A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages

Coccidiosis of the domestic fowl is a worldwide disease caused by seven species of protozoan parasites of the genus Eimeria. The genome of the model species, Eimeria tenella, presents a complexity of 55-60 MB distributed in 14 chromosomes. Relatively few studies have been undertaken to unravel the complexity of the transcriptome of Eimeria parasites. We report here the generation of more than 45,000 open reading frame expressed sequence tag (ORESTES) cDNA reads of E. tenella, Eimeria maxima and Eimeria acervulina, covering several developmental stages: unsporulated oocysts, sporoblastic oocysts, sporulated oocysts, sporozoites and second generation merozoites. All reads were assembled to constitute gene indices and submitted to a comprehensive functional annotation pipeline. In the case of E. tenella, we also incorporated publicly available ESTs to generate an integrated body of information. Orthology analyses have identified genes conserved across different apicomplexan parasites, as well as genes restricted to the genus Eimeria. Digital expression profiles obtained from ORESTES/EST countings, submitted to clustering analyses, revealed a high conservation pattern across the three Eimeria spp. Distance trees showed that unsporulated and sporoblastic oocysts constitute a distinct clade in all species, with sporulated oocysts forming a more external branch. This latter stage also shows a close relationship with sporozoites, whereas first and second generation merozoites are more closely related to each other than to sporozoites. The profiles were unambiguously associated with the distinct developmental stages and strongly correlated with the order of the stages in the parasite life cycle. Finally, we present The Eimeria Transcript Database (http://www.coccidia.icb.usp.br/eimeriatdb), a website that provides open access to all sequencing data, annotation and comparative analysis. We expect this repository to represent a useful resource to the Eimeria scientific community, helping to define potential candidates for the development of new strategies to control coccidiosis of the domestic fowl. (C) 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

PRoSPer: perceptual similarity queries in medical CBIR systems through user profiles

In this paper, we present a novel approach to perform similarity queries over medical images, maintaining the semantics of a given query posted by the user. Content-based image retrieval systems relying on relevance feedback techniques usually request the users to label relevant/irrelevant images. Thus, we present a highly effective strategy to survey user profiles, taking advantage of such labeling to implicitly gather the user perceptual similarity. The profiles maintain the settings desired for each user, allowing tuning of the similarity assessment, which encompasses the dynamic change of the distance function employed through an interactive process. Experiments on medical images show that the method is effective and can improve the decision making process during analysis.

Cold cloud climatology over Europe and the Mediterranean during the warm season from Meteosat IR imagery

Thermal infrared (IR, 10.5 – 12.5 m) images from the Meteosat Visible and Infrared Imager (MVIRI) of cold cloud episodes (cloud top brightness temperature < 241 K) are used as a proxy of precipitating clouds to derive a warm season (May-August) climatology of their coherency, duration, span, and speed over Europe and the Mediterranean. The analysis focuses over the 30°-54°N, 15°W-40°E domain in May-August 1996-2005. Harmonic analysis using discrete Fourier transforms is applied together with a statistical analysis and an investigation of the diurnal cycle. This study has the objective to make available a set of results on the propagation dynamics of the cloud systems with the aim of assist numerical modellers in improving summer convection parameterization. The zonal propagation of cold cloud systems is accompanied by a weak meridional component confined to narrow latitude belts. The persistence of cold clouds over the area evidences the role of orography, the Pyrenees, the Alps, the Balkans and Anatolia. A diurnal oscillation is found with a maximum marking the initiation of convection in the lee of the mountains and shifting from about 1400 UTC at 40°E to 1800 UTC at 0°. A moderate eastward propagation of the frequency maximum from all mountain chains across the domain exists and the diurnal maxima are completely suppressed west of 5°W. The mean power spectrum of the cold cloud frequency distribution evidences a period of one day all over Europe disappearing over the ocean (west of 10°W). Other maxima are found in correspondence of 6 to 10 days in the longitudes from 15° W to 0° and indicate the activity of the westerlies with frontal passage over the continent. Longer periods activities (from 15 up to 30 days) were stronger around 10° W and from 5° W to 15° E and are likely related to the Madden Julian Oscillation influence. The maxima of the diurnal signal are in phase with the presence of elevated terrain and with land masses. A median zonal phase speed of 16.1 ms-1 is found for all events ≥ 1000 km and ≥ 20 h and a full set of results divided by years and recurrence categories is also presented.

