mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Background The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. Results A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. Conclusions This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.

Inclusão da epistasia em modelo de avaliação genética de bovinos de corte compostos

Dados de bovinos compostos foram analisados para avaliar o efeito da epistasia nos modelos de avaliação genética. As características analisadas foram os pesos aos 205 (P205) e 390 dias (P390) e perímetro escrotal aos 390 dias (PE390). As análises foram realizadas pela metodologia de máxima verossimilhança considerando-se dois modelos: o modelo 1 incluiu como covariáveis os efeitos aditivos diretos e maternos, e os não aditivos das heterozigoses para os efeitos diretos e para o materno total, e o modelo 2 considerou também o efeito direto de epistasia. Para comparação dos modelos, foram utilizados o critério de informação de Akaike (AIC) e o critério de informação Bayesiano de Schwartz (BIC), e o teste de razão de verossimilhança. A inclusão da epistasia no modelo de avaliação genética pouco alterou as estimativas de componentes de (co)variâncias genéticas aditivas e, consequentemente, as herdabilidades. O teste de verossimilhança e o critério de Akaike sugeriram que o modelo 2, que inclui a epistasia, apresentou maior aderência aos dados para todas as características analisadas. O critério BIC indicou este modelo como o melhor apenas para P205. Para análise genética dessa população, o modelo que considerou o efeito de epistasia foi o mais adequado.

Power-law creep behavior of a semiflexible chain

Rheological properties of adherent cells are essential for their physiological functions, and microrheological measurements on living cells have shown that their viscoelastic responses follow a weak power law over a wide range of time scales. This power law is also influenced by mechanical prestress borne by the cytoskeleton, suggesting that cytoskeletal prestress determines the cell's viscoelasticity, but the biophysical origins of this behavior are largely unknown. We have recently developed a stochastic two-dimensional model of an elastically joined chain that links the power-law rheology to the prestress. Here we use a similar approach to study the creep response of a prestressed three-dimensional elastically jointed chain as a viscoelastic model of semiflexible polymers that comprise the prestressed cytoskeletal lattice. Using a Monte Carlo based algorithm, we show that numerical simulations of the chain's creep behavior closely correspond to the behavior observed experimentally in living cells. The power-law creep behavior results from a finite-speed propagation of free energy from the chain's end points toward the center of the chain in response to an externally applied stretching force. The property that links the power law to the prestress is the chain's stiffening with increasing prestress, which originates from entropic and enthalpic contributions. These results indicate that the essential features of cellular rheology can be explained by the viscoelastic behaviors of individual semiflexible polymers of the cytoskeleton.

Soil Carbon Turnover Measurement by Physical Fractionation at a Forest-to-Pasture Chronosequence in the Brazilian Amazon

The effect of conversion from forest-to-pasture upon soil carbon stocks has been intensively discussed, but few studies focus on how this land-use change affects carbon (C) distribution across soil fractions in the Amazon basin. We investigated this in the 20 cm depth along a chronosequence of sites from native forest to three successively older pastures. We performed a physicochemical fractionation of bulk soil samples to better understand the mechanisms by which soil C is stabilized and evaluate the contribution of each C fraction to total soil C. Additionally, we used a two-pool model to estimate the mean residence time (MRT) for the slow and active pool C in each fraction. Soil C increased with conversion from forest-to-pasture in the particulate organic matter (> 250 mu m), microaggregate (53-250 mu m), and d-clay (< 2 mu m) fractions. The microaggregate comprised the highest soil C content after the conversion from forest-to-pasture. The C content of the d-silt fraction decreased with time since conversion to pasture. Forest-derived C remained in all fractions with the highest concentration in the finest fractions, with the largest proportion of forest-derived soil C associated with clay minerals. Results from this work indicate that microaggregate formation is sensitive to changes in management and might serve as an indicator for management-induced soil carbon changes, and the soil C changes in the fractions are dependent on soil texture.

Stability analysis of core-annular flow and neutral stability wave number

A general transition criterion is proposed in order to locate the core-annular flow pattern in horizontal and vertical oil-water flows. It is based on a rigorous one-dimensional two-fluid model of liquid-liquid two-phase flow and considers the existence of critical interfacial wave numbers related to a non-negligible interfacial tension term to which the linear stability theory still applies. The viscous laminar-laminar flow problem is fully resolved and turbulence effects on the stability are analyzed through experimentally obtained shape factors. The proposed general transition criterion includes in its formulation the inviscid Kelvin-Helmholtz`s discriminator. If a theoretical maximum wavelength is considered as a necessary condition for stability, a stability criterion in terms of the Eotvos number is achieved. Effects of interfacial tension, viscosity ratio, density difference, and shape factors on the stability of core-annular flow are analyzed in detail. The more complete modeling allowed for the analysis of the neutral-stability wave number and the results strongly suggest that the interfacial tension term plays an indispensable role in the correct prediction of the stable region of core-annular flow pattern. The incorporation of a theoretical minimum wavelength into the transition model produced significantly better results. The criterion predictions were compared with recent data from the literature and the agreement is encouraging. (C) 2007 American Institute of Chemical Engineers.

