Organic geochemical parameters for estimation of petrogenic inputs in the coastal area of Kavala City,Greece

Background, aims, and scope  Sediments and soils in coastal areas are frequently polluted by anthropogenic contaminants as the result of both riverine or terrestrial discharge and autochthonic marine emissions. In order to determine petrogenic contamination in the coastal industrial area of Kavala City in northern Greece, a combination of polycyclic aromatic hydrocarbon (PAH) and organic geochemical petroleum biomarker analyses has been performed on marine and freshwater sediments as well as soils. Materials and methods  Soils, freshwater, and marine sediments have been treated by standard extraction methods. The dried and desulphurized sample extracts have been fractionated by column chromatography, followed by addition of surrogate standards. Qualitative and quantitative data were obtained by gas chromatograph connected with a flame ionization and electron capture detector (GC-FID/ECD) and by GC linked to a mass spectrometer (GC/MS), whereas identification of compounds was based on EI⁺-mass spectra and gas chromatographic retention times. Quantitative data were obtained by integration of specific ion chromatograms. Results  The total PAH concentrations measured in the area varied highly, showing different levels from 18 up to 318,000 ng g⁻¹ dry weight (dw). Several PAH ratios, as well as the ratio of pristane (Pr) to phytane (Phyt), have been considered. Out of 39 samples, 22 revealed a specific distribution of hopane fingerprints indicating petrogenic input. Finally, in numerous samples, the ratio of 17α(H)-22,29,30-trisnorhopane (Tm) and 18α(H)-22,29,30-trisnorhopane (Ts) was calculated, as well as the ratio of 22S-17α(H),21β(H)-30 homohopane (αβC₃₁-hopane 22S) and 22R-17α(H),21β(H)-30 homohopane (αβC₃₁-hopane 22R). Discussion  Based on the specific PAH ratios, a group of samples was clearly characterized to be contaminated dominantly by combustion-derived emissions, whereas a second group of samples exhibited mixed influence from petrogenic and pyrogenic PAHs. On the other hand, the exhibition of specific hopane fingerprints in many samples indicates a direct petrogenic input. Finally, the values of the ratio of Tm/(Ts + Tm) and of αβC₃₁-hopanes 22S/(22S+22R)-isomer demonstrated an input of highly mature organic matter that has to be clearly attributed to petroleum-derived contamination, while the ratio of Pr/Phyt showed that most samples exhibited an input of organic matter. Conclusions  The coastal area of Kavala is strongly affected by anthropogenic contaminants. Petrogenic emissions were pointed out firstly by PAH analyses that separated dominantly pyrogenic contaminated sites from areas affected by both pyrogenic and petrogenic emissions. However, analyses of organic geochemical biomarkers revealed a much higher sensitivity in identifying petroleum-derived contaminations and were successfully used to differentiate several petrogenic contaminations in the marine and terrestrial samples. Recommendations and perspectives  Based on this study, it was recommended to use a complementary approach of source-specific substances to successfully characterize petrogenic emissions. Generally, a PAH-based source identification of petrogenic versus pyrogenic contaminations should be combined with petroleum biomarker analysis. PAH and biomarker ratios as well as individual biomarker fingerprints revealed a more comprehensive view on the quality and quantity of petrogenic emissions in sediments and soils.     

Characterizing the Serum Proteome of Donkeys (Equus asinus)

Serum and plasma are commonly used in clinical practice considering the widely accepted fact that the “normal” protein expression pattern of a healthy animal changes under disease conditions. We herein used a label-free mass spectrometry–based quantitative proteomics approach to characterize the serum proteome of donkeys. A total of 277 unique proteins were identified from 2,388 unique peptides. Gene ontology analyses showed that the most frequent processes were related to metabolic activities and biological regulation, response to stimulus, and immune system processes. The main annotated areas of origin were the extracellular region, extracellular region part, and organelle, and their molecular functions included binding, catalytic activity, and molecular function regulator. Analyses using the Clusters of Orthologous Groups for Eukaryotic Complete Genomes database indicated that the identified proteins could be categorized into three main groups: signal transduction mechanisms, amino acid transport and metabolism, and defense mechanisms. Most of the unique proteins were associated with the complement and coagulation cascades, and they participated in several disease-related metabolic pathways. Our results should be crucial for further analyses of changes in different physiological and pathophysiological conditions in donkeys.     

Potential Proteomic-Based Strategies for Understanding Laminitis: Predictions and Pathogenesis

With today's understanding of the genome, advanced molecular techniques, and our growing ability to analyze complex biologic data, proteomics, the broad-based study of the repertoire of proteins expressed by cells or organisms, offers great promise for understanding the causes of complex diseases. Identifying and measuring novel protein biomarkers present in blood that predict the onset and resolution of laminitis would both aid clinical management of at-risk equine patients and shed light on underlying mechanisms with the intent of developing novel preventive strategies and therapeutic approaches. Identifying alterations in the profiles of proteins present in tissues of horses that develop laminitis or within in vitro model systems also can advance our understanding of this puzzling disease.     

