SnapShot: The Regulatory Genome

Enhancers switch genes on and off in response to a variety of intrinsic and external cellular signals. They are the cornerstone of gene regulation and the most pervasive constituents of the regulatory genome. Sequence polymorphisms in enhancer DNAs are a major source of population diversity and predilection to disease. To view this SnapShot, open or download the PDF.

The last frontier: Coupling technological developments with scientific challenges to improve hazard assessment of deep-sea mining

The growing economic interest in the exploitation of mineral resources on deep-ocean beds, including those in the vicinity of sensitive-rich habitats such as hydrothermal vents, raise a mounting concern about the damage that such actions might originate to these poorly-know ecosystems, which represent millions of years of evolution and adaptations to extreme environmental conditions. It has been suggested that mining may cause a major impact on vent ecosystems and other deep-sea areas. Yet, the scale and the nature of such impacts are unknown at present. Hence, building upon currently available scientific information it is crucial to develop new cost-effective technologies embedded into rigorous operating frameworks. The forward-thinking provided here will assist in the development of new technologies and tools to address the major challenges associated with deep sea-mining; technologies for in situ and ex situ observation and data acquisition, biogeochemical processes, hazard assessment of deep-sea mining to marine organisms and development of modeling tools in support of risk assessment scenarios. These technological developments are vital to validate a responsible and sustainable exploitation of the deep-sea mineral resources, based on the precautionary principle.

Abnormal mortality of octopus after a storm water event: Accumulated lead and lead isotopes as fingerprints

Octopus vulgaris is a sedentary organism that inhabits coastal waters being exposed to anthropogenic compounds. Lead concentration in coastal environments reflects many processes and activities namely weathering, industrial and domestic discharges, and atmospheric deposition. Since lead isotopic composition is little affected by kinetic processes occurring between source and sink, its signature has been used to identify different Pb sources. After a short-term heavy rainfall, hundreds of octopus appeared dead in two Portuguese coastal areas. Histopathology and Pb levels and its stable isotopes were determined in tissues, such as digestive gland, of stranded octopus and compared to alive specimens, sediments and runoff material from the same areas. Histology results showed severe damage in stranded octopus tissues suggesting that death was probably associated to multiple organ failure linked to hypertrophy and exudates input. In addition, Pb in stranded specimens reach concentrations up to one order of magnitude above the levels reported for alive octopus. Pb isotopic signatures in stranded organisms were closer to runoff material pointing to a similar origin of Pb. In summary, the results in this study showed that a short-term runoff event might change abruptly the salinity leading to the disruption of the osmoregulation function of octopus and consequently leading to its death. The analyses of stable isotopic Pb signature in octopus tissues corroborate these results and points to a change in the Pb source due to runoff after the storm water event. Pb stable isotopes in octopus proved to be an adequate tool to confirm the cause of death and linking it to the environment conditions.

The use of biomarkers as integrative tools for transitional water bodies monitoring in the Water Framework Directive context - A holistic approach in Minho river transitional waters

The Water Framework Directive (WFD) provides an important legislative opportunity to promote and implement an integrated approach for the protection of inland surface waters, transitional waters, coastal waters and groundwaters. The transitional waters constitute a central piece as they are usually under high environmental pressure and by their inherent characteristics present monitoring challenges. Integrating water quality monitoring with biological monitoring can increase the cost-effectiveness of monitoring efforts. One way of doing this is with biomarkers, which effectively integrate physical-chemical status and biological quality elements, dealing holistically with adverse consequences on the health of water bodies. The new Marine Strategy Framework Directive (MSFD) already incorporates the biomarker approach. Given the recent activities of OSPAR and HELCOM to harmonize existing monitoring guidelines between MSFD and WFD the use of similar methodologies should be fostered. To illustrate the potential of the biomarker approach, juveniles of flounder (Platichthys flesus) were used to evaluate the quality of the Minho river-estuary water bodies. The use of juveniles instead of adults eliminates several confounding factors such changes on the biological responses associated with reproduction. Here, a panel of well-established biomarkers, EROD, AChE, SOD, CAT, GST, LPO, ENA and FACs (1-Hydroxyrene) were selected and measured along with a gradient of different physical conditions, and integrated with trace elements characterization on both biota and sediments. In general, a clear profile along the water bodies was found, with low seasonal and spatial variation, consistent with a low impacted area. Overall, the results support the use of both the battery of biomarkers and the use of juvenile flounders in the monitoring of the water quality status within the WFD.

Major factors influencing the elemental composition of surface estuarine sediments: the case of 15 estuaries in Portugal

Upper sediments (0-5 cm) were sampled in 94 sites of water bodies of the fifteen Portuguese estuaries characterized by distinct settings of climate, topography and lithology, and marked by diverse anthropogenic pressures. Confined areas recognized as highly anthropogenic impacted, as well as areas dominated by erosion or frequently dredged were not sampled. Grain size, organic carbon (Corg), Al and trace elements (As, Cd, Co, Cr, Cu, Hg, Ni, Pb and Zn) were determined. Normalisation of trace element concentrations to Al and Corg, correlations between elements and Principal Component Analysis (PCA) allowed identifying elemental associations and the relevance of grain-size, lithology and anthropogenic inputs on sediment chemical composition. Whereas grain-size is the dominant effect for the majority of the studied estuaries, the southern estuaries Mira, Arade and Guadiana are dominated by specific lithologies of their river basins, and anthropogenic effects are identified in Ave, Leça, Tagus and Sado. This study emphasizes how baseline values of trace elements in sediments may vary within and among estuarine systems.