Genetics and race variability of the lucerne - Colletotrichum trifolii pathosystem in Australia

The Australian-bred lucerne cultivars, Trifecta and Sequel, were found to possess useful levels of resistance to both Colletotrichum trifolii races 1 and 2. Race 2 has only been previously observed in the United States and surveys did not reveal its presence in Australia. Multilocus fingerprinting using random amplified polymorphic DNA (RAPDs) analysis revealed low diversity (<10% dissimilarity) within Australian C. trifolii collections, and between the Australian race 1 isolates and a US race 2 isolate. Studies on the inheritance of resistance to C. trifolii race 1 in individual clones from Trifecta and Sequel revealed the presence of 2 different genetic mechanisms. One inheritance was for resistance as a recessive trait, and the other indicated that resistance was dominant. The recessive system has never been previously reported, whereas in the US, 2 completely dominant and independent tetrasomic genes Anl and Ant have been reported to condition C. trifolii resistance. It was not possible to fit the observed segregations from our studies to a single-gene model. In contrast to US studies, clones of cv. Sequel exhibiting the recessive resistance reacted differently to spray and stem injection with C. trifolii inoculum, being resistant to the former and susceptible to the latter, providing additional evidence for the presence of a different genetic mechanism conditioning resistance to those previously reported in the US. As C. trifolii is one of the most serious diseases of lucerne worldwide, the future development of molecular markers closely linked to the dominant and recessive resistances identified in these studies, and the relationships between these resistances and Anl and Ans as determined by genetic mapping, appear to be useful areas of future study.

Kinetics of propranolol uptake in muscle, skin, and fat of the isolated perfused rat hindlimb

The tissue distribution kinetics of a highly bound solute, propranolol, was investigated in a heterogeneous organ, the isolated perfused limb, using the impulse-response technique and destructive sampling. The propranolol concentration in muscle, skin, and fat as well as in outflow perfusate was measured up to 30 min after injection. The resulting data were analysed assuming (1) vascular, muscle, skin and fat compartments as well mixed (compartmental model) and (2) using a distributed-in-space model which accounts for the noninstantaneous intravascular mixing and tissue distribution processes but consists only of a vascular and extravascular phase (two-phase model). The compartmental model adequately described propranolol concentration-time data in the three tissue compartments and the outflow concentration-time curve (except of the early mixing phase). In contrast, the two-phase model better described the outflow concentration-time curve but is limited in accounting only for the distribution kinetics in the dominant tissue, the muscle. The two-phase model well described the time course of propranolol concentration in muscle tissue, with parameter estimates similar to those obtained with the compartmental model. The results suggest, first that the uptake kinetics of propranolol into skin and fat cannot be analysed on the basis of outflow data alone and, second that the assumption of well-mixed compartments is a valid approximation from a practical point of view las, e.g., in physiological based pharmacokinetic modelling). The steady-state distribution volumes of skin and fat were only 16 and 4%, respectively, of that of muscle tissue (16.7 ml), with higher partition coefficient in fat (6.36) than in skin (2.64) and muscle (2.79. (C) 2000 Elsevier Science B.V. All rights reserved.

The role of impulsivity in the development of substance use and eating disorders

Impulsivity is now widely viewed as a multidimensional construct consisting of a number of related dimensions. Although many measures of impulsivity are correlated, most recent factor analyses support at least a two-factor model. In the current paper, these two factors have been labelled reward sensitivity, reflecting one of the primary dimensions of Gray's personality theory, and rash-spontaneous impulsiveness. The evidence supporting the existence of two dimensions of impulsivity is reviewed in relation to substance misuse and binge eating. (C) 2004 Elsevier Ltd. All rights reserved.

