A snapshot of suspended sediment and fluid mud occurrence in a mixed-energy embayment, Tijucas Bay, Brazil

Along the southern Brazilian coast, Tijucas Bay is known for its unique muddy tidal flats associated with chenier plains. Previous field observations pointed to very high suspended sediment concentrations (SSCs) in the inner parts of the bay, and in the estuary of the Tijucas River, suggesting the presence of fluid mud. In this study, the occurrences of suspended sediments and fluid mud were examined during a larger-scale, high-resolution 2-day field campaign on 1-2 May 2007, encompassing survey lines spanning nearly 80 km, 75 water sampling stations for near-bottom density estimates, and ten sediment sampling stations. Wave refraction modeling provided qualitative wave energy estimates as a function of different incidence directions. The results show that SSC increases toward the inner bay near the water surface, but seaward near the bottom. This suggests that suspended sediment is supplied by the local rivers, in particular the Tijucas. Near-surface SSCs were of the order of 50 mg l(-1) close to the shore, but exceeded 100 mg l(-1) near the bottom in the deeper parts of the bay. Fluid mud thickness and location given by densimetry and echo-sounding agreed in some places, although being mostly discordant. The best agreement was observed where wave energy was high during the campaign. The discrepancy between the two methods may be an indication for the existence of fluid mud, which is recorded by one method but not the other. Agreement is considered to be an indication of fluidization, whereas disagreement indicates more consolidation. Wave modeling suggests that waves from the ENE and SE are the most effective in supplying energy to the inner bay, which may induce the liquefaction of mud deposits to form fluid mud. Nearshore mud resuspension and weak horizontal currents result in sediment-laden offshore flow, which explains the higher SSCs measured in the deeper parts of the bay, besides providing a mechanism for fine-sediment export to the inner shelf.

Impacts of interruption of the Agulhas leakage on the tropical Atlantic in coupled ocean-atmosphere simulations

In this paper we use a coupled ocean-atmosphere model to investigate the impact of the interruption of Agulhas leakage of Indian ocean water on the tropical Atlantic, a region where strong coupled ocean-atmosphere interactions occur. The effect of a shut down of leakage of Indian ocean water is isolated from the effect of a collapse of the MOC. In our experiments, the ocean model is forced with boundary conditions in the southeastern corner of the domain that correspond to no interocean exchange of Indian ocean water into the Atlantic. The southern boundary condition is taken from the Levitus data and ensures an MOC in the Atlantic. Within this configuration, instead of warm and salty Indian ocean water temperature (cold) and salinity (fresh) anomalies of southern ocean origin propagate into the South Atlantic and eventually reach the equatorial region, mainly in the thermocline. This set up mimics the closure of the ""warm water path"" in favor of the ""cold water path"". As part of the atmospheric response, there is a northward shift of the intertropical convergence zone (ITCZ). The changes in trade winds lead to reduced Ekman pumping in the equatorial region. This leads to a freshening and warming of the surface waters along the equator. Especially in the Cold Tongue region, the cold and fresh subsurface anomalies do not reach the surface due to the reduced upwelling. The anomaly signals are transported by the equatorial undercurrent and spread away from the equator within the thermocline. Part of the anomaly eventually reaches the Tropical North Atlantic, where it affects the Guinea Dome. Surprisingly, the main effect at the surface is small on the equator and relatively large at the Guinea Dome. In the atmosphere, the northward shift of the ITCZ is associated with a band of negative precipitation anomalies and higher salinities over the Tropical South Atlantic. An important implication of these results is that the modified water characteristics due to a shut down of the Agulhas leakage remain largely unaffected when crossing the equatorial Atlantic and therefore can affect the deepwater formation in the North Atlantic. This supports the hypothesis that the Agulhas leakage is an important source region for climate change and decadal variability of the Atlantic.

Submesoscale activity over the Argentinian shelf

Submesoscale activity over the Argentinian shelf is investigated by means of high resolution primitive equation numerical solutions. These reveal energetic turbulent activity (visually similar to the one occasionally seen in satellite images) at scales O(5 km) in fall and winter that is linked to mixed layer baroclinic instability. The air-sea heat flux responsible for (i) deepening the upper ocean boundary layer (at these seasons) and (ii) maintaining a cross-shelf background density gradient is the key environmental parameter controlling submesoscale activity. Implications of submesoscale turbulence are investigated. Its mixing efficiency estimated by computing a diffusivity coefficient is above 30 m(2) s(-1) away from the shallowest regions. Aggregation of surface buoyant material by submesoscale currents occurs within hours and is presumably important to the ecosystem.

In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements

In silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens' biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L major, L infantum, and L braziliensis. We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters. and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile oft. donovani genes during promastigote-amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania. (C) 2012 Elsevier B.V. All rights reserved.

