Exposure assessment of potentially toxic trace elements via consumption of fruits and vegetables grown under the impact of Alaverdi's mining complex

This study is aimed to investigate the transfer of potentially toxic trace elements from soils to plants grown under the impact of Alaverdi's mining complex and assess the related dietary exposure to local residents. Contamination levels of potentially toxic trace elements (Cu, Ni, Pb, Zn, Hg, As, Cd) in soils and plants were determined and afterwards, transfer factors, estimated daily intakes, target hazard quotients, and hazard indexes were calculated.

Some trace elements (Pb, Zn, Cd) exceeded the maximum allowable levels. EDIs of Cu, Ni, Hg for the majority of studied fruits and vegetables exceeded the health-based guideline values. Meanwhile, in case of combined consumption of the studied food items, the estimated cumulative daily intakes exceeded health-based guideline values not only for the aforementioned trace elements but also for Zn in the following sequence: Zn > Hg > Ni > Cu. HI > 1 values highlighted the potential adverse health effects for local population through more than one trace element.

Detailed investigations need to be done for the overall assessment of health risks, taking into consideration not only adverse health effects posed by more than one toxic trace element but also through other exposure pathways.     

Recent advances in proteomic applications for schistosomiasis research: potential clinical impact

Introduction: Schistosomiasis is a neglected tropical disease affecting hundreds of millions of people worldwide. Recent advances in the field of proteomics and the development of new and highly sensitive mass spectrometers and quantitative techniques have provided new tools for advancing the molecular biology, cell biology, diagnosis and vaccine development for public health threats such as schistosomiasis.

Areas covered: In this review we describe the latest advances in research that utilizes proteomics-based tools to address some of the key challenges to developing effective interventions against schistosomiasis. We also provide information about the potential of extracellular vesicles to advance the fight against this devastating disease.

Expert commentary: Different proteins are already being tested as vaccines against schistosomiasis with promising results. The re-analysis of the Schistosoma spp. proteomes using new and more sensitive mass spectrometers as well as better separation approaches will help identify more vaccine targets in a rational and informed manner. In addition, the recent development of new proteome microarrays will facilitate characterisation of novel markers of infection as well as new vaccine and diagnostic candidate antigens.     

The role of elevation and soil chemistry in the distribution and ion accumulation of floral morphs of Streptanthus polygaloides Gray (Brassicaceae), a Californian nickel hyperaccumulator

Background: The flora of serpentine/ultramafic soils provides an excellent model system for the study of natural selection in plant populations. Streptanthus polygaloides is a nickel hyperaccumulator that is endemic to serpentine soils in the Sierra Nevada of California, and has four floral morphs (yellow, purple, yellow-to-purple and undulate).

Aims: We investigate three hypotheses: (1) the purple morph occurs in colder, wetter climates than the yellow morph; (2) tissue–soil ionic relationships differ among morphs; and (3) morphs occur on soils with differing elemental concentrations.

Methods: We queried herbarium records to investigate patterns of occurrence among the yellow and purple floral morphs, and analysed soil and tissue samples from wild populations of all four morphs.

Results: The purple morph inhabited serpentine outcrops with colder temperatures and greater precipitation levels than the yellow morph. Concentrations of elements in leaf tissue and rhizosphere soil differed little among populations of the morphs, but showed substantial within-site variation.

Conclusions: Our results suggest that a climatic gradient may be responsible for divergence in floral colour among populations of S. polygaloides. Because of the large within-site variation in soil and tissue elemental concentrations, plants appear to have a varied physiological response to edaphic factors, regardless of morph membership.     

Multiple biomarker approach in the fiddler crab to assess anthropogenic pollution in tropical coastal environments

Context: Fiddler crabs are important to the ecology of estuarine systems around the world, however, few studies have incorporated them as bioindicators. Urias estuary represents one of the most urbanized lagoons in the Gulf of California region and received discharges from different sources: shrimp farm, thermoelectric plant, fish processing plants, and untreated domestic and sewage wastes.

