannot, and that this capability is associated with the presence of a betaproteobacterial endosymbiont in the flagellate's cytoplasm. However, the specific mechanisms involved in this process remained obscure. In this work, we sequence and phylogenetically analyze the heme pathway genes from the symbionts and from their hosts, as well as from a number of heme synthesis-deficient Kinetoplastida. Our results show that the enzymes responsible for synthesis of heme are encoded on the symbiont genomes and produced in close cooperation with the flagellate host. Our evidence suggests that this synergistic relationship is the end result of a history of extensive gene loss and multiple lateral gene transfer events in different branches of the phylogeny of the Trypanosomatidae.

Crystallization and preliminary X-ray diffraction analysis of recombinant chlorocatechol 1,2-dioxygenase from Pseudomonas putida

Chlorocatechol 1,2-dioxygenase from the Gram-negative bacterium Pseudomonas putida (Pp 1,2-CCD) is considered to be an important biotechnological tool owing to its ability to process a broad spectrum of organic pollutants. In the current work, the crystallization, crystallographic characterization and phasing of the recombinant Pp 1,2-CCD enzyme are described. Reddish-brown crystals were obtained in the presence of polyethylene glycol and magnesium acetate by utilizing the vapour-diffusion technique in sitting drops. Crystal dehydration was the key step in obtaining data sets, which were collected on the D03B-MX2 beamline at the CNPEM/MCT - LNLS using a MAR CCD detector. Pp 1,2-CCD crystals belonged to space group P6(1)22 and the crystallographic structure of Pp 1,2-CCD has been solved by the MR-SAD technique using Fe atoms as scattering centres and the coordinates of 3-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus (PDB entry 2boy) as the search model. The initial model, which contains three molecules in the asymmetric unit, has been refined to 3.4 A resolution.

Simultaneous optimization by neuro-genetic approach for analysis of plant materials by laser induced breakdown spectroscopy

A simultaneous optimization strategy based on a neuro-genetic approach is proposed for selection of laser induced breakdown spectroscopy operational conditions for the simultaneous determination of macronutrients (Ca, Mg and P), micro-nutrients (B, Cu, Fe, Mn and Zn), Al and Si in plant samples. A laser induced breakdown spectroscopy system equipped with a 10 Hz Q-switched Nd:YAG laser (12 ns, 532 nm, 140 mJ) and an Echelle spectrometer with intensified coupled-charge device was used. Integration time gate, delay time, amplification gain and number of pulses were optimized. Pellets of spinach leaves (NIST 1570a) were employed as laboratory samples. In order to find a model that could correlate laser induced breakdown spectroscopy operational conditions with compromised high peak areas of all elements simultaneously, a Bayesian Regularized Artificial Neural Network approach was employed. Subsequently, a genetic algorithm was applied to find optimal conditions for the neural network model, in an approach called neuro-genetic, A single laser induced breakdown spectroscopy working condition that maximizes peak areas of all elements simultaneously, was obtained with the following optimized parameters: 9.0 mu s integration time gate, 1.1 mu s delay time, 225 (a.u.) amplification gain and 30 accumulated laser pulses. The proposed approach is a useful and a suitable tool for the optimization process of such a complex analytical problem. (C) 2009 Elsevier B.V. All rights reserved.

Experimental Analysis of Structural Change and Rheological Behavior of Macromolecular Solutions with Guar and Xanthan Gums in Crossflow Microfiltration Processing

The present paper reports on the structural change and rheological behavior of mixtures of macromolecular suspensions (guar and xanthan gums) in crossflow microfiltration processing. Mixtures in suspension of guar and xanthan gums at low concentrations (1,000 ppm) and different proportions were processed by microfiltration with membrane of nominal pore size of 0.4 mu m. The rheological behavior of the mixtures was investigated in rotational viscometers at two different temperatures, 25 and 40 C, at the beginning and at the end of each experiment. The shear stress (t) in function of the shear rate (gamma) was fitted and analyzed with the power-law model. All the mixtures showed flow behavior index values (n) lower than 1, characterizing non-Newtonian fluids (pseudoplastic). The samples of both mixtures and permeates were also analyzed by absorbency spectroscopy in infrared radiation. The absorbency analysis showed that there is good synergism between xanthan and guar gums without structure modifications or gel formation in the concentration process by microfiltration.

