Variation in Polycyclic Aromatic Hydrocarbon Contamination Between Native and Introduced Species of Fishes of Pallikaranai Wetland, Chennai, Tamil Nadu, India

The impacts of invasive fish species on recipient communities are mostly considered a threat to the biodiversity of freshwater systems. A characteristic of introduced species turning invasive is their higher tolerance to environmental stressors. To understand if non-native fishes in Pallikaranai wetland, Tamil Nadu, India, are more tolerant to anthropogenic pressures in the Wetland, we assessed the variation in Polycyclic Aromatic Hydrocarbon contamination between introduced and native fish species. Mean levels of Naphthalene, fluorene, phenanthrene, anthracene, pyrene, and total PAH in samples of introduced species were higher than native species, while High Molecular weight PAH and carcinogenic PAH4 were higher in native fish species. The data was also analysed to assess if co-variates (organs, seasons, and sex) affected PAH accumulation patterns in non-native species. It was observed that only organs, sex, and year contributed significantly.

Changes in Antioxidant System during Grain Development of Wheat (Triticum aestivum L.) and Relationship with Protein Composition under FHB Stress

Fusarium head blight (FHB) is found in both temperate and semi-tropical regions and causes losses in wheat (Triticum aestivum L.) resulting in reduced yield, deteriorated grain quality, and contamination of the grains with mycotoxins, primarily deoxynivalenol (DON). In this study, we focused on the identification of protein components in Fusarium-inoculated and non-inoculated wheat samples along with the major antioxidant enzymes that Fusarium can encounter during FHB infection process in six winter wheat varieties when FHB symptoms started to occur. Our hypothesis was that wheat antioxidants and H₂O₂ may play a role against Fusarium infections, consequently preserving protein grain components. Results showed that in more resistant varieties (Olimpija and Vulkan) DON content of inoculated flour was less accumulated and thus the major gluten network was not significantly attacked by Fusarium spp. The maximum increase in guaiacol peroxidase (POD) activity in response to FHB treatment was detected in the FHB-resistant varieties Olimpija and Vulkan, while the lowest increase in H₂O₂ content was detected in the FHB-susceptible variety Golubica. A particular reduction in the content of both total glutenin and high-molecular-weight glutenin subunits was detected in susceptible wheat varieties after serious artificial infection, along with increased DON accumulation. The defense mechanism in wheat varieties differed, where resistant varieties’ protein composition depended on POD activity as a detoxification agent.

FGF-2 isoforms influence the development of dopaminergic neurons in the murine substantia nigra, but not anxiety-like behavior, stress susceptibility, or locomotor behavior

BACKGROUND

Loss of fibroblast growth factor 2 (FGF-2) is responsible for the development of an increased number of dopaminergic (DA) neurons in the murine substantia nigra pars compacta (SNpc). Furthermore, dysregulation of its expression patterns within the central nervous system (CNS) is associated with behavioral abnormalities in mice. Until now, the contributions of the individual FGF-2 isoforms (one low (LMW) and two high molecular weight (HMW) isoforms) in the CNS are elusive.

METHODS

To unravel the specific effects of FGF-2 isoforms, we compared three knockout mouse lines, one only deficient for LMW, one deficient for HMW and another lacking both isoforms, regarding DA neuronal development. With this regard, three time points of ontogenic development of the SNpc were stereologically investigated. Furthermore, behavioral aspects were analyzed in young adult mice, supplemented by corticosterone measurements.

RESULTS

Juvenile mice lacking either LMW or HMW develop equal supernumerary DA neuron numbers in the SNpc. Compensatory increased LMW expression is observed in animals lacking HMW. Meanwhile, no knockout mouse line demonstrated changes in anxiety-like behavior, stress susceptibility, or locomotor behavior.

CONCLUSIONS

Both FGF-2 isoforms crucially influence DA neuronal development in the murine SNpc. However, absence of LMW or HMW alone alters neither anxiety-like nor locomotor behavior, or stress susceptibility. Therefore, FGF-2 is not a determinant and causative factor for behavioral alterations alone, but probably in combination with appropriate conditions, like environmental or genetic factors.

Concentration of Polycyclic Aromatic Hydrocarbons and Estimated Human Health Risk of Water Samples Around Atlas Cove, Lagos, Nigeria

BACKGROUND

Polycyclic aromatic hydrocarbons (PAHs) are common pollutants in water and have been reported to cause severe health effects in humans as well as the ecosystem.