Potential of a neutrino detector in the ANDES underground laboratory for geophysics and astrophysics of neutrinos

The construction of the Agua Negra tunnels that will link Argentina and Chile under the Andes, the world's longest mountain range, opens the possibility of building the first deep underground laboratory in the Southern Hemisphere. This laboratory has the acronym ANDES (Agua Negra Deep Experiment Site) and its overburden could be as large as similar to 1.7 km of rock, or 4500 mwe, providing an excellent low background environment to study physics of rare events like the ones induced by neutrinos and/or dark matter. In this paper we investigate the physics potential of a few kiloton size liquid scintillator detector, which could be constructed in the ANDES laboratory as one of its possible scientific programs. In particular, we evaluate the impact of such a detector for the studies of geoneutrinos and Galactic supernova neutrinos, assuming a fiducial volume of 3 kilotons as a reference size. We emphasize the complementary roles of such a detector to the ones of the Northern Hemisphere neutrino facilities, given the advantages of its geographical location.

Heavy metal distribution in recent sediments along the Tiete River basin (Sao Pauro, Brazil)

The distribution of heavy metals in recent sediments deposited along the Tiete River, a highly polluted river in southeast region of Brazil was studied. Around the metropolitan area of Silo Paulo city (25 million people), the pollution is related to municipal wastes and industrial effluents with reinforced downstream by agricultural activities. The observed increase of heavy metal concentrations is particularly important for Zn in the upper basin and Cu, Co and Cr at mouth. Geo-accumulation index calculation, related to the regional background, showed that the sediments along the basin are seriously polluted by heavy metals of anthropogenic origin, mainly Cu, Co, Cr and Zn. Calculated index suggests medium to very strongly pollution.

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Background: Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results: Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion: Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.

Global gene expression profiling of oral cavity cancers suggests molecular heterogeneity within anatomic subsites

Abstract Background Oral squamous cell carcinoma (OSCC) is a frequent neoplasm, which is usually aggressive and has unpredictable biological behavior and unfavorable prognosis. The comprehension of the molecular basis of this variability should lead to the development of targeted therapies as well as to improvements in specificity and sensitivity of diagnosis. Results Samples of primary OSCCs and their corresponding surgical margins were obtained from male patients during surgery and their gene expression profiles were screened using whole-genome microarray technology. Hierarchical clustering and Principal Components Analysis were used for data visualization and One-way Analysis of Variance was used to identify differentially expressed genes. Samples clustered mostly according to disease subsite, suggesting molecular heterogeneity within tumor stages. In order to corroborate our results, two publicly available datasets of microarray experiments were assessed. We found significant molecular differences between OSCC anatomic subsites concerning groups of genes presently or potentially important for drug development, including mRNA processing, cytoskeleton organization and biogenesis, metabolic process, cell cycle and apoptosis. Conclusion Our results corroborate literature data on molecular heterogeneity of OSCCs. Differences between disease subsites and among samples belonging to the same TNM class highlight the importance of gene expression-based classification and challenge the development of targeted therapies.

Functional characterisation of the non-essential protein kinases and phosphatases regulating Aspergillus nidulans hydrolytic enzyme production

Abstract Background Despite recent advances in the understanding of lignocellulolytic enzyme regulation, less is known about how different carbon sources are sensed and the signaling cascades that result in the adaptation of cellular metabolism and hydrolase secretion. Therefore, the role played by non-essential protein kinases (NPK) and phosphatases (NPP) in the sensing of carbon and/or energetic status was investigated in the model filamentous fungus Aspergillus nidulans. Results Eleven NPKs and seven NPPs were identified as being involved in cellulase, and in some cases also hemicellulase, production in A. nidulans. The regulation of CreA-mediated carbon catabolite repression (CCR) in the parental strain was determined by fluorescence microscopy, utilising a CreA: GFP fusion protein. The sensing of phosphorylated glucose, via the RAS signalling pathway induced CreA repression, while carbon starvation resulted in derepression. Growth on cellulose represented carbon starvation and derepressing conditions. The involvement of the identified NPKs in the regulation of cellulose-induced responses and CreA derepression was assessed by genome-wide transcriptomics (GEO accession 47810). CreA:GFP localisation and the restoration of endocellulase activity via the introduction of the ∆creA mutation, was assessed in the NPK-deficient backgrounds. The absence of either the schA or snfA kinase dramatically reduced cellulose-induced transcriptional responses, including the expression of hydrolytic enzymes and transporters. The mechanism by which these two NPKs controlled gene transcription was identified, as the NPK-deficient mutants were not able to unlock CreA-mediated carbon catabolite repression under derepressing conditions, such as carbon starvation or growth on cellulose. Conclusions Collectively, this study identified multiple kinases and phosphatases involved in the sensing of carbon and/or energetic status, while demonstrating the overlapping, synergistic roles of schA and snfA in the regulation of CreA derepression and hydrolytic enzyme production in A. nidulans. The importance of a carbon starvation-induced signal for CreA derepression, permitting transcriptional activator binding, appeared paramount for hydrolase secretion.

