GeNets: a unified web platform for network-based genomic analyses.

Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.

Occurrence of halogenated transformation products of selected pharmaceuticals and personal care products in secondary and tertiary treated wastewaters from southern California.

Final effluent samples from 10 southern California (United States) wastewater treatment facilities, employing four distinct treatment schemes, were surveyed for selected pharmaceuticals, personal care products (PPCPs), alkylphenols, and 21 of their halogenated disinfection byproducts. Chlorinated and brominated standards and isotopically labeled internal standards were synthesized and purified to confirm and more accurately quantify selected disinfection byproducts of salicylic acid, bisphenol A, gemfibrozil, naproxen, diclofenac, technical 4-nonylphenol, and 4-tert-octylphenol using high-performance liquid chromatography and tandem mass spectrometry. Concentrations of parent compounds ranged from <10 to 3830 ng/L (gemfibrozil), and those of chloro/bromo byproducts ranged from <4 to 370 ng/L (dibromo nonylphenol). The highest concentrations of parent compounds were measured in effluent that was not subjected to tertiary treatment. The chlorinated and brominated byproduct concentration may be affected by the influent concentration of parent compounds, hydraulic retention times, and chlorine contact times. Salicylic acid was readily halogenated, which is evident from the ratio of halogenated to nonhalogenated species. There were no measured chlorinated byproducts of bisphenol A despite occasionally high concentrations of the parent compound. Not surprisingly, higher concentrations of most brominated species were measured in the treatment plant with the highest bromide concentrations. These results demonstrate the occurrence of novel halogenated byproducts of PPCPs that have limited toxicological data and significant uncertainty with regard to their risk to ecological systems.

Diurnal variability of pharmaceutical, personal care product, estrogen and alkylphenol concentrations in effluent from a tertiary wastewater treatment facility.

Hourly samples of tertiary wastewater effluent were analyzed for 30 pharmaceuticals, personal care products, estrogenic steroids, and alkylphenols in order to better understand the rate at which these compounds enter the environment. Several distinct patterns of daily cycling were observed, and were characterized as three separate categories. The concentrations of compounds such as trimethoprim, sulfamethoxazole, naproxen, estrone, and triclosan varied greatly during a daily cycle, with relative standard deviations exceeding 100% of their daily mean. Less extreme daily cycles were seen for other compounds such as azithromycin, atenolol, tert-octylphenol, iopromide and gemfibrozil. Peak concentrations for most compounds occurred in the early evening (5-8 pm). However, some compounds including carbamazepine, primidone, fluoxetine, and triclocarban exhibited little or no variability.

Isolation and Extraction of Microplastics from Environmental Samples: An Evaluation of Practical Approaches and Recommendations for Further Harmonization.

Researchers have been identifying microplastics in environmental samples dating back to the 1970s. Today, microplastics are a recognized environmental pollutant attracting a large amount of public and government attention, and in the last few years the number of scientific publications has grown exponentially. An underlying theme within this research field is to achieve a consensus for adopting a set of appropriate procedures to accurately identify and quantify microplastics within diverse matrices. These methods should then be harmonized to produce quantifiable data that is reproducible and comparable around the world. In addition, clear and concise guidelines for standard analytical protocols should be made available to researchers. In keeping with the theme of this special issue, the goals of this focal point review are to provide researchers with an overview of approaches to isolate and extract microplastics from different matrices, highlight associated methodological constraints and the necessary steps for conducting procedural controls and quality assurance. Simple samples, including water and sediments with low organic content, can be filtered and sieved. Stepwise procedures require density separation or digestion before filtration. Finally, complex matrices require more extensive steps with both digestion and density adjustments to assist plastic isolation. Implementing appropriate methods with a harmonized approach from sample collection to data analysis will allow comparisons across the research community.

Sampling and Quality Assurance and Quality Control: A Guide for Scientists Investigating the Occurrence of Microplastics Across Matrices.