OBJECTIVES

This study examined the concentrations of polycyclic aromatic hydrocarbons and estimated the human health risk from water samples around Atlas Cove jetty, Lagos, Nigeria.

METHODS

Physical and chemical parameters and PAHs were determined in Atlas Cove jetty water using standard methods from June to August 2016 at five different points of activity. Chronic daily intake through ingestion, exposure dose via dermal absorption and carcinogenic risks were calculated for children and adults.

RESULTS

Electrical conductivity values ranged from 23,600±57.74 - 30,000±57.74 μS/cm. Dissolved oxygen ranged from 6.27±0.46 - 9.60±0.00 mg/L. Biochemical oxygen demand levels ranged from 2.93±0.61 - 7.33±0.23 mg/L and total dissolved solid ranged from 17,500±57.74 - 20,000±57.74 mg/L for the water samples, which was higher than permissible limits. The values obtained for pH, chemical oxygen demand, nitrate, sulphate and phosphate for the water samples were within World Health Organization (WHO) limits except for pH at point 2 (3.18±0.02). A total of eleven PAH congeners were detected in the water samples. The concentrations of total PAHs observed in water samples ranged from 46 - 507 μg/L. Low molecular weight PAHs were more dominant in all samples. It was observed that 2-3 ring PAHs accounted for 63.64% of PAHs, 4-rings PAHs accounted for 27.27% of PAHs, and 5-6 ring PAHs accounted for 9.09% of PAHs.

CONCLUSIONS

Carcinogenic risks calculated for both adults and children were higher than the United States Environmental Protection Agency (USEPA) acceptable cancer risk, and much higher for children, which suggests that children could be prone to cancer through ingestion. Fauna and flora around the Atlas Cove jetty may be at risk due to water pollution.

COMPETING INTERESTS

The authors declare no competing financial interests.

Characterization of the Low-Molecular-Weight Human Plasma Peptidome

The human plasma proteome represents an important secreted sub-proteome. Proteomic analysis of blood plasma with mass spectrometry is a challenging task. The high complexity and wide dynamic range of proteins as well as the presence of several proteins at very high concentrations complicate the profiling of the human plasma proteome. The peptidome (or low-molecular-weight fraction, LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based markers of disease. Peptides are generated by active synthesis and proteolytic processing, often yielding proteolytic fragments that mediate a variety of physiological and pathological functions. As such, degradomic studies, investigating cleavage products via peptidomics and top-down proteomics in particular, have warranted significant research interest. However, due to their molecular weight, abundance, and solubility, issues with identifying specific cleavage sites and coverage of peptide fragments remain challenging. Peptidomics is currently focused toward comprehensively studying peptides cleaved from precursor proteins by endogenous proteases. This protocol outlines a standardized rapid and reproducible procedure for peptidomic profiling of human plasma using centrifugal ultrafiltration and mass spectrometry. Ultrafiltration is a convective process that uses anisotropic semipermeable membranes to separate macromolecular species on the basis of size. We have optimized centrifugal ultrafiltration (cellulose triacetate membrane) for plasma fractionation with respect to buffer and solvent composition, centrifugal force, duration, and temperature to facilitate recovery >95% and enrichment of the human plasma peptidome. This method serves as a comprehensive and facile process to enrich and identify a key, underrepresented sub-proteome of human blood plasma.

The prediction of PAHs bioavailability in soils using chemical methods: state of the art and future challenges

The evaluation of the available fraction of hydrophobic organic contaminants (HOCs) is extremely important for assessing their risk to the environment and human health. This available fraction, which can be solubilized and/or easily extracted, is believed to be the most accessible for bioaccumulation, biosorption and/or transformation by organisms. Based on this, two main types of chemical methods have been developed, closely related to the concepts of bioaccessibility and freely available concentrations: non-exhaustive extractions and biomimetic methods. Since bioavailability is species and compound specific, this work focused only in one of the most widespread group of HOCs in soils: polycyclic aromatic hydrocarbons (PAHs). This study aims at producing a state of the art knowledge base on bioavailability and chemical availability of PAHs in soils, clarifying which chemical methods can provide a better prediction of an organism exposure, and which are the most promising ones. Therefore, a review of the processes involved on PAHs availability to microorganisms, earthworms and plants was performed and the outputs given by the different chemical methods were evaluated. The suitability of chemical methods to predict bioavailability of the 16 US EPA PAHs in dissimilar naturally contaminated soils was not yet demonstrated, being especially difficult for high molecular weight compounds. Even though the potential to predict microbial mineralization using non-exhaustive extractions is promising, it will be very difficult to achieve for earthworms and plants, due to the complexity of accumulation mechanisms which are not taken into account by chemical methods. Yet, the existing models could be improved by determining compound, species and site specific parameters. Moreover, chemical availability can be very useful to understand the bioavailability processes and the behavior of PAHs in soils. The inclusion of chemical methods on risk assessment has been suggested and it is promising, despite some methods overpredict risks.