Objective: Assess the effects on anthropogenic contamination on female fiddler crabs reproduction, survival and genetic stability.

Methods: Exposition of wild crabs from a less impacted (reference) site to naturally contaminated sediments on under controlled laboratory conditions. Reproductive parameters, levels of DNA damage and mortality rates were measured, together with chemical analyses of sediments.

Results: The most contaminated sediments corresponded to the site where fish processing plants were located and the integrated biomarker response analysis revealed that the most adverse effects were produced by exposure to sediments from this site; these crabs showed higher mortality (67%) and poorer ovarian development than those crabs exposed to sediments from other sites.

Conclusions: Female crabs under pollution stress are able to trade-off reproduction for survival, and surviving animals were able to restore genetic stability possibly by activating DNA repair mechanisms. Multiple biomarker approach discriminates different coastal contamination scenarios.     

Employing proteomics in the study of antigen presentation: an update

Introduction: Our immune system discriminates self from non-self by examining the peptide cargo of human leukocyte antigen (HLA) molecules displayed on the cell surface. Successful recognition of HLA-bound non-self peptides can induce T cell responses leading to, for example, the destruction of infected cells. Today, largely due to advances in technology, we have an unprecedented capability to identify the nature of these presented peptides and unravel the true complexity of antigen presentation.

Areas covered: In addition to conventional linear peptides, HLA molecules also present post-translationally modified sequences comprising a wealth of chemical and structural modifications, including a novel class of noncontiguous spliced peptides. This review focuses on these emerging themes in antigen presentation and how mass spectrometry in particular has contributed to a new view of the antigenic landscape that is presented to the immune system.

Expert Commentary: Advances in the sensitivity of mass spectrometers and use of hybrid fragmentation technologies will provide more information-rich spectra of HLA bound peptides leading to more definitive identification of T cell epitopes. Coupled with improvements in sample preparation and new informatics workflows, studies will access novel classes of peptide antigen and allow interrogation of rare and clinically relevant samples.     

Long-Term Biomonitoring of Soil Contamination Using Poplar Trees: Accumulation of Trace Elements in Leaves and Fruits

Phytostabilization aims to immobilize soil contaminants using higher plants. The accumulation of trace elements in Populus alba leaves was monitored for 12 years after a mine spill. Concentrations of As and Pb significantly decreased, while concentrations of Cd and Zn did not significantly over time. Soil concentrations extracted by CaCl₂ were measured by ICP-OES and results of As and Pb were below the detection limit. Long-term biomonitoring of soil contamination using poplar leaves was proven to be better suited for the study of trace elements. Plants suitable for phytostabilization must also be able to survive and reproduce in contaminated soils. Concentrations of trace elements were also measured in P. alba fruiting catkins to determine the effect on its reproduction potential. Cadmium and Zn were found to accumulate in fruiting catkins, with the transfer coefficient for Cd significantly greater than Zn. It is possible for trace elements to translocate to seed, which presents a concern for seed germination, establishment and colonization. We conclude that white poplar is a suitable tree for long-term monitoring of soil contaminated with Cd and Zn, and for phytostabilization in riparian habitats, although some caution should be taken with the possible effects on the food web.

Supplemental materials are available for this article. Go to the publisher's online edition of International Journal of Phytoremediation to view the supplemental file.     

Solubilization and Plant Uptake of Zinc and Cadmium from Soils Treated with Elemental Sulfur

In growth chamber experiments we studied the potential use of elemental sulfur (S₈) as an acidifying agent to enhance the uptake of Cd and Zn from three different polluted soils by candidate phytoremediation plants (Brassica juncea, Helianthus annuus, Salix viminalis). Two of the three soils were calcareous, the other slightly acidic. One of the calcareous soils had been contaminated by dust emissions from a nearby brass smelter. The pollution of the other two soils had resulted from sewage sludge applications.

