Validation of reference genes for gene expression studies in the honey bee, Apis mellifera, by quantitative real-time RT-PCR

For obtaining accurate and reliable gene expression results it is essential that quantitative real-time RT-PCR (qRT-PCR) data are normalized with appropriate reference genes. The current exponential increase in postgenomic studies on the honey bee, Apis mellifera, makes the standardization of qRT-PCR results an important task for ongoing community efforts. For this aim we selected four candidate reference genes (actin, ribosomal protein 49, elongation factor 1-alpha, tbp-association factor) and used three software-based approaches (geNorm, BestKeeper and NormFinder) to evaluate the suitability of these genes as endogenous controls. Their expression was examined during honey bee development, in different tissues, and after juvenile hormone exposure. Furthermore, the importance of choosing an appropriate reference gene was investigated for two developmentally regulated target genes. The results led us to consider all four candidate genes as suitable genes for normalization in A. mellifera. However, each condition evaluated in this study revealed a specific set of genes as the most appropriated ones.

Extending Bell's beables to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories

In this paper, employing the Ito stochastic Schrodinger equation, we extend Bell's beable interpretation of quantum mechanics to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories. For a particular choice of the source of stochasticity, the one leading to a dissipative Lindblad-type correction to the Hamiltonian dynamics, we find that the diffusive terms in Nelsons stochastic trajectories are naturally incorporated into Bohm's causal dynamics, yielding a unified Bohm-Nelson theory. In particular, by analyzing the interference between quantum trajectories, we clearly identify the decoherence time, as estimated from the quantum formalism. We also observe the quantum-to-classical transition in the convergence of the infinite ensemble of quantum trajectories to their classical counterparts. Finally, we show that our extended beables circumvent the problems in Bohm's causal dynamics regarding stationary states in quantum mechanics.

Evaluation of rock mechanical behaviors under uniaxial compression with reference to assessed weathering grades

A weathering classification for granitic rock materials from southeastern Brazil was framed based on core characteristics. The classification was substantiated by a detailed petrographic study. Indirect assessment of weathering grades by density, ultrasonic and Schmidt hammer index tests was performed. Rebound values due to Schmidt hammer multiple impacts at one representative point were more efficient in predicting weathering grades than averaged single impact rebound values, P-wave velocities and densities. Uniaxial compression tests revealed that a large range of uniaxial compressive strength (214-153 MPa) exists in Grade I category where weathering does not seem to have played any role. It was concluded that variability in occurrences of quartz intragranular cracks and in biotite percentage, distribution and orientation might have played a key role in accelerating or decelerating the failure processes of the Grade I specimens. Deterioration of uniaxial compressive strength and elastic modulus and increase in Poisson`s ratio with increasing weathering intensity could be attributed to alteration of minerals, disruption of rock skeleton and microcrack augmentation. A crude relation between failure modes and weathering grades also emerged.

Defining Nutrient and Biochemical Oxygen Demand Baselines for Tropical Rivers and Streams in So Paulo State (Brazil): A Comparison Between Reference and Impacted Sites

Determining reference concentrations in rivers and streams is an important tool for environmental management. Reference conditions for eutrophication-related water variables are unavailable for Brazilian freshwaters. We aimed to establish reference baselines for So Paulo State tropical rivers and streams for total phosphorus (TP) and nitrogen (TN), nitrogen-ammonia (NH(4) (+)) and Biochemical Oxygen Demand (BOD) through the best professional judgment and the trisection methods. Data from 319 sites monitored by the So Paulo State Environmental Company (2005 to 2009) and from the 22 Water Resources Management Units in So Paulo State were assessed (N = 27,131). We verified that data from different management units dominated by similar land cover could be analyzed together (Analysis of Variance, P = 0.504). Cumulative frequency diagrams showed that industrialized management units were characterized by the worst water quality (e.g. average TP of 0.51 mg/L), followed by agricultural watersheds. TN and NH(4) (+) were associated with urban percentages and population density (Spearman Rank Correlation Test, P < 0.05). Best professional judgment and trisection (median of lower third of all sites) methods for determining reference concentrations showed agreement: 0.03 & 0.04 mg/L (TP), 0.31 & 0.34 mg/L (TN), 0.06 & 0.10 mg-N/L (NH(4) (+)) and 2 & 2 mg/L (BOD), respectively. Our reference concentrations were similar to TP and TN reference values proposed for temperate water bodies. These baselines can help with water management in So Paulo State, as well as providing some of the first such information for tropical ecosystems.