A BEM model applied to failure analysis of multi-fractured structures

Due to manufacturing or damage process, brittle materials present a large number of micro-cracks which are randomly distributed. The lifetime of these materials is governed by crack propagation under the applied mechanical and thermal loadings. In order to deal with these kinds of materials, the present work develops a boundary element method (BEM) model allowing for the analysis of multiple random crack propagation in plane structures. The adopted formulation is based on the dual BEM, for which singular and hyper-singular integral equations are used. An iterative scheme to predict the crack growth path and crack length increment is proposed. This scheme enables us to simulate the localization and coalescence phenomena, which are the main contribution of this paper. Considering the fracture mechanics approach, the displacement correlation technique is applied to evaluate the stress intensity factors. The propagation angle and the equivalent stress intensity factor are calculated using the theory of maximum circumferential stress. Examples of multi-fractured domains, loaded up to rupture, are considered to illustrate the applicability of the proposed method. (C) 2011 Elsevier Ltd. All rights reserved.

Interface shear strength of geosynthetics: Evaluation and analysis of inclined plane tests

The inclined plane test (IPT) is commonly performed to measure the interface shear strength between different materials as those used in cover systems of landfills. The test, when interpreted according to European test Standards provides the static interface friction angle, usually assumed for 50 mm displacement and denoted as phi(stat)(50). However, if interpreted considering the several phases of the sliding process, the test is capable of yielding more realistic information about the interface shear strength such as differentiating interfaces which exhibit the same value of phi(stat)(50) but different behavior for displacement less than 50 mm. In this paper, the IPT is used to evaluate the interface shear strength of some materials usually present in cover liner systems of landfill. The results of the tests were analyzed for both, the static and the dynamic phases of the sliding and were interpreted based on the static initial friction angle, phi(0), and the limit friction angle, phi(lim). It is shown that depending on the sliding behavior of the interfaces, phi(stat)(50), which is usually adopted as the designing parameter in stability analysis, can be larger than phi(0) and phi(lim). (C) 2009 Elsevier Ltd. All rights reserved.

Motivations for the establishment of PNHRs and analysis of the incentives for their creation and management in Mato Grosso do Sul

The development of efficient programs of incentive to voluntary conservation in private lands require an extensive knowledge on the motivations of land owners for conservation and their degree of acceptance on the benefits offered. Thus, this paper intended to evaluate the motivations for the establishment of PNHRs, the difficulties faced by their recognition and the incentives received for their establishment and management in Mato Grosso do Sul, and also to discuss some possibilities of widening the benefits offered. To this end, people responsible for 34 PNHRs were interviewed between March/2008 and March/2009. The results show that conservation is among the main reasons for the creation of these areas, in spite of economical and personal factors also being mentioned. The slowness and the red tape during the process of recognition were also emphasized as problems; on the other hand, several PNHRs received or receive support for their creation or management. Finally, some considerations are made on the benefits offered to owners of PNHRs and their possibilities of widening throughout the state.

Learning Profile Identification Based on the Analysis of the User Context of Interaction

One of the e-learning environment goal is to attend the individual needs of students during the learning process. The adaptation of contents, activities and tools into different visualization or in a variety of content types is an important feature of this environment, bringing to the user the sensation that there are suitable workplaces to his profile in the same system. Nevertheless, it is important the investigation of student behaviour aspects, considering the context where the interaction happens, to achieve an efficient personalization process. The paper goal is to present an approach to identify the student learning profile analyzing the context of interaction. Besides this, the learning profile could be analyzed in different dimensions allows the system to deal with the different focus of the learning.

Finite element analysis of concrete cracking at early age

The study of the early age concrete properties is becoming more important, as the thermal effects and the shrinkage, even in the first hours, could generate cracks, increasing the permeability of the structure and being able to induce problems of durability and functionality in the same ones. The detailed study of the stresses development during the construction process can be decisive to keep low the cracking levels. In this work a computational model, based on the finite element method, was implemented to simulate the early age concrete behavior and, specially, the evaluation of the cracking risk. The finite element analysis encloses the computational modeling of the following phenomena: chemical, thermal, moisture diffusion and mechanical which occur at the first days after the concrete cast. The developed software results were compared with experimental values found in the literature, demonstrating an excellent approach for all the implemented analysis.

Integrated analysis of cooling water systems: Modeling and experimental validation

Cooling towers are widely used in many industrial and utility plants as a cooling medium, whose thermal performance is of vital importance. Despite the wide interest in cooling tower design, rating and its importance in energy conservation, there are few investigations concerning the integrated analysis of cooling systems. This work presents an approach for the systemic performance analysis of a cooling water system. The approach combines experimental design with mathematical modeling. An experimental investigation was carried out to characterize the mass transfer in the packing of the cooling tower as a function of the liquid and gas flow rates, whose results were within the range of the measurement accuracy. Then, an integrated model was developed that relies on the mass and heat transfer of the cooling tower, as well as on the hydraulic and thermal interactions with a heat exchanger network. The integrated model for the cooling water system was simulated and the temperature results agree with the experimental data of the real operation of the pilot plant. A case study illustrates the interaction in the system and the need for a systemic analysis of cooling water system. The proposed mathematical and experimental analysis should be useful for performance analysis of real-world cooling water systems. (C) 2009 Elsevier Ltd. All rights reserved.