Transport in bidisperse adsorbents: Significance of the macroscopic adsorbate flux

Transport in bidisperse adsorbents is investigated here, while incorporating a two-dimensional model for adsorbate diffusion in the microparticles. The latter treatment permits consideration of the macropore concentration variation around the microparticle surface, and thereby predicts an adsorbate through-flux on the macroscopic coordinate. Such a through-flux has earlier been postulated in the literature, but with unrealistic mechanistic justification. The new model therefore resolves the existing ambiguity in this regard, and covers the entire spectrum of behaviour between microparticle and macropore diffusion control. Computational results show that if the macroscopic adsorbate flux, ignored in the conventional analysis, has a significant contribution to the total flux under macropore control conditions then it is always important even when the microparticle diffusion resistance is not negligible. The effect of various parameters such as relative microparticle size and isotherm heterogeneity on the uptake is also studied and discussed. (C) 1997 Elsevier Science Ltd.

Methimazole and propylthiouracil equally cross the perfused human term placental lobule

Propylthiouracil (PTU) is widely believed to cross the placenta less freely than methimazole (MMI) and is therefore regarded as the preferred drug for treatment of hyperthyroidism in pregnancy. Clinical studies comparing the two drugs show, however, no differences in maternal or fetal thyroid function. We investigated transfer from the maternal to the fetal circuit in the isolated perfused term human placental lobule of low and high doses of PTU (4 mu g/mL and 40 mu g/mL) and MMI(1.5 mu g/mL and 15 mu g/mL) in protein-free perfusate and low doses of both drugs with addition of 40 g/L of bovine albumin. Both drugs readily crossed the placenta, reaching equilibrium in all experiments in about 2 h. Drug concentrations in the two circuits fitted a two compartmental model. Transfer kinetics for the two drugs were similar, nonsaturable, and unaffected by addition of albumin. Clearances (mL.min(-1).g(-1), means +/- SD) of PTU from maternal to fetal circuits were: 0.229 +/- 0.110, 0.216 +/- 0.065, and 0.170 +/- 0.032; and for transfer of MMI: 0.165 +/- 0.025, 0.232 +/- 0.153, and 0.174 +/- 0.009 (for low doses without, low doses with, and high doses without albumin, respectively). Clearances of PTU from fetal to maternal circuits were: 0.147 +/- 0.072, 0.109 +/- 0.014, and 0.116 +/- 0.028; and for transfer of MMI: 0.095 +/- 0.029, 0.122 +/- 0.088, and 0.12 +/- 0.005 (in the same experiments). There was no significant difference between drugs or drug doses and no effect of addition of albumin. We conclude that PTU and MMI have similar placental transfer kinetics.

Lexical decision in Parkinson's disease: A reply to Brown, McDonald, and Spicer (1999)

Recent semantic priming investigations in Parkinsons disease (PD) employed variants of Neelys (1977) lexical decision paradigm to dissociate the automatic and attentional aspects of semantic activation (McDonald, Brown, Gorell, 1996; Spicer, Brown, Gorell, 1994). In our earlier review, we claimed that the results of Spicer, McDonald and colleagues normal control participants violated the two-process model of information processing (Posner Snyder, 1975) upon which their experimental paradigm had been based (Arnott Chenery, 1999). We argued that, even at the shortest SOA employed, key design modifications to Neelys original experiments biased the tasks employed by Spicer et al. and McDonald et al. towards being assessments of attention-dependent processes. Accordingly, we contended that experimental procedures did not speak to issues of automaticity and, therefore, Spicer, McDonald and colleagues claims of robust automatic semantic activation in PD must be treated with caution.

Drop penetration into porous powder beds

The kinetics of drop penetration were studied by filming single drops of several different fluids (water, PEG200, PEG600, and HPC solutions) as they penetrated into loosely packed beds of glass ballotini, lactose, zinc oxide, and titanium dioxide powders. Measured times ranged from 0.45 to 126 s and depended on the powder particle size,viscosity, surface tensions, and contact angle. The experimental drop penetration times were compared to existing theoretical predictions by M. Denesuk et al. (J. Colloid Interface Sci. 158, 114, 1993) and S. Middleman (Modeling Axisymmetric Flows: Dynamics of Films, Jets, and Drops, Academic Press, San Diego, 1995) but did not agree. Loosely packed powder beds tend to have a heterogeneous bed structure containing large macrovoids which do not participate in liquid flow but are included implicitly in the existing approach to estimating powder pore size. A new two-phase model was proposed where the total volume of the macrovoids was assumed to be the difference between the bed porosity and the tap porosity. A new parameter, the effective porosity (epsilon)eff, was defined as the tap porosity multiplied by the fraction of pores that terminate at a macrovoid and are effectively blocked pores. The improved drop penetration model was much more successful at estimating the drop penetration time on all powders and the predicted times were generally within an order of magnitude of the experimental results. (C) 2002 Elsevier Science (USA).