A reference business process for ecological niche modelling

Ecological niche modelling combines species occurrence points with environmental raster layers in order to obtain models for describing the probabilistic distribution of species. The process to generate an ecological niche model is complex. It requires dealing with a large amount of data, use of different software packages for data conversion, for model generation and for different types of processing and analyses, among other functionalities. A software platform that integrates all requirements under a single and seamless interface would be very helpful for users. Furthermore, since biodiversity modelling is constantly evolving, new requirements are constantly being added in terms of functions, algorithms and data formats. This evolution must be accompanied by any software intended to be used in this area. In this scenario, a Service-Oriented Architecture (SOA) is an appropriate choice for designing such systems. According to SOA best practices and methodologies, the design of a reference business process must be performed prior to the architecture definition. The purpose is to understand the complexities of the process (business process in this context refers to the ecological niche modelling problem) and to design an architecture able to offer a comprehensive solution, called a reference architecture, that can be further detailed when implementing specific systems. This paper presents a reference business process for ecological niche modelling, as part of a major work focused on the definition of a reference architecture based on SOA concepts that will be used to evolve the openModeller software package for species modelling. The basic steps that are performed while developing a model are described, highlighting important aspects, based on the knowledge of modelling experts. In order to illustrate the steps defined for the process, an experiment was developed, modelling the distribution of Ouratea spectabilis (Mart.) Engl. (Ochnaceae) using openModeller. As a consequence of the knowledge gained with this work, many desirable improvements on the modelling software packages have been identified and are presented. Also, a discussion on the potential for large-scale experimentation in ecological niche modelling is provided, highlighting opportunities for research. The results obtained are very important for those involved in the development of modelling tools and systems, for requirement analysis and to provide insight on new features and trends for this category of systems. They can also be very helpful for beginners in modelling research, who can use the process and the experiment example as a guide to this complex activity. (c) 2008 Elsevier B.V. All rights reserved.

Evaluation of FAO Penman-Monteith and alternative methods for estimating reference evapotranspiration with missing data in Southern Ontario, Canada

Grass reference evapotranspiration (ETo) is an important agrometeorological parameter for climatological and hydrological studies, as well as for irrigation planning and management. There are several methods to estimate ETo, but their performance in different environments is diverse, since all of them have some empirical background. The FAO Penman-Monteith (FAD PM) method has been considered as a universal standard to estimate ETo for more than a decade. This method considers many parameters related to the evapotranspiration process: net radiation (Rn), air temperature (7), vapor pressure deficit (Delta e), and wind speed (U); and has presented very good results when compared to data from lysimeters Populated with short grass or alfalfa. In some conditions, the use of the FAO PM method is restricted by the lack of input variables. In these cases, when data are missing, the option is to calculate ETo by the FAD PM method using estimated input variables, as recommended by FAD Irrigation and Drainage Paper 56. Based on that, the objective of this study was to evaluate the performance of the FAO PM method to estimate ETo when Rn, Delta e, and U data are missing, in Southern Ontario, Canada. Other alternative methods were also tested for the region: Priestley-Taylor, Hargreaves, and Thornthwaite. Data from 12 locations across Southern Ontario, Canada, were used to compare ETo estimated by the FAD PM method with a complete data set and with missing data. The alternative ETo equations were also tested and calibrated for each location. When relative humidity (RH) and U data were missing, the FAD PM method was still a very good option for estimating ETo for Southern Ontario, with RMSE smaller than 0.53 mm day(-1). For these cases, U data were replaced by the normal values for the region and Delta e was estimated from temperature data. The Priestley-Taylor method was also a good option for estimating ETo when U and Delta e data were missing, mainly when calibrated locally (RMSE = 0.40 mm day(-1)). When Rn was missing, the FAD PM method was not good enough for estimating ETo, with RMSE increasing to 0.79 mm day(-1). When only T data were available, adjusted Hargreaves and modified Thornthwaite methods were better options to estimate ETo than the FAO) PM method, since RMSEs from these methods, respectively 0.79 and 0.83 mm day(-1), were significantly smaller than that obtained by FAO PM (RMSE = 1.12 mm day(-1). (C) 2009 Elsevier B.V. All rights reserved.