Plastic pollution is a defining environmental contaminant and is considered to be one of the greatest environmental threats of the Anthropocene, with its presence documented across aquatic and terrestrial ecosystems. The majority of this plastic debris falls into the micro (1 µm-5 mm) or nano (1-1000 nm) size range and comes from primary and secondary sources. Its small size makes it cumbersome to isolate and analyze reproducibly, and its ubiquitous distribution creates numerous challenges when controlling for background contamination across matrices (e.g., sediment, tissue, water, air). Although research on microplastics represents a relatively nascent subfield, burgeoning interest in questions surrounding the fate and effects of these debris items creates a pressing need for harmonized sampling protocols and quality control approaches. For results across laboratories to be reproducible and comparable, it is imperative that guidelines based on vetted protocols be readily available to research groups, many of which are either new to plastics research or, as with any new subfield, have arrived at current approaches through a process of trial-and-error rather than in consultation with the greater scientific community. The goals of this manuscript are to (i) outline the steps necessary to conduct general as well as matrix-specific quality assurance and quality control based on sample type and associated constraints, (ii) briefly review current findings across matrices, and (iii) provide guidance for the design of sampling regimes. Specific attention is paid to the source of microplastic pollution as well as the pathway by which contamination occurs, with details provided regarding each step in the process from generating appropriate questions to sampling design and collection.

Cyanide generation during preservation of chlorinated wastewater effluent samples for total cyanide analysis.

Dechlorinating agents and pH adjustment are often used to preserve wastewater samples for cyanide analysis. The effects of four approved preservation protocols on the results of the total cyanide analysis of effluents from four water reclamation plants were examined. The results differed widely, and a clear pattern emerged. Immediate analysis without pH adjustment generally gave total cyanide concentrations below the reporting limit of 5 microg/L, irrespective of the dechlorinating agents used. When the pH was adjusted to > or =12, a slight increase in the measured total cyanide concentration was observed when thiosulfate was used to dechlorinate the samples, and a significant increase (>10 microg/L) was observed when arsenite was used as the dechlorinating agent. These results provide evidence that approved preservation protocols may give rise to cyanide formation in chlorinated wastewater effluent matrices.

Sources and dispersive modes of micro-fibers in the environment.

Understanding the sources and distribution of microfibers (MFs) in the environment is critical if control and remediation measures are to be effective. Microfibers comprise an overwhelming fraction (>85%) of microplastic debris found on shorelines around the world. Although primary sources have not been fully vetted, until recently it was widely believed that domestic laundry discharges were the major source. It was also thought that synthetic fibers and particles having dimensions <5 mm easily bypassed filtration and other solid separation processes at wastewater treatment plants (WWTPs) and entered oceans and surface waters. A more thorough assessment of WWTP effluent discharges indicates, however, that fiber and particulate counts do not support the belief that plants are the primary vectors for fibers entering the environment. This finding may bolster concerns that active and pervasive shedding of fibers from common fabrics and textiles could be contributing significantly, via direct pathways, to burgeoning environmental loads. Integr Environ Assess Manag 2017;13:466-469. © 2017 SETAC.

Transport and fate of microplastic particles in wastewater treatment plants.

Municipal wastewater treatment plants (WWTPs) are frequently suspected as significant point sources or conduits of microplastics to the environment. To directly investigate these suspicions, effluent discharges from seven tertiary plants and one secondary plant in Southern California were studied. The study also looked at influent loads, particle size/type, conveyance, and removal at these wastewater treatment facilities. Over 0.189 million liters of effluent at each of the seven tertiary plants were filtered using an assembled stack of sieves with mesh sizes between 400 and 45 µm. Additionally, the surface of 28.4 million liters of final effluent at three tertiary plants was skimmed using a 125 µm filtering assembly. The results suggest that tertiary effluent is not a significant source of microplastics and that these plastic pollutants are effectively removed during the skimming and settling treatment processes. However, at a downstream secondary plant, an average of one micro-particle in every 1.14 thousand liters of final effluent was counted. The majority of microplastics identified in this study had a profile (color, shape, and size) similar to the blue polyethylene particles present in toothpaste formulations. Existing treatment processes were determined to be very effective for removal of microplastic contaminants entering typical municipal WWTPs.

Screening estrogenic oxidized by-products by combining ER binding and ultrafiltration.

Ozonation and chlorination of 17ß-estradiol (E2), 17α-ethynylestradiol (EE2), bisphenol A (BPA), and nonylphenol (NP) were performed to evaluate the estrogenic activity of the by-products of these endocrine disrupting chemicals (EDCs). After 15min oxidation, samples were extracted using solid phase extraction (SPE) cartridges, and tested in vitro to measure the estrogenic activities of the oxidized products. MCF-7 cell proliferation assay showed that chlorinated BPA solution displayed slightly stronger estrogenicity than BPA, while chlorinated NP retained about one-tenth of its bioactivity. The estrogenic mono-, di-, tri-, and tetra-ClBPAs and di-ClNP were screened out from the corresponding chlorinated products by a combined application of estrogen receptor (ER) binding with ultrafiltration and identified by high performance liquid chromatography coupled with mass spectrometry (LC/MS). Ozonation of the above four estrogens and chlorination of E2 and EE2 significantly decreased their estrogenic activities under the applied conditions.