Sulfur was added to soils in quantities of 20 to 400 mmol sulfur kg^-1 soil. Plants were grown under fluorescent light in 1.5 l ($OS 13 cm) pots for 28 d.

Within 700 h soil pH decreased significantly in all soils, depending on S₈ dosage. In the acid soil, pH decreased from pH 6.5 to about 4 at the highest treatment level, while pH in one of the calcareous soils dropped even below pH 4. The effect was smaller in the second calcareous soil.

NaNO₃-extractable Cd and Zn increased up to 26-and 13-fold, respectively, in the acid soil, while in the calcareous soils, maximum increases were 9-and 11-fold, respectively.

Increased NaNO₃-extractable concentrations translated well into shoot concentrations (dry matter) in plants. Shoot Zn concentrations in H. annuus, for example, increased from 930 in the controls to 4300 mg kg^-1 in the highest S₈ treatment. However, effects observed in the plants were generally smaller than in the soils. In addition, in some variants growth was negatively affected, resulting in reduced metal removal from the soils.     

Glycosylation and its implications in breast cancer

Introduction: For decades, the role of glycans and glycoproteins in the progression of breast cancer and other cancers have been evaluated. Through extensive studies focused on elucidating the biological functions of glycosylation, researchers have been able to implicate alterations in these functions to tumor formation and metastasis.

Areas covered: In this review, we summarize how changes in glycosylation are associated with tumorigenesis, with emphasis on breast cancers. An overview of the changes in N-linked and O-linked glycans associated with breast cancer tumors and biofluids are described. Recent advances in glycomics are emphasized in the context of continuing to decipher the glycosylation changes associated with breast cancer progression.

Expert opinion: While changes in glycosylation have been studied in breast cancer for many years, the clinical relevance of these studies has been limited. This reflects the inherent biological and clinical heterogeneity of breast cancers. Glycomics analysis lags behind the advances in genomics and proteomics, but new approaches are emerging. A summary of known glycosylation changes associated with breast cancer is necessary to implement new findings in the context of clinical outcomes and therapeutic strategies. A better understanding of the dynamics of tumor and immune glycosylation is critical to improving emerging immunotherapeutic treatments.     

Application of Diffusive Gradient in Thin Film to Estimate Available Copper in Soil Solution

In Chile, there are several agricultural areas with soils containing high levels of copper of both anthropic and geochemical origin. The diffusive gradient in thin film (DGT) technique is a promising tool for the evaluation of the bioavailability of metals in situ in different environmental systems. The objective of this study was the preparation, validation, and application of DGT to soil solutions and soil containing copper over 1000 mg kg^?1.

The results show that a resin gel thickness of 0.3 mm gives the best reproducibility and response in the absorption of copper by DGT. The amount of copper extracted in a period of 4 h by the devices from the soil solution corresponds to 13% of the total metal present in the solution.

The DGT allowed a more representative estimation of the amount of Cu available in the soil, more in agreement with the absence of symptoms of phytotoxicity in cultivated species. This shows that the determination of available Cu by DTPA must be handled cautiously because in soils with high Cu content the amount of metal that can have direct influence on absorption by the plant is overestimated.     

A Contribution to the Determination of Polychlorobenzenes in Sediments

A full analytical procedure involving extraction and clean-up is presented for the determination of the tri-, tetra-, penta- and hexa-chlorobenzenes in sediments. For this study, the gas chromatography coupled to electronic capture detection was used.

The samples were dried with sodium sulphate and Soxhlet extracted for 16 hours with dichloromethane. Then this solvent was replaced by hexane and the resulting solution was concentrated in a rotary evaporator. The clean-up process consisted of elution through a mixed silica column followed by a treatment with activated copper turnings to remove the sulphur. The sample was then concentrated down to 2 mL by nitrogen stream. The internal standard, 1,4-dibromobenzene, was added to the sample prior to the extraction, whereas the injection standard, 1,3,5-tribromobenzene, was added right before the sample was injected through the chromatographic system.