UV-MALDI mass spectrometric quantitation of uracil based pesticides in fruit soft drinks along with matrix effects evaluation

This study focused on the development of the accurate and precise quantitative method for the determination of pesticides bromacil (1), terbacil (2), lenacil (3), butafenacil (4) and flupropacil (5) in fruit based soft drinks. Three different types of drinks are bought from market; huddled orange fruit drink (100%) (I), red-oranges (II) and multivitamin drink containing strawberry, orange, banana and maracuja (III). Samples were analyzed "with" and "without" pulp utilizing LC-ESI (or APCI) MS/MS, HPLC-ESI-(or APCI)-MS/MS and UV-MALDI-Orbitrap-MS methods. The effect of high complexity of the food matrix on the analysis was discussed. Study focuses on the advantages of the UV-MALDI-Orbitrap-MS method compared to the traditionally involved GC alone or hybrid methods such as GC-MS and LC-MS/MS for quantification of pesticides in water and soft drinks. The developed method included the techniques performed for validation, calibration and standardization. The target pesticides are widely used for the treatment of citrus fruits and pineapples, but for soft drink products, there are still no clear regulations on pesticide residues limits. The matrix effects in the analysis of fruit drinks required implementation of the exact standard reference material corresponds to the variety of food matrices. This paper contributed to the broad analytical implementation of the UV-MALDI-Orbitrap-MS method in the quality control and assessment programs for monitoring of pesticide contamination in fruit based sodas.

Isolation and quantitation of adiponectin higher order complexes

Adiponectin is a circulating bioactive hormone secreted by adipocytes as oligomers ranging in size from 90 kDa trimers and 180 kDa hexamers to larger high molecular weight oligomers that may reach 18- or 36-mers in size. While total circulating adiponectin levels correlate well with metabolic health, it is the relative distribution of adiponectin complexes that is most clinically relevant to glucose sensitivity and inflammation. High molecular weight adiponectin best mirrors insulin sensitivity, while trimeric adiponectin dominates with insulin resistance and adipose tissue inflammation. Experimental animal and in vitro models have also linked the relative fraction of high molecular weight adiponectin to its positive effects. Quantitating adiponectin size distribution thus provides a window into metabolic health and can serve as a surrogate marker for adipose tissue fitness. Here, we present a detailed protocol for isolating and quantitating adiponectin complexes in serum or plasma that has been extensively utilized for both human clinical samples and numerous animal models under various experimental conditions. Examples are presented of different adiponectin distributions and tips are provided for optimization using available equipment. Comparison of this rigorous approach to other available methods is also discussed. In total, this summary is a blueprint for the expanded quantitation and study of adiponectin complexes.

Experimental investigation and modeling of dissolved organic carbon removal by coagulation from seawater

Coagulation removes colloidal matters and dissolved organic carbon (DOC) which can cause irreversible membrane fouling. However, how DOC is removed by coagulant is not well-known. Jar test was used to study the removal of hydrophobic and hydrophilic DOC fractions at various doses (0.5-8.0 mg-Fe(+3) L(-1)) of ferric chloride (FeCl3) and pH (5.0-9.0). Natural organic matter (NOM) in seawater and treated seawater were fractionated by liquid chromatography-organic carbon detector (LC-OCD). Compared to surface water, the removal of DOC in seawater by coagulation was remarkably different. Majority of DOC could be easily removed with very low coagulant dose (<5.0 mg-Fe(+3) L(-1)) and the removal efficiency did not vary with pH, but the DOC composition in treated water had significantly changed. Hydrophobic fraction (HB) was better removed at high pH while hydrophilic fraction (HF) was better removed at low pH. A modified model of Kastl et al. (2004) which assumed that the removal occurred by adsorption of un-dissociated compounds onto ferric hydroxide was formulated and successfully validated against the jar test data.

