Formation of genotoxic compounds by medium pressure ultra violet treatment of nitrate rich water

Genotoxic compounds were produced by full-scale medium pressure (MP) ultraviolet hydrogen peroxide (UV/H2O2) treatment of nitrate-rich pretreated surface water. It was hypothesized that this formation was caused by the reaction of nitrate photolysis intermediates with natural organic matter (NOM). An increase in the Ames test response was also found after MP UV photolysis of water containing Pony Lake NOM from the International Humic Substances Society (IHSS) and nitrate, while no increase in the Ames test response was found when nitrate was absent. The same trend in an Ames test response and nitrite formation was observed for both nitrate-rich pretreated surface water and reconstituted water containing NOM and nitrate. Therefore, the conversion of nitrate by MP UV photolysis was studied in several water types. In organic-free water, nitrate was completely converted into nitrite, while no inorganic nitrogen was lost. Also in nitrate-rich surface water, nitrite was found as the only inorganic reaction product, while a small decrease of the inorganic nitrogen content was observed. When NOM was replaced by phenol, MP UV photolysis caused a restricted nitrite formation only, together with a large loss of inorganic nitrogen. The formation of the nitrated phenol derivatives, 2- and 4-nitrophenol and 4-nitrocatechol, was observed with highest concentrations under practical UV conditions. It is hypothesized that the formation of nitrated aromatic compounds is the cause of the increased Ames test response by MP UV treatment

Dual-color bioluminescent sensor proteins for therapeutic drug monitoring of antitumor antibodies

\u3cp\u3eMonitoring the levels of therapeutic antibodies in individual patients would allow patient-specific dose optimization, with the potential for major therapeutic and financial benefits. Our group recently developed a new platform of bioluminescent sensor proteins (LUMABS; LUMinescent AntiBody Sensor) that allow antibody detection directly in blood plasma. In this study, we targeted four clinically important therapeutic antibodies, the Her2-receptor targeting trastuzumab, the anti-CD20 antibodies rituximab and obinutuzumab, and the EGFR-blocking cetuximab. A strong correlation was found between the affinity of the antibody binding peptide and sensor performance. LUMABS sensors with physiologically relevant affinities and decent sensor responses were obtained for trastuzumab and cetuximab using mimotope and meditope peptides, respectively, with affinities in the 10\u3csup\u3e-7\u3c/sup\u3e M range. The lower affinity of the CD20-derived cyclic peptide employed in the anti-CD20 LUMABS sensor (K\u3csub\u3ed\u3c/sub\u3e = 10\u3csup\u3e-5\u3c/sup\u3e M), translated in a LUMABS sensor with a strongly attenuated sensor response. The trastuzumab and cetuximab sensors were further characterized with respect to binding kinetics and their performance in undiluted blood plasma. For both antibodies, LUMABS-based detection directly in plasma compared well to the analytical performance of commercial ELISA kits. Besides identifying important design parameters for the development of new LUMABS sensors, this work demonstrates the potential of the LUMABS platform for point-of-care detection of therapeutic antibodies.\u3c/p\u3

Dual-Color Bioluminescent Sensor Proteins for Therapeutic Drug Monitoring of Antitumor Antibodies

Monitoring the levels of therapeutic antibodies in individual patients would allow patient-specific dose optimization, with the potential for major therapeutic and financial benefits. Our group recently developed a new platform of bioluminescent sensor proteins (LUMABS; LUMinescent AntiBody Sensor) that allow antibody detection directly in blood plasma. In this study, we targeted four clinically important therapeutic antibodies, the Her2-receptor targeting trastuzumab, the anti-CD20 antibodies rituximab and obinutuzumab, and the EGFR-blocking cetuximab. A strong correlation was found between the affinity of the antibody binding peptide and sensor performance. LUMABS sensors with physiologically relevant affinities and decent sensor responses were obtained for trastuzumab and cetuximab using mimotope and meditope peptides, respectively, with affinities in the 10^–7 M range. The lower affinity of the CD20-derived cyclic peptide employed in the anti-CD20 LUMABS sensor (<i>K</i>_d = 10^–5 M), translated in a LUMABS sensor with a strongly attenuated sensor response. The trastuzumab and cetuximab sensors were further characterized with respect to binding kinetics and their performance in undiluted blood plasma. For both antibodies, LUMABS-based detection directly in plasma compared well to the analytical performance of commercial ELISA kits. Besides identifying important design parameters for the development of new LUMABS sensors, this work demonstrates the potential of the LUMABS platform for point-of-care detection of therapeutic antibodies

Analysis of RET promoter CpG island methylation using methylation-specific PCR (MSP), pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM): impact on stage II colon cancer patient outcome.