The limits of quantification ranged from 71 to 500 pg g^?1 (dry weight). The reproducibility in the peak areas within a day was better for the compounds with increasing number of chlorines, whereas the reproducibility over time studies provided no significant differences in the peak areas in consecutive days.

The method was successfully applied to the determination of polychlorobenzenes in a certified sediment and, finally, it was applied to the determination of these compounds in several sections of a sediment core from Esthwaite Water Lake (United Kingdom).     

Trace Elements in Edible Rocky Shore Species: Effect of Sewage Discharges and Human Health Risk Implications

Sewage pollution is a worldwide concern and can result in increasing levels of trace elements in the environment that can pose serious risks both to wildlife and human health. This highlights the importance of studying the role of sewage discharges in the contamination of aquatic systems, especially in rocky shores, since part of our food resources is directly collected from coastal waters. For this purpose, the accumulation of trace elements (Cu, Zn, Pb, Ni, Co, Cd, Fe, Mn, and As) by edible molluscs (Mytilus galloprovincialis, Patella ulyssiponensis, and Phorcus lineatus) was compared between one sewage-impacted area and two reference areas.

This study suggests that the concentrations of trace elements in the soft tissues of the selected molluscs can be affected by the presence of sewage discharges, and that limpets seem to be the best bioindicator. Moreover, the sewage pollution increased the concentrations of As in the mollusc species, emphasizing its potential damaging effects on natural systems and on edible species.     

Patterns of seed dispersal syndromes on serpentine soils: examining the roles of habitat patchiness,soil infertility and correlated functional traits

Background: It is critical to understand the ecological factors shaping seed dispersal in plant communities in order to predict their fate in the face of global change. Communities restricted to patchy habitats may contain more species with ‘directed’ dispersal syndromes that facilitate successful seed dispersal to other patches; however, habitat quality may constrain the presence of and efficiency of dispersal syndromes found within those habitats.

Aims: The aim of this study was to hypothesise that if habitat patchiness is an important filter on dispersal syndromes, ‘directed’ vertebrate dispersal should be more prevalent in serpentine habitats because of their patchiness. Alternatively, if habitat quality is more important, wind dispersal should be more prevalent in serpentine habitats because of their low fertility.

Methods: Using three datasets representing grassland, chaparral and forest vegetation types, we analysed differences in the composition of dispersal syndromes (vertebrate, wind, passive, water and ant) between communities on patchy infertile serpentine soils and on continuous, fertile non-serpentine soils. Our analyses also accounted for correlated functional traits and phylogenetic relatedness.

Results: Across and within all three vegetation types, serpentine communities had significantly higher proportions of wind dispersed and lower proportions of vertebrate-dispersed species. These patterns were not independent of functional traits. Proportions of the other dispersal syndromes did not differ.

Conclusions: Our results suggest that on low-fertility soils, habitat quality may outweigh habitat patchiness as a filter on the availability of dispersal syndromes, potentially adding to the vulnerability of such communities to stochastic extinctions and global change.     

Improvements in algal lipid production: a systems biology and gene editing approach

Background: In the wake of rising energy demands, microalgae have emerged as potential sources of sustainable and renewable carbon-neutral fuels, such as bio-hydrogen and bio-oil.

Purpose: For rational metabolic engineering, the elucidation of metabolic pathways in fine detail and their manipulation according to requirements is the key to exploiting the use of microalgae. Emergence of site-specific nucleases have revolutionized applied research leading to biotechnological gains. Genome engineering as well as modulation of the endogenous genome with high precision using CRISPR systems is being gradually employed in microalgal research. Further, to optimize and produce better algal platforms, use of systems biology network analysis and integration of omics data is required. This review discusses two important approaches: systems biology and gene editing strategies used on microalgal systems with a focus on biofuel production and sustainable solutions. It also emphasizes that the integration of such systems would contribute and compliment applied research on microalgae.