Computational identification of microRNAs in the strawberry (Fragaria x ananassa) genome sequence and validation of their precise sequences by miR-RACE

In plants, microRNAs (miRNAs) play significant roles in post-transcriptional gene regulation and have been found to control many genes involved in different biological and metabolic processes. Extensive studies were carried out to discover miRNAs and analyze their functions in model plant species, such as in Arabidopsis and rice that have been reported. In this research, we used bioinformatics to predict microRNAs in an important strawberry rootstock cultivar to discover and validate precise sequences of microRNAs in strawberry. By adopting a range of filtering criteria, we obtained 59 potential miRNAs belonging to 40 miRNA families from the Fragaria vesca genome. Using two specific 5' and 3' miRNA RACE PCR reactions and a sequence-directed cloning method, we accurately determined 34 precise sequences of candidate miRNAs, while six other sequences exhibited some minor divergence in their termini nucleotides, and 19 miRNAs that could not be cloned owing to expression abundance may be too low or these mirRNAs predicted could not be existing in strawberry. Potential target genes were further predicted for the miRNAs above. The expression of the 16 miRNAs unreported and having exact sequences and their targets by experiment could be detected in different tissues of strawberry ranging from roots, stems, leaves, flowers and fruits by qRT-PCR and some of them showed differential expression in various tissues. The functional analysis of 16 miRNAs and their targets was carried out. Finally, we conclude that there are 34 mirRNAs in strawberry and their targets play vital roles not only in growth and development, but also in diverse physiological processes. These results show that regulatory miRNAs exist in agronomically important strawberry and might have an important function in strawberry growth and development.

PacBio sequencing of gene families - a case study with wheat gluten genes

Amino acids in wheat (Triticum aestivum) seeds mainly accumulate in storage proteins called gliadins and glutenins. Gliadins contain α/β-, γ- and ω-types whereas glutenins contain HMW- and LMW-types. Known gliadin and glutenin sequences were largely determined through cloning and sequencing by capillary electrophoresis. This time-consuming process prevents us to intensively study the variation of each orthologous gene copy among cultivars. The throughput and sequencing length of Pacific Bioscience RS (PacBio) single molecule sequencing platform make it feasible to construct contiguous and non-chimeric RNA sequences. We assembled 424 wheat storage protein transcripts from ten wheat cultivars by using just one single-molecule-real-time cell. The protein genes from wheat cultivar Chinese Spring are comparable to known sequences from NCBI. We demonstrated real-time sequencing of gene families with high-throughput and low-cost. This method can be applied to studies of gene amplification and copy number variation among species and cultivars.

Computer models versus reality: how well do in silico models currently predict the sensitization potential of a substance

National legislations for the assessment of the skin sensitization potential of chemicals are increasingly based on the globally harmonized system (GHS). In this study, experimental data on 55 non-sensitizing and 45 sensitizing chemicals were evaluated according to GHS criteria and used to test the performance of computer (in silico) models for the prediction of skin sensitization. Statistic models (Vega, Case Ultra, TOPKAT), mechanistic models (Toxtree, OECD (Q)SAR toolbox, DEREK) or a hybrid model (TIMES-SS) were evaluated. Between three and nine of the substances evaluated were found in the individual training sets of various models. Mechanism based models performed better than statistical models and gave better predictivities depending on the stringency of the domain definition. Best performance was achieved by TIMES-SS, with a perfect prediction, whereby only 16% of the substances were within its reliability domain. Some models offer modules for potency; however predictions did not correlate well with the GHS sensitization subcategory derived from the experimental data. In conclusion, although mechanistic models can be used to a certain degree under well-defined conditions, at the present, the in silico models are not sufficiently accurate for broad application to predict skin sensitization potentials.

Urinary phthalates are associated with higher blood pressure in childhood

OBJECTIVE

To examine associations of urinary phthalate levels with blood pressure (BP) and serum triglyceride and lipoprotein levels in children.

STUDY DESIGN

We performed a cross-sectional analysis of a subsample of US children aged 6-19 years who participated in the National Health and Nutrition Examination Survey between 2003 and 2008. We quantified exposure to 3 families of phthalates--low molecular weight, high molecular weight and di-2-ethylhexylphthalate (DEHP)--based on molar concentration of urinary metabolites. We assessed descriptive, bivariate, and multivariate associations with BP and lipid levels.

RESULTS

Controlling for an array of sociodemographic and behavioral factors, as well as diet and body mass index, levels of metabolites of DEHP, a phthalate commonly found in processed foods, were associated with higher age-, sex-, and height-standardized BP. For each log unit (roughly 3-fold) increase in DEHP metabolites, a 0.041 SD unit increase in systolic BP z-score was identified (P = .047). Metabolites of low molecular weight phthalates commonly found in cosmetics and personal care products were not associated with BP. Phthalate metabolites were not associated with triglyceride levels, high-density lipoprotein level, or prehypertension.