Critical comparison of Julius Kruttschnitt Mineral Research Centre (JKMRC) blast fragmentation models

Blast fragmentation can have a significant impact on the profitability of a mine. An optimum run of mine (ROM) size distribution is required to maximise the performance of downstream processes. If this fragmentation size distribution can be modelled and controlled, the operation will have made a significant advancement towards improving its performance. Blast fragmentation modelling is an important step in Mine to Mill™ optimisation. It allows the estimation of blast fragmentation distributions for a number of different rock mass, blast geometry, and explosive parameters. These distributions can then be modelled in downstream mining and milling processes to determine the optimum blast design. When a blast hole is detonated rock breakage occurs in two different stress regions - compressive and tensile. In the-first region, compressive stress waves form a 'crushed zone' directly adjacent to the blast hole. The second region, termed the 'cracked zone', occurs outside the crush one. The widely used Kuz-Ram model does not recognise these two blast regions. In the Kuz-Ram model the mean fragment size from the blast is approximated and is then used to estimate the remaining size distribution. Experience has shown that this model predicts the coarse end reasonably accurately, but it can significantly underestimate the amount of fines generated. As part of the Australian Mineral Industries Research Association (AMIRA) P483A Mine to Mill™ project, the Two-Component Model (TCM) and Crush Zone Model (CZM), developed by the Julius Kruttschnitt Mineral Research Centre (JKMRC), were compared and evaluated to measured ROM fragmentation distributions. An important criteria for this comparison was the variation of model results from measured ROM in the-fine to intermediate section (1-100 mm) of the fragmentation curve. This region of the distribution is important for Mine to Mill™ optimisation. The comparison of modelled and Split ROM fragmentation distributions has been conducted in harder ores (UCS greater than 80 MPa). Further work involves modelling softer ores. The comparisons will be continued with future site surveys to increase confidence in the comparison of the CZM and TCM to Split results. Stochastic fragmentation modelling will then be conducted to take into account variation of input parameters. A window of possible fragmentation distributions can be compared to those obtained by Split . Following this work, an improved fragmentation model will be developed in response to these findings.

An electromagnetic-field method modeling of a radial line planar antenna with coupling probes

This communications describes an electromagnetic model of a radial line planar antenna consisting of a radial guide with one central probe and many peripheral probes arranged in concentric circles feeding an array of antenna elements such as patches or wire curls. The model takes into account interactions between the coupling probes while assuming isolation of radiating elements. Based on this model, computer programs are developed to determine equivalent circuit parameters of the feed network and the radiation pattern of the radial line planar antenna. Comparisons are made between the present model and the two-probe model developed earlier by other researchers.

The development of a scale to measure concepts of schizophrenia: experience among Brazilian psychiatrists

INTRODUCTION: Among psychiatric disorders schizophrenia is often said to be the condition with the most disputed definition.The Bleulerian and Schneiderian approaches have given rise to diagnostic formulations that have varied with time and place. Controversies over the concept of schizophrenia were examined within European/North American settings in the early 1970s but little has since been reported on the views of psychiatrists in developing countries. In Brazil both concepts are referred to in the literature. A scale was developed to measure adherence to Bleulerian and Schneiderian concepts among psychiatrists working in S. Paulo. METHODOLOGY: A self-reported questionnaire comprising seventeen visual analogue-scale statements related to Bleulerian and Schneiderian definitions of Shizophrenia, plus sociodemographic and training characteristics, was distributed to a non-randomised sample of 150 psychiatrists. The two sub-scales were assessed by psychometric methods for internal consistency, sub-scale structure and test-retest reliability. Items selected according to internal consistency were examined by a two-factor model exploratory factor analysis. Intraclass correlation coefficients described the stability of the scale. RESULTS: Replies were received from 117 psychiatrists (mean age 36 (SD 7.9)), 74% of whom were made and 26% female. The Schneiderian scale showed better overall internal consistency than the Bleulerian scale. Intra-class correlation coefficients for test-retest comparisons were between 0.5 and 0.7 for Schneiderian items and 0.2 and 0.7 for Bleulerian items. There was no negative association between Bleulerian and Schneiderian scale scores, suggesting that respondents may hold both concepts. Place of training was significantly associated with the respondent's opinion; disagreement with a Bleulerian standpoint predominated for those trained at the University of S. Paulo. CONCLUSIONS: The less satisfactory reliability for the Bleulerian sub-scale limits confidence in the whole scale but on the other hand this questionnaire contributes to the understanding of the controversy over Bleulerian and Schneiderian models for conceptualisation of schizophrenia, the former requiring more inference and therefore being prone to unreliability.