Conclusions: Recent advances in microalgae are discussed, including systems biology, gene editing approaches in lipid bio-synthesis, and antenna engineering. Lastly, it has been attempted here to showcase how CRISPR/Cas systems are a better editing tool than existing techniques that can be utilized for gene modulation and engineering during biofuel production.     

Growth and Cadmium Phytoextraction by Swiss Chard,Maize, Rice,Noccaea caerulescens,and Alyssum murale in pH Adjusted Biosolids Amended Soils

Past applications of biosolids to soils at some locations added higher Cd levels than presently permitted. Cadmium phytoextraction would alleviate current land use constraints. Unamended farm soil, and biosolids amended farm and mine soils were obtained from a Fulton Co., IL biosolids management facility. Soils contained 0.16, 22.8, 45.3 mg Cd kg^–1 and 43.1, 482, 812 mg Zn kg^–1 respectively with initial pH 6.0, 6.1, 6.4. In greenhouse studies, Swiss chard (Beta vulgaris var. cicla), a Cd-accumulator maize (inbred B37 Zea mays) and a southern France Cd-hyperaccumulator genotype of Noccaea caerulescens were tested for Cd accumulation and phytoextraction. Soil pH was adjusted from ～5.5–7.0. Additionally 100 rice (Oryza sativa) genotypes and the Ni-hyperaccumulator Alyssum murale were screened for potential phytoextraction use.

Chard suffered phytotoxicity at low pH and accumulated up to 90 mg Cd kg^–1 on the biosolids amended mine soil. The maize inbred accumulated up to 45 mg Cd kg^–1 with only mild phytotoxicity symptoms during early growth at pH > 6.0. N. caerulescens did not exhibit phytotoxicity symptoms at any pH, and accumulated up to 235 mg Cd kg^–1 in 3 months. Reharvested N. caerulescens accumulated up to 900 mg Cd kg^–1 after 10 months. Neither Alyssum nor 90% of rice genotypes survived acceptably.

Both N. caerulescens and B37 maize show promise for Cd phytoextraction in IL and require field evaluation; both plants could be utilized for nearly continuous Cd removal. Other maize inbreds may offer higher Cd phytoextraction at lower pH, and mono-cross hybrids higher shoot biomass yields. Further, maize grown only for biomass Cd maximum removal could be double-cropped.     

Laboratory studies of steam stripping of LNAPL‐contaminated soils

Bench‐scale laboratory experiments were conducted to evaluate the effectiveness of steam injection for in situ remediation of soils contaminated by light nonaqueous‐phase liquids (LNAPLs). Several parametric studies were performed with various combinations of soils, LNAPLs, and steam injection conditions.

An increase in steam injection pressure produced a significant increase in LNAPL recovery efficiency. An increase in steam injection pressure from 12.4 to 44.8 kPa resulted in increased LNAPL recovery efficiency from 86 to 95% after one pore volume of steam injection. Higher steam injection pressure yielded maximum LNAPL recovery efficiency in significantly less time and required a smaller amount of steam than at low pressure.

An increase in soil grain size or an increase in grain‐size‐distribution slope resulted in increased LNAPL recovery efficiency. The final LNAPL residual saturation was approximately 0.5% for coarse‐grained soils and 1.8% for soils with finer grain sizes. Soils with finer grains required more time for treatment than soils with coarser grains.

Steam injection experiments with No. 2 heating oil and with jet fuel showed no significant variation in steam front propagation, temperature profile, and maximum LNAPL recovery efficiency. The LNAPL residual saturation after steam injection was essentially independent of the starting LNAPL saturation.     

Mycorrhizal ecology on serpentine soils

Background: Serpentine ecosystems support different, often unique, plant communities; however, we know little about the soil organisms that associate with these ecosystems. Mycorrhizas, mutualistic symbioses between fungi and roots, are critical to nutrient cycling and energy exchange below ground.

Aims: We address three hypotheses: H1, diversity of mycorrhizal fungi in serpentine soils mirrors above-ground plant diversity; H2, the morphology of mycorrhizas and fungi on serpentine soils differs from that on non-serpentine; and H3, mycorrhizal fungal communities of the same or closely related hosts differ between serpentine and non-serpentine soils.