International audienceBackground: Already since the 1990s, promoter CpG island methylation markers have been considered promising diagnostic, prognostic, and predictive cancer biomarkers. However, so far, only a limited number of DNA methylation markers have been introduced into clinical practice. One reason why the vast majority of methylation markers do not translate into clinical applications is lack of independent validation of methylation markers, often caused by differences in methylation analysis techniques. We recently described RET promoter CpG island methylation as a potential prognostic marker in stage II colorectal cancer (CRC) patients of two independent series.Methods: In the current study, we analyzed the RET promoter CpG island methylation of 241 stage II colon cancer patients by direct methylation-specific PCR (MSP), nested-MSP, pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM). All primers were designed as close as possible to the same genomic region. In order to investigate the effect of different DNA methylation assays on patient outcome, we assessed the clinical sensitivity and specificity as well as the association of RET methylation with overall survival for three and five years of follow-up.Results: Using direct-MSP and nested-MSP, 12.0 % (25/209) and 29.6 % (71/240) of the patients showed RET promoter CpG island methylation. Methylation frequencies detected by pyrosequencing were related to the threshold for positivity that defined RET methylation. Methylation frequencies obtained by pyrosequencing (threshold for positivity at 20 %) and MS-HRM were 13.3 % (32/240) and 13.8 % (33/239), respectively. The pyrosequencing threshold for positivity of 20 % showed the best correlation with MS-HRM and direct-MSP results. Nested-MSP detected RET promoter CpG island methylation in deceased patients with a higher sensitivity (33.1 %) compared to direct-MSP (10.7 %), pyrosequencing (14.4 %), and MS-HRM (15.4 %). While RET methylation frequencies detected by nested-MSP, pyrosequencing, and MS-HRM varied, the prognostic effect seemed similar (HR 1.74, 95 % CI 0.97-3.15; HR 1.85, 95 % CI 0.93-3.86; HR 1.83, 95 % CI 0.92-3.65, respectively).Conclusions: Our results show that upon optimizing and aligning four RET methylation assays with regard to primer location and sensitivity, differences in methylation frequencies and clinical sensitivities are observed; however, the effect on the marker's prognostic outcome is minimal

Characterization of the habitat-and season-independent increase in fungal biomass induced by the invasive giant goldenrod and its impact on the fungivorous nematode community

Outside its native range, the invasive plant species giant goldenrod (Solidago gigantea) has been shown to increase belowground fungal biomass. This non-obvious effect is poorly character-ized; we don’t know whether it is plant developmental stage-dependent, which fractions of the fungal community are affected, and whether it is reflected in the next trophic level. To address these questions, fungal assemblages in soil samples collected from invaded and uninvaded plots in two soil types were compared. Although using ergosterol as a marker for fungal biomass demonstrated a significant increase in fungal biomass, specific quantitative PCR (qPCR) assays did not point at a quantitative shift. MiSeq-based characterization of the belowground effects of giant goldenrod revealed a local increase of mainly Cladosporiaceae and Glomeraceae. This asymmetric boost in the fungal community was reflected in a specific shift in the fungivorous nematode community. Our findings provide insight into the potential impact of invasive plants on local fungal communities

Disparate gain and loss of parasitic abilities among nematode lineages - Fig 1

<p><b>Pictures of the head (A, C) and the middle regions (B, D) of two relatively basal representatives of the Tylenchida</b>. This speciose nematode order harbours most of the economically high impact plant-parasitic nematode species. Morphometrics of the stylet, an injection-needle like device used to puncture the plant cell wall (A, C), and the lateral field, indentations in the cuticle present in both sides of the nematode (B, D), are used for species identification. For these pictures, standard light microscopy was combined with differential interference contrast (DIC) optics (magnification: 1,000x).</p

Complexity and Diversity of the Mammalian Sialome Revealed by Nidovirus Virolectins.

Sialic acids (Sias), 9-carbon-backbone sugars, are among the most complex and versatile molecules of life. As terminal residues of glycans on proteins and lipids, Sias are key elements of glycotopes of both cellular and microbial lectins and thus act as important molecular tags in cell recognition and signaling events. Their functions in such interactions can be regulated by post-synthetic modifications, the most common of which is differential Sia-O-acetylation (O-Ac-Sias). The biology of O-Ac-Sias remains mostly unexplored, largely because of limitations associated with their specific in situ detection. Here, we show that dual-function hemagglutinin-esterase envelope proteins of nidoviruses distinguish between a variety of closely related O-Ac-Sias. By using soluble forms of hemagglutinin-esterases as lectins and sialate-O-acetylesterases, we demonstrate differential expression of distinct O-Ac-sialoglycan populations in an organ-, tissue- and cell-specific fashion. Our findings indicate that programmed Sia-O-acetylation/de-O-acetylation may be critical to key aspects of cell development, homeostasis, and/or function

A generalized overview of the phylogenetic relationships within the phylum Nematoda based on (nearly) full-length small subunit ribosomal DNA (SSU rDNA) sequences.

<p>For clade designation, we adhered to Holterman et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185445#pone.0185445.ref007" target="_blank">7</a>]. Plant parasites are found in Clades 1, 2, 10 and 12, and icons are used to distinguish four types of plant-parasitic nematodes: ectoparasites, semi-endoparasites, migratory endoparasites, and sedentary endoparasites.</p

Taxon coverage for the four plant parasite-harboring nematode lineages.

<p>Taxon coverage for the four plant parasite-harboring nematode lineages.</p