(Table 1) Position and astronomical ages of sedimentary cycles in the eastern Mediterranean Sea

An astronomically calibrated timescale has recently been established [Hilgen, 1991, doi:10.1016/0012-821X(91)90082-S; doi:10.1016/0012-821X(91)90206-W] for the Pliocene and earliest Pleistocene based on the correlation of dominantly precession controlled sedimentary cycles (sapropels and carbonate cycles) in Mediterranean marine sequences to the precession time series of the astronomical solution of Berger and Loutre [1991, doi:10.1016/0277-3791(91)90033-Q ] (hereinafter referred to as Ber90). Here we evaluate the accuracy of this timescale by (1) comparing the sedimentary cycle patterns with 65°N summer insolation time series of different astronomical solutions and (2) a cross-spectral comparison between the obliquity-related components in the 65°N summer insolation curves and high-resolution paleoclimatic records derived from the same sections used to construct the timescale. Our results show that the carbonate cycles older than 3.5 m.y. should be calibrated to one precession cycle older than previously proposed. Application of the astronomical solution of Laskar [1990, doi:10.1016/0019-1035(90)90084-M], (hereinafter referred to as La90) with present-day values for the dynamical ellipticity of the Earth and tidal dissipation by the Sun and Moon results in the best fit with the geological record, indicating that this solution is the most accurate from a geological point of view. Application of Ber90, or La90 solutions with dynamical ellipticity values smaller or larger than the present-day value, results in a less obvious fit with the geological record. This implies that the change in the planetary shape of the Earth associated with ice loading and unloading near the poles during the last 5.3 million years was too small to drive the precession into resonance with the perturbation term, s6-g6+g5, of Jupiter and Saturn. Our new timescale results in a slight but significant modification of all ages of the sedimentary cycles, bioevents, reversal boundaries, chronostratigraphic boundaries, and glacial cycles. Moreover, a comparison of this timescale with the astronomical timescales of ODP site 846 [Shackleton et al., 1995, doi:10.2973/odp.proc.sr.138.106.1995; doi:10.2973/odp.proc.sr.138.117.1995] and ODP site 659 [Tiedemann et al., 1994, doi:10.1029/94PA00208] indicates that all obliquity-related glacial cycles prior to ~4.7 Ma in ODP sites 659 and 846 should be correlated with one obliquity cycle older than previously proposed.

Surface time series of nitrate, silicate and chlorophyll a (1999-2011) and CTD profiles (1999) at the PhytoCly station, Bay of Calvi, Corsica, Mediterranean Sea

This work is based on a long time series of data collected in the well-preserved Bay of Calvi (Corsica island, Ligurian Sea, NW Mediterranean) between 1979 and 2011, which include physical characteristics (31 years), chlorophyll a (chl a, 15 years), and inorganic nutrients (13 years). Because samples were collected at relatively high frequencies, which ranged from daily to biweekly during the winter-spring period, it was possible to (1) evidence the key role of two interacting physical variables, i.e. water temperature and wind intensity, on nutrient replenishment and phytoplankton dynamics during the winter-spring period, (2) determine critical values of physical factors that explained interannual variability in the replenishment of surface nutrients and the winter-spring phytoplankton bloom, and (3) identify previously unrecognized characteristics of the planktonic ecosystem. Over the >30 year observation period, the main driver of nutrient replenishment and phytoplankton (chl a) development was the number of wind events (mean daily wind speed >5 m s-1) during the cold-water period (subsurface water <13.5°C). According to winter intensity, there were strong differences in both the duration and intensity of nutrient fertilization and phytoplankton blooms (chl a). The trophic character of the Bay of Calvi changed according to years, and ranged from very oligotrophic (i.e. subtropical regime, characterized by low seasonal variability) to mesotrophic (i.e. temperate regime, with a well-marked increase in nutrient concentrations and chl a during the winter-spring period) during mild and moderate winters, respectively. A third regime occurred during severe winters characterized by specific wind conditions (i.e. high frequency of northeasterly winds), when Mediterranean "high nutrient - low chlorophyll" conditions occurred as a result of enhanced crossshore exchanges and associated offshore export of the nutrient-rich water. There was no long-term trend (e.g. climatic) in either nutrient replenishment or the winter-spring phytoplankton bloom between 1979 and 2011, but both nutrients and chl a reflected interannual and decadal changes in winter intensity.