Methods: This review focuses on whether plant diversity on serpentine soils correlates with the below ground diversity of mycorrhizal fungi.

Results: Studies show that plants and fungi formed abundant ectomycorrhizal and arbuscular mycorrhizal symbioses on and off serpentine soils. No serpentine-endemic fungi were identified. Molecular analyses indicate distinct serpentine isolates for Cenococcum geophilum and for Acaulospora, suggesting adaptation to serpentine soils. While fungal sporocarp assemblages on serpentine sites resembled those off serpentine, fruiting of hypogeous fungi was greatly reduced.

Conclusions: Ectomycorrhizal fungal communities did not differ between soil types; however, arbuscular mycorrhizal communities differed in some cases but not others. The additive response to multiple factors, described as the serpentine syndrome, may explain part of the response by fungi.     

Mass spectrometric analysis of glycosylated viral proteins

Introduction: Viral diseases contribute much to human and animal suffering and enormous efforts are directed at developing appropriate vaccines for protection. Glycoproteins constitute much of the viral surfaces and are obvious targets for such vaccine development. This review describes mass spectrometric methods used for the structural determination of these compounds.

Areas covered: The review describes the structures of the N- and O-linked glycans found on glycoproteins and mass spectrometric methods for their ionization and fragmentation. The steps, such as determination of glycan attachment sites and the structures of the attached glycans following their release from the glycoproteins are described and examples are given of the uses of the various analytical methods using mainly influenza, Ebola and HIV as representative examples. Also included are tables listing work on many other viruses.

Expert commentary: Recent technological advances, such as the introduction of ion mobility techniques, have greatly improved analyses in this area and have enabled larger amounts of information to be gathered in shorter time periods on ever smaller amounts of material. Such techniques should greatly accelerate the discovery of vaccine targets and lead to the production of vaccines for diseases not currently available.     

Evaluation of Heavy Metals Pollution Loadings in the Sediments of the Ave River Basin (Portugal)

Sediment samples from the Ave river basin were collected with the aim of determining metal total pollution contents. Cr, Cu, Fe, Mn, Pb, Zn and VM at 550 °C were determined. Some physico-chemical parameters were also quantified in water samples collected in the water column just above the sediments.

Metal contamination factors (CF) indicated that sediments were not contaminated with Cu and Pb, slightly with Zn and moderately with Cr.

For sediments with high metal pollution loadings, the original BCR (Community Bureau of Reference) metal speciation protocol was also applied. Speciation studies showed that chromium was mainly associated with the oxidisable plus residual fractions (>85%). These results suggest that changes in the physico-chemical properties of the river water (e.g. pH, Eh) should not be accompanied by a significative release of chromium from sediments.

The relationships between chromium speciation fractions, physic-chemical parameters of the sediments and water samples were studied by Principal Component Analysis, and allowed to reduce the dimensionality of the data matrix from 14 to 3 significant components accounting for 89% of the variance. It was found that hydrous Fe/Mn oxides and organic matter are the “carriers” of chromium associated to fractions exchangeable and oxidable.     

Integral membrane proteins: bottom-up,top-down and structural proteomics

Introduction: Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review.

Areas covered: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome. However, this coverage relies upon hydrophilic loop regions while transmembrane domains are generally poorly covered in peptide-based strategies. Top-down mass spectrometry where the intact membrane protein is fragmented in the gas phase gives good coverage in transmembrane regions, and membrane fractions are yielding to high-throughput top-down proteomics. Exciting progress in native mass spectrometry of membrane protein complexes is providing insights into subunit stoichiometry and lipid binding, and cross-linking strategies are contributing critical in-vivo information.

Expert commentary: It is clear from the literature that integral membrane proteins have yielded to advanced techniques in protein chemistry and mass spectrometry, with applications limited only by the imagination of investigators. Key advances toward translation to the clinic are emphasized.