Sources and fate of nitrosodimethylamine and its precursors in municipal wastewater treatment plants.

To assess the occurrence and fate of nitrosodimethylamine (NDMA) and its precursors in wastewater treatment plants, samples from wastewater treatment plants and industrial sources were analyzed for NDMA, total NDMA precursors, and dimethylamine (DMA). The median concentration of NDMA in untreated wastewater was approximately 80 ng/L, with maximum concentrations up to 790 ng/L presumably occuring because of sources unrelated to domestic wastewater. Concentrations of DMA in untreated wastewater ranged from approximately 50 to 120 microg/L and accounted for a majority of the NDMA precursors. The removal of NDMA during secondary biological treatment exhibited considerable variability, with overall removal ranging from 0 to 75%. In contrast, removal of NDMA precursors and DMA generally exceeded 70%. The median concentration of NDMA in secondary effluent before disinfection was 46 ng/L. Although DMA was removed during secondary treatment, other NDMA precursors in wastewater effluent will result in formation of additional NDMA upon disinfection with chloramines.

Phytochemical Analysis and Anti-Inflammatory Activity of the Extracts of the African Medicinal Plant Ximenia caffra.

A method was developed for identification and quantification of polyphenols in the leaves of Ximenia caffra using HPLC/UV/MS. Based on analyzing the MS and UV data and in comparison to the authentic standards, a total of 10 polyphenols were identified and quantified, including gallic acid, catechin, quercetin, kaempferol, and their derivatives. The total content of these compounds was found to be approximately 19.45 mg/g in the leaf and the most abundant is quercetin-rutinoside (9.08 mg/g). The total phenolic content as measured by Folin-Ciocalteu assay was 261.87 ± 7.11 mg GAE/g and the total antioxidant capacity as measured in vitro was 1.46 ± 0.01 mmol Trolox/g. The antiproliferative effect of the leaf extract was measured by MTS assay with IC50 value of 239.0 ± 44.5 µg/mL. Cell-based assays show that the leaf extract inhibits the mRNA expression of proinflammatory genes (IL-6, iNOS, and TNF-α) by using RT-qPCR, implying its anti-inflammatory effects. It was further demonstrated that the underlying therapeutic mechanism involves the suppression of NF-κB, a shared pathway between cell death and inflammation.

Cdc5 influences phosphorylation of Net1 and disassembly of the RENT complex.

BACKGROUND: In S. cerevisiae, the mitotic exit network (MEN) proteins, including the Polo-like protein kinase Cdc5 and the protein phosphatase Cdc14, are required for exit from mitosis. In pre-anaphase cells, Cdc14 is sequestered to the nucleolus by Net1 as a part of the RENT complex. When cells are primed to exit mitosis, the RENT complex is disassembled and Cdc14 is released from the nucleolus. RESULTS: Here, we show that Cdc5 is necessary to free nucleolar Cdc14 in late mitosis, that elevated Cdc5 activity provokes ectopic release of Cdc14 in pre-anaphase cells, and that the phosphorylation state of Net1 is regulated by Cdc5 during anaphase. Furthermore, recombinant Cdc5 and Xenopus Polo-like kinase can disassemble the RENT complex in vitro by phosphorylating Net1 and thereby reducing its affinity for Cdc14. Surprisingly, although RENT complexes containing Net1 mutants (Net1(7m) and Net1(19m') lacking sites phosphorylated by Cdc5 in vitro are refractory to disassembly by Polo-like kinases in vitro, net1(7m) and net1(19m') cells grow normally and exhibit only minor defects in releasing Cdc14 during anaphase. However, net1(19m') cells exhibit a synergistic growth defect when combined with mutations in CDC5 or DBF2 (another MEN gene). CONCLUSIONS: We propose that although Cdc5 potentially disassembles RENT by directly phosphorylating Net1, Cdc5 mediates exit from mitosis primarily by phosphorylating other targets. Our study suggests that Cdc5/Polo is unusually promiscuous and highlights the need to validate Cdc5/Polo in vitro phosphorylation sites by direct in vivo mapping experiments.