CONCLUSIONS

Dietary phthalate exposure is associated with higher systolic BP in children and adolescents. Further work is needed to confirm these associations, as well as to evaluate opportunities for intervention.

Beyond gene expression: the impact of protein post-translational modifications in bacteria

The post-translational modification (PTM) of proteins plays a critical role in the regulation of a broad range of cellular processes in eukaryotes. Yet their role in governing similar systems in the conventionally presumed 'simpler' forms of life has been largely neglected and, until recently, was thought to occur only rarely, with some modifications assumed to be limited to higher organisms alone. Recent developments in mass spectrometry-based proteomics have provided an unparalleled power to enrich, identify and quantify peptides with PTMs. Additional modifications to biological molecules such as lipids and carbohydrates that are essential for bacterial pathophysiology have only recently been detected on proteins. Here we review bacterial protein PTMs, focusing on phosphorylation, acetylation, proteolytic degradation, methylation and lipidation and the roles they play in bacterial adaptation - thus highlighting the importance of proteomic techniques in a field that is only just in its infancy. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Low-molecular-weight DNA replication intermediates in Escherichia coli: mechanism of formation and strand specificity

Chromosomal DNA replication intermediates, revealed in ligase-deficient conditions in vivo, are of low molecular weight (LMW) independently of the organism, suggesting discontinuous replication of both the leading and the lagging DNA strands. Yet, in vitro experiments with purified enzymes replicating sigma-structured substrates show continuous synthesis of the leading DNA strand in complete absence of ligase, supporting the textbook model of semi-discontinuous DNA replication. The discrepancy between the in vivo and in vitro results is rationalized by proposing that various excision repair events nick continuously synthesized leading strands after synthesis, producing the observed LMW intermediates. Here, we show that, in an Escherichia coli ligase-deficient strain with all known excision repair pathways inactivated, new DNA is still synthesized discontinuously. Furthermore, hybridization to strand-specific targets demonstrates that the LMW replication intermediates come from both the lagging and the leading strands. These results support the model of discontinuous leading strand synthesis in E. coli.

Advanced glycation endproducts in food and their effects on health

Advanced glycation endproducts (AGEs) form by Maillard-reactions after initial binding of aldehydes with amines or amides in heated foods or in living organisms. The mechanisms of formation may include ionic as well as oxidative and radical pathways. The reactions may proceed within proteins to form high-molecular weight (HMW) AGEs or among small molecules to form low-molecular weight (LMW) AGEs. All free amino acids form AGEs, but lysine or arginine side chains dominate AGE formation within proteins. The analysis of AGEs in foods and body fluids is most often performed by ELISA or LC-MS; however, none of the methodologies cover all HMW and LMW AGEs. Most research is, therefore, carried out using 'representative' AGE compounds, most often N(ε)-carboxymethyl-lysine (CML). Only LMW AGEs, including peptide-bound forms, and carbonyls may be absorbed from the gut and contribute to the body burden of AGEs. Some AGEs interact with specific pro- or anti-inflammatory receptors. Most studies on the biological effects of AGEs have been carried out by administering heated foods. The pro-inflammatory and deteriorating biological effects of AGEs in these studies, therefore, need further confirmation. The current review points out several research needs in order to address important questions on AGEs in foods and health.

Physicochemical characterization of the staphylolytic LysK enzyme in complexes with polycationic polymers as a potent antimicrobial

Staphylococcus aureus causes many serious visceral, skin, and respiratory diseases. About 90% of its clinical strains are multi-drug resistant, but the use of bacteriophage lytic enzymes offers a viable alternative to antibiotic therapy. LysK, the phage K endolysin, can lyse S. aureus when purified and exposed externally. It has been investigated in its complexes with polycationic polymers (poly-l-lysines (PLLs) of molecular weights 2.5, 9.6, and 55.2 kDa and their block copolymers with polyethylene glycol PLL10-PEG114, PLL30-PEG114, and PLL30-PEG23) as a basis for creating active and stable antimicrobial. Complexing with polycationic PLLs produces a stabilizing effect on LysK due to structure ordering in its molecules and break-down of aggregates as a result of electrostatic interaction. The stability of LysK in the presence of PLL-PEG block copolymers improves by both electrostatic and hydrophobic mechanisms. Complexes of LysK with 2.5, 9.6, 55.2 kDa poly-l-lysines and PLL30-PEG114 have demonstrated sufficient stability at the temperatures of physiological activity (37 °C) and storage (4 °C and 22 °C).