Association of Zn, Cu, Cd and Pb with protein fractions and sub-cellular partitioning in the digestive gland of Octopus vulgaris living in habitats with different metal levels

Zinc, Cu, Cd and Pb concentrations were determined in protein fractions of digestive gland and in the whole digestive gland of Octopus vulgaris collected from two areas of the Portuguese coast. Approximately 95% of Zn, 99% of Cu, 85-96% of Cd and 77-86% of Pb were stored in the cytosol, suggesting the predominance of cytosolic proteins in the trapping these elements. Gel filtration chromatography evidenced the presence of two major groups of proteins, with high molecular weight (HMW, 144 000-130 000 Da) and low molecular weight (LMW, 11000-6000 Da). The following metal-protein associations were found: Zn was distributed between HMW and LMW; Cu and Cd in LMW proteins with a minor association with HMW; and Pb in HMW proteins. The strong positive correlations between Cd, Zn and Cu and LMW proteins point to the presence of metalloproteins with high affinity to these elements. A shift was registered between the maximum of the ratio 254:280 nm and metal concentrations in the chromatographic profiles. This shift may result from metallothioneins having a small participation in the metal binding or protein purification was insufficient and various LMW proteins may be interfering.

Metallothioneins and trace elements in digestive gland, gills, kidney and gonads of Octopus vulgaris

Metallothionein-like proteins (MT) and V, Cr, Co, Ni, Zn, Cu, As and Cd were determined in digestive gland, gills, kidney and gonads of Octopus vulgaris, from the Portuguese coast. To our knowledge these are the first data on MT in octopus. High concentrations (microgg(-1), dry mass) of Zn (48050) and Cd (555) were found in digestive gland, and MT reached levels one order of magnitude above the ones registered in wild bivalves. Significantly higher levels of MT in digestive gland and gills of specimens from A and B were in line with elevated Cd concentrations. Principal component analyses (PCA) point to MT-Cd and MT-Cr associations in digestive gland and gills. Despite the high levels of Zn in specimens from B, association with Zn was not obtained. Due to the affinity of MT to various elements, it should not be excluded the possibility of Cd replacing Zn in Zn-MT. Kidney presented higher levels of Cd, Co, Ni and As than gills and gonads, and in the case of As surpassing the levels in digestive gland, but PCA showed no relation with MT. Likewise the MT levels in gonads had no correspondence to the metal concentration variation.

Sub-cellular partitioning of Zn, Cu, Cd and Pb in the digestive gland of native Octopus vulgaris exposed to different metal concentrations (Portugal)

Concentrations of Zn, Cu, Cd and Pb and their sub-cellular distributions were determined in composite samples of digestive glands of the common octopus, Octopus vulgaris caught from two areas of the Portuguese coast characterised by contrasting metal contamination. Minor contents of Zn (1%), Cu (2%), Cd (6%) and Pb (7%) were found in the insoluble fraction, consisting of nuclei, mitochondria, lysosomes and microsome operationally separated from the whole digestive gland through a sequential centrifugation. A tendency for linear relationships between metal concentrations in nuclei, mitochondria, lysosomes and whole digestive gland was observed. These relationships suggest that despite low metal content organelles responded to the increasing accumulated metals, which means that detoxifying mechanism in cytosol was incomplete. Poorer correlations between microsome and whole digestive gland did not point to metal toxicity in the analysed compartments. However, the high accumulated Cd indicated that O. vulgaris is an important vehicle of this element to its predators in the coastal environment.

Geographical variation and partition of metals in tissues of Octopus vulgaris along the Portuguese coast

Zinc, Cu, Cd, Pb and Hg were determined in mantle, arm and digestive gland of 59 individuals of Octopus vulgaris captured at six sites along the Portuguese coast. Metal concentrations in tissues did not vary significantly (P<0.05) with size/weight, sex or sexual stage. The abundance of metals in each analysed tissue was: Zn>Cu>>Cd>Pb>Hg. Concentrations in the digestive gland reached one (Pb, Hg) and two (Zn, Cu, Cd) orders of magnitude higher than those found in arm and mantle, which indicates that the digestive gland contains the major storage sites for these elements, acting as a detoxification organ. However, concentrations in the digestive gland showed contrasting geographic patterns: Zn, Pb, Cu and Hg were higher in the Southern stations, while Cd levels increased drastically in Northern stations. This increase is in line with the contrasting Cd distribution in coastal waters. The lack of relations between metal concentration in tissues and biological parameters facilitates the recognition of those spatial patterns. The geographical contrast of Cd is extended to the accumulation in mantle and arm. A possible explanation for these enhanced values is that threshold level for Cd accumulation in digestive gland was attained and detoxification processes eventually modified.