Retinal and lenticular ultrastructure in the aestivating salamanderfish, Lepidogalaxias salamandroides (Galaxiidae, Teleostei) with special reference to a new type of photoreceptor mosaic

The salamanderfish, Lepidogalaxias salamandroides (Galaxiidae, Teleostei) is endemic to southwestern Australia and inhabits shallow, freshwater pools which evaporate during the hot summer months. Burrowing into the substrate in response to falling water levels allows these fish to aestivate for extended periods of time while encapsulated in a mucous cocoon even when the pools contain no water. Only a few minutes after a major rainfall, these fish emerge into relatively clear water which subsequently becomes laden with tannin, turning the water black and reducing the pH to approximately 4.3. As part of a large study of the visual adaptations of this unique species, the retinal and lenticular morphology of the aestivating salamanderfish is examined at the level of the light and electron microscopes. The inner retina is highly vascularised by a complex system of vitreal blood vessels, while the outer retina receives a blood supply by diffusion from a choriocapillaris. This increased retinal blood supply may be an adaptation for reducing the oxygen tension during critical periods of aestivation. Large numbers of Muller cells traverse the thickness of the retina from the inner to the outer limiting membranes. The ganglion cells are arranged in two ill-defined layers, separated from a thick inner nuclear layer containing two layers of horizontal cells by a soma-free inner plexiform layer. The photoreceptors can be divided into three types typical of many early actinopterygian representatives; equal double cones, small single cones and large rods (2:1:1). These photoreceptors are arranged into a unique regular square mosaic comprising a large rod bordered by four equal double cones with a small single cone located at the corner of each repeating unit. The double cones may optimise perception of mobile prey which it tracks by flexion of its head and neck and the large rods may increase sensitivity in the dark tannin-rich waters in which it lives. Each single cone also possesses a dense collection of polysomes and glycogen (a paraboloid) beneath its ellipsoid, the first such finding in teleosts. The retinal pigment epithelium possesses melanosomes, pha,oocytes and a large number of mitochondria. The anatomy of the retina and the photoreceptor mosaic is discussed in relation to the primitive phylogeny of this species and its unique life history.

Assessment of transient gene expression in plant tissues using the green fluorescent protein as a reference

Four different promoters (35S and enhanced 35S of the cauliflower mosaic virus, polyubiquitin of maize and actin1 of rice) were compared in a transient assay using maize leaves and particle bombardment. A gene encoding the jellyfish green fluorescent protein (GFP) driven by the 358 promoter was used as an internal standard to monitor the effectiveness of each bombardment. Normalisation of the transient expression assay using the GFP reference significantly reduced the variability between separate bombardments and allowed for a rapid and accurate evaluation of different promoters in microprojectile-bombarded leaves.

Predicting composition of leg sections with anthropometry and bioelectrical impedance analysis using magnetic resonance imaging as reference

Magnetic resonance imaging (MRI) was used to evaluate and compare with anthropometry a fundamental bioelectrical impedance analysis (BIA) method for predicting muscle and adipose tissue composition in the lower limb. Healthy volunteers (eight men and eight women), aged 41 to 62 years, with mean (S.D.) body mass indices of 28.6 (5.4) kg/m(2) and 25.1 (5.4) kg/m(2) respectively, were subjected to MRI leg scans, from which 20-cm sections of thigh and IO-cm sections of lower leg (calf) were analysed for muscle and adipose tissue content, using specifically developed software. Muscle and adipose tissue were also predicted from anthropometric measurements of circumferences and skinfold thicknesses, and by use of fundamental BIA equations involving section impedance at 50 kHz and tissue-specific resistivities. Anthropometric assessments of circumferences, cross-sectional areas and volumes for total constituent tissues matched closely MRI estimates. Muscle volume was substantially overestimated (bias: thigh, -40%; calf, -18%) and adipose tissue underestimated (bias: thigh, 43%; calf, 8%) by anthropometry, in contrast to generally better predictions by the fundamental BIA approach for muscle (bias:thigh, -12%; calf, 5%) and adipose tissue (bias:thigh, 17%; calf, -28%). However, both methods demonstrated considerable individual variability (95% limits of agreement 20-77%). In general, there was similar reproducibility for anthropometric and fundamental BIA methods in the thigh (inter-observer residual coefficient of variation for muscle 3.5% versus 3.8%), but the latter was better in the calf (inter-observer residual coefficient of variation for muscle 8.2% versus 4.5%). This study suggests that the fundamental BIA method has advantages over anthropometry for measuring lower limb tissue composition in healthy individuals.