Sensing the "LUV" with HST+COS in Cycle 20 and beyond

New Cosmic Origins Spectrograph (COS) observing modes have extended the Hubble Space Telescope's spectral range to wavelengths between 900-1150 Å. However, the G140L/1280 and the Cycle 19 available G130M central wavelengths (1055 and 1096) that sample below 1150 Å were only available at focus positions which provided low-resolution (R<3,000). For HST Cycle 20, we introduced a new G130M/1222 central wavelength that covers 1065-1365 Å with R>10,000 everywhere, but optimized for 15000 from 1080-1200 Å. This mode places geo-coronal Lyα between the COS FUV detector segments to minimize detector gain sag. Also for Cycle 20, the resolution of the G130M/1055 and 1096 modes will be increased by a factor of 3-4 by optimizing the focus positions for these modes. This will give HST approximately the effective area of FUSE over the FUSE bandpass at 10,000. Here we present the current calibration status of the COS G130M/1055, 1096, and 1222 central wavelength settings at the original and second FUV lifetime positions with an emphasis on observing over the "Lyman UV", or "LUV", 912-1216 Å.

Estudios tafonómicos en foraminíferos bentónicos como proxy de hidrodinámica y sedimentología en el gradiente Río de La Plata – Océano Atlántico Sur Occidental

Los foraminíferos bentónicos representan un excelente proxy geológico, ya que sus caparazones son incorporados en el sedimento y pasan a comportarse como granos sedimentares durante los eventos de transporte y erosión, permitiendo así, el registro de condiciones y eventos que ocurren en los océanos. De este modo, son usados para describir patrones de hidrodinámica y evaluar índices de deposición, erosión y retrabajamiento del sedimento en los ambientes marinos. Concretamente, las regiones costeras representan zonas de alta complejidad ambiental, debido a que en ellas se da la mezcla de agua tanto de origen continental como marino, y a su vez, al efecto de la descarga fluvial que aporta material particulado del continente para el océano. El Río de la Plata (RdLP) representa el cuarto mayor estuario del mundo y el segundo del continente americano, lo cual convierte al sistema RdLP-Océano Atlántico en un complejo gradiente estuarino de interés en estudios sedimentológicos con posteriores aplicaciones paleo-climáticas y paleo-ecológicas del Cuaternario Superior. En el presente estudio, se registra a partir de las asociaciones muertas, para la región del estuario entrada de agua marina hasta la zona del frente termohalino. Dichas asociaciones se caracterizaron por especies típicas de plataforma y aguas frías. La región marina del RdlP registró los mayores porcentajes de abrasión y fragmentación de caparazones, indicando una zona de alta energía. Por otro lado, en la región más oceánica las asociaciones muertas reflejaron un transporte en dirección norte, influenciado por la pluma del RdlP. Cabe resaltar la presencia en esta región de una isla barrera, vestigio de una paleo-costa producto de una regresión Holocénica. Este local se caracterizó por un aumento de la abrasión y fragmentación mostrando la gran hidrodinámica presente. En todos los casos existió correlación entre las señales tafonómicas y los datos geo-químicos (sedimentología, pH, oxígeno disuelto, carbono orgánico y nitrógeno total)

Estudios tafonómicos en foraminíferos bentónicos como proxy de hidrodinámica y sedimentología en el gradiente Río de La Plata – Océano Atlántico Sur Occidental

Los foraminíferos bentónicos representan un excelente proxy geológico, ya que sus caparazones son incorporados en el sedimento y pasan a comportarse como granos sedimentares durante los eventos de transporte y erosión, permitiendo así, el registro de condiciones y eventos que ocurren en los océanos. De este modo, son usados para describir patrones de hidrodinámica y evaluar índices de deposición, erosión y retrabajamiento del sedimento en los ambientes marinos. Concretamente, las regiones costeras representan zonas de alta complejidad ambiental, debido a que en ellas se da la mezcla de agua tanto de origen continental como marino, y a su vez, al efecto de la descarga fluvial que aporta material particulado del continente para el océano. El Río de la Plata (RdLP) representa el cuarto mayor estuario del mundo y el segundo del continente americano, lo cual convierte al sistema RdLP-Océano Atlántico en un complejo gradiente estuarino de interés en estudios sedimentológicos con posteriores aplicaciones paleo-climáticas y paleo-ecológicas del Cuaternario Superior. En el presente estudio, se registra a partir de las asociaciones muertas, para la región del estuario entrada de agua marina hasta la zona del frente termohalino. Dichas asociaciones se caracterizaron por especies típicas de plataforma y aguas frías. La región marina del RdlP registró los mayores porcentajes de abrasión y fragmentación de caparazones, indicando una zona de alta energía. Por otro lado, en la región más oceánica las asociaciones muertas reflejaron un transporte en dirección norte, influenciado por la pluma del RdlP. Cabe resaltar la presencia en esta región de una isla barrera, vestigio de una paleo-costa producto de una regresión Holocénica. Este local se caracterizó por un aumento de la abrasión y fragmentación mostrando la gran hidrodinámica presente. En todos los casos existió correlación entre las señales tafonómicas y los datos geo-químicos (sedimentología, pH, oxígeno disuelto, carbono orgánico y nitrógeno total).