Harmonic distortion analysis of double gate graded-channel MOSFETs operating in saturation

In this work we present an analysis of harmonic distortion (HD) in graded-channel (GC) gate-all-a round (GAA) devices operating in saturation region for analog applications. The study has been performed through device characterization and two-dimensional process and device simulations. The overall study has been done on the total and third order HDs. When applied in the saturation regime as an amplifier, the GC outperforms conventional GAA transistors presenting simultaneously higher transconductance, lower drain output conductance and more than 15 dB improved linearity. The influence of channel length reduction on the H D is also analyzed. Although slight linearity degradation is observed in both the conventional and the GC devices when reducing the channel length, the HD presented by the GC transistor is significantly lower than the one showed by conventional device for any Studied channel length. This allows AC input signal amplitude up to 20 times higher than the conventional GAA for a same specified distortion level. (C) 2008 Elsevier Ltd. All rights reserved.

In silico analysis of candidate genes involved in light sensing and signal transduction pathways in soybean

Several aspects of photoperception and light signal transduction have been elucidated by studies with model plants. However, the information available for economically important crops, such as Fabaceae species, is scarce. In order to incorporate the existing genomic tools into a strategy to advance soybean research, we have investigated publicly available expressed sequence tag ( EST) sequence databases in order to identify Glycine max sequences related to genes involved in light-regulated developmental control in model plants. Approximately 38,000 sequences from open-access databases were investigated, and all bona fide and putative photoreceptor gene families were found in soybean sequence databases. We have identified G. max orthologs for several families of transcriptional regulators and cytoplasmic proteins mediating photoreceptor-induced responses, although some important Arabidopsis phytochrome-signaling components are absent. Moreover, soybean and Arabidopsis gene-family homologs appear to have undergone a distinct expansion process in some cases. We propose a working model of light perception, signal transduction and response-eliciting in G. max, based on the identified key components from Arabidopsis. These results demonstrate the power of comparative genomics between model systems and crop species to elucidate several aspects of plant physiology and metabolism.

Analysis of chemokines and reactive oxygen species formation by rat and human neutrophils induced by microcystin-LA, -YR and -LR

Microcystins (MC), a family of heptapeptide toxins produced by some genera of Cyanobacteria, have potent hepatotoxicity and tumor-promoting activity. Leukocyte infiltration in the liver was observed in MC-induced acute intoxication. Although the mechanisms of hepatotoxicity are still unclear, neutrophil infiltration in the liver may play an important role in triggering toxic injury and tumor development. The present study reports the effects of MC-LA, MC-YR and MC-LR (1 and 1000 nM) on human and rat neutrophils functions in vitro. Cell viability, DNA fragmentation, mitochondrial membrane depolarization and intracellular reactive oxygen species (ROS) levels were measured by flow cytometry. Extracellular ROS content was measured by lucigenin-amplified chemiluminescence, and cytokines were determined by ELISA. We found that these MC increased interleukin-8 (IL-8), cytokine-induced neutrophil chemoattractant-2 alpha beta (CINC-2 alpha beta) and extracellular ROS levels in human and rat neutrophils. Apart from neutrophil presence during the inflammatory process of MC-induced injury, our results suggest that hepatic neutrophil accumulation is further increased by MC-induced neutrophil-derived chemokine. (c) 2008 Elsevier Ltd. All rights reserved.

Gene expression analysis of Paracoccidioides brasiliensis transition from conidium to yeast cell

Paracoccidioides brasiliensis infectious process relies on the initial expression of virulence faactors that are assumed to be controlled by molecular mechanisms through which the conidia and/or mycelial fragments convert to yeast cells. In order to analyze the profile of the thermally-induced dimorphic gene expression, 48 h C-L transition cultures which had been incubated at 36 degrees C were studied. By this time approximately 50% of the conidial population had already reverted to yeast form cells. At this transition time, an EST-Orestes library was constructed and characterized. As a result, 79 sequences were obtained, of which 39 (49.4%) had not been described previously in other libraries of this fungus and which could represent novel exclusive C-Y transition genes. Two of these sequences are, among others, cholestanol delta-isomerase, and electron transfer flavoprotein-ubiquinoneoxidoreductase (ETF-QO). The other 40 (50.6%) sequences were shared with Mycelia (M), Yeast (Y) or Mycelia to yest transition (M-Y) libraries. An important component of this group of sequences is a putative response regulator receiver SKN7, a protein of high importance in stress adaptation and a regulator of virulence in some bacteria and fungi. This is the first report identifying genes expressed during the C-Y transition process, the initial step required to understand the natural history of P brasiliensis conidia induced infection.