The ocular morphology of the southern hemisphere lamprey Geotria australis gray with special reference to optical specialisations and the characterisation and phylogeny of photoreceptor types

This paper describes the ocular morphology of young adults of the southern hemisphere lamprey Geotria australis, the sole representative of the Geotriidae, and makes comparisons with those of holarctic lampreys (Petromyzontidae). As previously reported for the holarctic lamprey Ichthyomyzon unicuspis [Collin and Fritzsch, 1993], the lens of G. australis is non-spherical and possesses a cone-shaped posterior that may be capable of mediating variable focus. The avascular retina of G. australis is well differentiated, containing three retinal ganglion cell populations, three layers of horizontal cells and three photoreceptor types, in contrast to petromyzontids that contain only two photoreceptor types (short and long), G. australis possesses one rod-like (R1) and two cone-like (C1 and C2) photoreceptors. Although the rodlike receptor in G. australis may be homologous with the short receptors of holarctic lampreys, the two cone-like receptors have morphological characteristics that differ markedly from those of the long receptors of their holarctic counterparts. The features which distinguish the two cone-like receptors from those of the long receptor type in holarctic lampreys are the characteristics of the mitochondria and the presence of large amounts of two different types of stored secretory material in the endoplasmic reticulum of the myoid (refractile bodies). The endoplasmic reticulum of each receptor type has a different shape and staining profile and is polymorphic, each showing a continuum of distension. It is proposed that the presence of two cone-like photoreceptors with different characteristics would increase the spectral range of G. australis and thus be of value during the parasitic phase, when this lamprey lives in the surface marine waters. The irideal flap, present in G. australis but not petromyzontids, would assist in reducing intraocular flare during life in surface waters. The results of this study, which are discussed in the context of the proposed evolution of lampreys, emphasise that it is important to take into account the characteristics of the eyes of southern hemisphere lampreys when making generalizations about the eyes of lampreys as a whole.

Global trajectories of the long-term decline of coral reef ecosystems

Degradation of coral reef ecosystems began centuries ago, but there is no global summary of the magnitude of change. We compiled records, extending back thousands of years, of the status and trends of seven major guilds of carnivores, herbivores, and architectural species from 14 regions. Large animals declined before small animals and architectural species, and Atlantic reefs declined before reefs in the Red Sea and Australia, but the trajectories of decline were markedly similar worldwide. All reefs were substantially degraded long before outbreaks of coral disease and bleaching. Regardless of these new threats, reefs will not survive without immediate protection from human exploitation over large spatial scales.

Molecular phylogenetics of Chaetodon and the Chaetodontidae (Teleostei : Perciformes) with reference to morphology