Compilation of quality controlled nutrient profiles from the Mediterranean Sea

In the last decades, a striking amount of hydrographic data, covering the most part of Mediterranean basin, have been generated by the efforts made to characterize the oceanography and ecology of the basin. On the other side, the improvement in technologies, and the consequent perfecting of sampling and analytical techniques, provided data even more reliable than in the past. Nutrient data enter fully in this context, but suffer of the fact of having been produced by a large number of uncoordinated research programs and of being often deficient in quality control, with data bases lacking of intercalibration. In this study we present a computational procedure based on robust statistical parameters and on the physical dynamic properties of the Mediterranean sea and its morphological characteristics, to partially overcome the above limits in the existing data sets. Through a data pre filtering based on the outlier analysis, and thanks to the subsequent shape analysis, the procedure identifies the inconsistent data and for each basin area identifies a characteristic set of shapes (vertical profiles). Rejecting all the profiles that do not follow any of the spotted shapes, the procedure identifies all the reliable profiles and allows us to obtain a data set that can be considered more internally consistent than the existing ones.

Radar profiles from South Shetland Islands/Western Antarctic Peninsula

The sedimentary architecture of polar gravel-beach ridges is presented and it is shown that ridge internal geometries reflect past wave-climate conditions. Ground-penetrating radar (GPR) data obtained along the coasts of Potter Peninsula (King George Island) show that beach ridges unconformably overlie the prograding strand plain. Development of individual ridges is seen to result from multiple storms in periods of increased storm-wave impact on the coast. Strand-plain progradation, by contrast, is the result of swash sedimentation at the beach-face under persistent calm conditions. The sedimentary architecture of beach ridges in sheltered parts of the coast is characterized by seaward-dipping prograding beds, being the result of swash deposition under stormy conditions, or aggrading beds formed by wave overtopping. By contrast, ridges exposed to high-energy waves are composed of seaward- as well as landward-dipping strata, bundled by numerous erosional unconformities. These erosional unconformities are the result of sediment starvation or partial reworking of ridge material during exceptional strong storms. The number of individual ridges which are preserved from a given time interval varies along the coast depending on the morphodynamic setting: sheltered coasts are characterized by numerous small ridges, whereas fewer but larger ridges develop on exposed beaches. The frequency of ridge building ranges from decades in the low-energy settings up to 1600 years under high-energy conditions. Beach ridges in the study area cluster at 9.5, 7.5, 5.5, and below 3.5 m above the present-day storm beach. Based on radiocarbon data, this is interpreted to reflect distinct periods of increased storminess and/or shortened annual sea-ice coverage in the area of the South Shetland Islands for the times around 4.3, c. 3.1, 1.9 ka cal BP, and after 0.65 ka cal BP. Ages further indicate that even ridges at higher elevations can be subject to later reactivation and reworking. A careful investigation of the stratigraphic architecture is therefore essential prior to sampling for dating purposes.

Sedimentation across the Great Barrier Reef

The continental margin off northeast Australia, comprising the Great Barrier Reef (GBR) platform and Queensland Trough, is the largest tropical mixed siliciclastic/carbonate depositional system in existence. We describe a suite of 35 piston cores and two Ocean Drilling Program (ODP) sites from a 130*240 km rectangular area of the Queensland Trough, the slope and basin setting east of the central GBR platform. Oxygen isotope records, physical property (magnetic susceptibility and greyscale) logs, analyses of bulk carbonate content and radiocarbon ages at these locations are used to construct a high resolution stratigraphy. This information is used to quantify mass accumulation rates (MARs) for siliciclastic and carbonate sediments accumulating in the Queensland Trough over the last 31,000 years. For the slope, highest MARs of siliciclastic sediment occur during transgression (1.0 Million Tonnes per year; MT/yr), and lowest MARs of siliciclastic (<0.1 MT/yr) and carbonate (0.2 MT/yr) sediment occur during sea level lowstand. Carbonate MARs are similar to siliciclastic MARs for transgression and highstand (1.1-1.4 MT/yr). In contrast, for the basin, MARs of siliciclastic (0-0.1 MT/yr) and carbonate sediment (0.2-0.4 MT/yr) are continuously low, and within a factor of two, for lowstand, transgression, and highstand. Generic models for carbonate margins predict that maximum and minimum carbonate MARs on the slope will occur during highstand and lowstand, respectively. Conversely, most models for siliciclastic margins suggest maximum and minimum siliciclastic MARs will occur during lowstand and transgression, respectively. Although carbonate MARs in the Queensland Trough are similar to those predicted for carbonate depositional systems, siliciclastic MARs are the opposite. Given uniform siliciclastic MARs in the basin through time, we conclude that terrigenous material is stored on the shelf during sea level lowstand, and released to the slope during transgression as wave driven currents transport shelf sediment offshore.