Utilizing earthworm and microbial assays to assess the ecotoxicity of chromium mine wastes

Mining plays an important role in the South African economy which results in environmental impacts. This holds a potential hazard for ecosystems surrounding mining areas and also for public health in the surrounding communities. The aim of this study was to use soil enzymatic analyses and earthworm (Eisenia andrei) responses viz. growth, reproduction, lysosomal membrane stability and tissue metal concentrations to determine the effect caused by chromium mine waste on the activity of soil microbial community and soil invertebrates. Results indicated that chromium mining did have an ecotoxic effect on enzymatic activity, as the material which exceeded the Cr benchmark for microorganisms showed the least amount of enzymatic activity. Significant differences in enzymatic activity were observed between the different samples. Earthworm biomass increases were low in the mining material exposed worms and might have been correlated with the low enzymatic activities in the materials. Biomass was however not considered a sensitive endpoint. Lysosomal membrane stability, measured as NRRT, proved to be a sensitive endpoint, showing the same pattern from day 7 up to day 28. Hatching success of cocoons was not considered a sensitive endpoint, due to the low cocoon production in the mining material exposed worms. Since mine waste materials often contain complex mixtures of metals that might be toxic on their own or in combination with other factors, it is difficult to attribute any observed effect to any of the specific metals analyzed. The metal concentrations were however compared to benchmarks in order to determine which of the metals could have had a toxic effect on the soil organisms. The only benchmark exceeded, was the PNEC for microorganisms, for Cr in the unrehabilitated silt (TDF1) material. None of the other benchmarks were exceeded, indicating that perhaps granular composition of the materials might have had a greater influence than the metals.     

Comparison of methods for depletion of albumin and IgG from equine serum

Background: Disease‐specific biomarkers hold diagnostic promise in both human and veterinary medicine, but serum biomarkers in low concentrations may be masked by the presence of abundant proteins, mostly albumin and IgG. Methods to deplete albumin and IgG exist, but efficacy of these methods for depleting equine serum of these proteins has not been established. Objective: The aim of this study was to determine if albumin and IgG could be depleted from equine serum using several commercially available kits and procedures. Methods: One‐dimensional gel electrophoresis followed by densitometry was used to determine percent of albumin, IgG, and both in pooled serum from 3 horses before and after application of 7 depletion methods. Repeatability was determined by applying the 2 best methods to serum samples from 6 grade horses. Results: For pooled serum, depletion rates varied from 35–90% for albumin and 0–94% for IgG. In the repeatability study, the ProteoExtract method combined with protein G Sepharose beads to remove additional IgG provided the best overall performance with 66% albumin depletion and 100% IgG depletion. A protocol using protein G Sepharose beads to remove IgG followed by ethanol precipitation of nonalbumin proteins with albumin remaining in the supernatant was the second most effective, with 85% albumin depletion and 55% IgG depletion. Although a multiprotein immunodepletion column effectively removed 90% of the albumin, the method was ineffective at removing IgG. Conclusion: Albumin and IgG removal kits optimized for human use have variable efficacy for equine serum. Combined use of the ProteoExtract kit and manual incubation with protein G Sepharose beads provided the most effective depletion.     

Biochemistry of hexose and pentose transformations in soil analyzed by position-specific labeling and 13C-PLFA

Microbial transformations are key processes of soil organic matter (SOM) formation, stabilization and decomposition. Combination of position-specific ¹³C labeling with compound-specific ¹³C-PLFA analysis is a novel tool to trace metabolic pathways. This combination was used to analyze short-term transformations (3 and 10 days after tracer application) of two key monosaccharides: glucose and ribose in soil under field conditions. Transformations of sugars were quantified by the incorporation of ¹³C from individual molecule positions in bulk soil, microbial biomass (by CFE) and in cell membranes of microbial groups classified by ¹³C-PLFA.The ¹³C incorporation in the Gram negative bacteria was higher by one order of magnitude compared to all other microbial groups. All of the ¹³C recovered in soil on day 3 was allocated in microbial biomass. On day 10 however, a part of the ¹³C was recovered in non-extractable microbial cell components or microbial excretions. As sugars are not absorbed by mineral particles due to a lack of charged functional groups, their quick mineralization from soil solution is generally expected. However, microorganisms transformed sugars to metabolites with a slower turnover. The ¹³C incorporation from the individual glucose positions into soil and microbial biomass showed that the two main glucose utilizing pathways in organisms – glycolysis and the pentose phosphate pathway – exist in soils in parallel. However, the pattern of ¹³C incorporation from individual glucose positions into PLFAs showed intensive recycling of the added ¹³C via gluconeogenesis and a mixing of both glucose utilizing pathways. The pattern of position-specific incorporation of ribose C also shows initial utilization in the pentose phosphate pathway but is overprinted on day 10, again due to intensive recycling and mixing. This shows that glucose and ribose – as ubiquitous substrates – are used in various metabolic pathways and their C is intensively recycled in microbial biomass.Analyzing the fate of individual C atoms by position-specific labeling deeply improves our understanding of the pathways of microbial utilization of sugars (and other compounds) by microbial groups and so, of soil C fluxes.