Butterflyfish are colourful, pan-tropical coastal fish that are important and distinctive members of coral reef communities. A successful systematic scheme and a robust phylogeny is considered essential in understanding further their biogeography and ecology, although recent cladistic treatments of butterflyfish phylogeny, based on soft tissue and bone morphology and coded at the generic and subgeneric levels, differ in character coding and subsequently tree topology. This study provides an independent test of the morphologically based hypotheses, using molecular systematic data from two partial mitochondrial gene fragments, cytochrome b (cytb) and small subunit rRNA (rrnS), for 52 ingroup chaetodontids and seven pomacanthids used to root the molecular trees. Individual gene trees were largely compatible and a combined molecular phylogeny, inferred from Bayesian analysis, was used to test alternative hypotheses suggested by morphological analyses. The tree was also used to map the latest morphological matrix in order to evaluate potential synapomorphies for various nodes defining butterflyfish interrelationships. A clade comprised of Chelmon and Coradion was sister group to other chaetodontids. Heniochus and Hemitaurichthys were each resolved as monophyletic groups, and as sister taxa Of the taxa sampled, Prognothodes was resolved as the sister genus to Chaeotodon. Of the ten Chaetodon subgenera sampled, all were monophyletic but their interrelationships differed significantly from that inferred from morphological characters. Lepidochaetodon was the most basal subgenus followed by Exornator and the remaining subgenera. Molecular data support the sister group relationship between Corallochaetodon and Citharoedus suggested by morphology, but major differences occur among the remaining more derived taxa. Chaetodon trifascialis and C. oligacanthus were resolved as sister taxa adding weight to the inclusion of the latter in C. Megaprotodon. Of those pairs of taxa known to hybridize and sampled with molecular data, all were closely related phylogenetically, except those hybrids known to occur in the Rabdophorus subgenus. Two base changes separated C. pelewensis from C. paucifasciatus which have been regarded previously as a single species. Cytb provided greater resolution than rrnS and will likely provide additional resolution with greater taxon sampling.

Reference Values of Tissue Doppler Imaging and Pulsed Doppler Echocardiography for Analysis of Left Ventricular Diastolic Function in Healthy Adults

To determine reference values for tissue Doppler imaging (TDI) and pulsed Doppler echocardiography for left ventricular diastolic function analysis in a healthy Brazilian adult population. Observations were based on a randomly selected healthy population from the city of Vitoria, Espirito Santo, Brazil. Healthy volunteers (n = 275, 61.7% women) without prior histories of cardiovascular disease underwent transthoracic echocardiography. We analyzed 175 individuals by TDI and evaluated mitral annulus E`- and A`-waves from the septum (S) and lateral wall (L) to calculate E`/A` ratios. Using pulsed Doppler echocardiography, we further analyzed the mitral E- and A-waves, E/A ratios, isovolumetric relaxation times (IRTs), and deceleration times (DTs) of 275 individuals. Pulsed Doppler mitral inflow mean values for men were as follows: E-wave: 71 +/- 16 cm/sec, A-wave: 68 +/- 15 cm/sec, IRT: 74.8 +/- 9.2 ms, DT: 206 +/- 32.3 ms, E/A ratio: 1.1 +/- 0.3. Pulsed Doppler mitral inflow mean values for women were as follows: E-wave: 76 +/- 17, A-wave: 69 +/- 14 cm/sec, IRT: 71.2 +/- 10.5 ms, DT: 197 +/- 33.3 ms, E/A ratio: 1.1 +/- 0.3. IRT and DT values were higher in men than in women (P = 0.04 and P = 0.007, respectively). TDI values in men were as follows: E`S: 11 +/- 3 cm/sec, A`S: 13 +/- 2 cm/sec, E`S/A`S: 0.89 +/- 0.2, E`L: 14 +/- 3 cm/sec, A`L: 14 +/- 2 cm/sec, E`L/A`L: 1.1 +/- 0.4. E-wave/ E`S ratio: 6.9 +/- 2.2; E-wave / E`L ratio: 4.9 +/- 1.7. In this study, we determined pulsed Doppler and TDI derived parameters for left ventricular diastolic function in a large sample of healthy Brazilian adults. (Echocardiography 2010;27:777-782).

Optimal quantum trajectories for discrete measurements

Using the method of quantum trajectories we show that a known pure state can be optimally monitored through time when subject to a sequence of discrete measurements. By modifying the way that we extract information from the measurement apparatus we can minimize the average algorithmic information of the measurement record, without changing the unconditional evolution of the measured system. We define an optimal measurement scheme as one which has the lowest average algorithmic information allowed. We also show how it is possible to extract information about system operator averages from the measurement records and their probabilities. The optimal measurement scheme, in the limit of weak coupling, determines the statistics of the variance of the measured variable directly. We discuss the relevance of such measurements for recent experiments in quantum optics.