Biotic transformation products of sulfonamides in environmental water samples: High-resolution mass spectrometry-based tentative identification by a suspect screening approach.

The presence of pharmaceuticals in the aquatic environment is mainly due to their release from the effluents of the wastewater treatment plants (WWTPs), which are unable to completely remove them and their transformation products (TPs). Sulfonamides (SAs) are a synthetic antibacterial class used for the treatment of both human and animal infections; they have often been reported in surface water, thus contributing to the antibiotic resistance emergency. Monitoring SA TPs should be important as well because they could still exert some pharmaceutical activity; however, many TPs are still unknown since several transformation processes are possible (e. g. human and animal metabolism, WWTP activities, environmental factors etc.). In this work, three of the most used SAs, i.e., sulfamethoxazole (SMX), sulfapyridine (SPY), and sulfadiazine (SDZ), were incubated for 20 days in a batch reactor with activated sludge under controlled conditions. Then, the water sample was extracted and analyzed by ultra-high performance liquid chromatography-high resolution mass spectrometry in the data dependent acquisition (DDA) mode. Starting from the literature data, the possible transformation pathways were studied, and for each SA, a list of TPs was hypothesized and used for the identification. The raw data files were processed with Compound Discoverer, and 44 TPs (18, 13, and 13 TPs for SMX, SPY, and SDZ, respectively), including multiple TPs, were manually validated. To overcome the limitation of the DDA, the identified TPs were used in an inclusion list to analyze WWTP samples by a suspect screening approach. In this way, 4 SMX TPs and 5 SPY TPs were tentatively identified together with their parent compounds. Among these TPs, 5 of 9 were acetylated forms, in agreement with previous literature reporting that acetylation is the predominant SA transformation.

Electro-fermentation: Sustainable bioproductions steered by electricity.

The market of biobased products obtainable via fermentation processes has steadily increased over the past few years, driven by the need to create a decarbonized economy. To date, industrial fermentation (IF) employs either pure or mixed microbial cultures (MMC), whereby the type of the microbial catalysts and the used feedstock affect metabolic pathways and, in turn, the type of product(s) generated. In many cases, especially when dealing with MMC, the economic viability of IF is still hindered by factors such as the low attained product titer and selectivity, which ultimately challenge the downstream recovery and purification steps. In this context, electro-fermentation (EF) represents an innovative approach, based on the use of a polarized electrode interface to trigger changes in the rate, yield, titer or product distribution deriving from traditional fermentation processes. In principle, the electrode in EF can act as an electron acceptor (i.e., anodic electro-fermentation, AEF) or donor (i.e., cathodic electro-fermentation, CEF), or simply as a means to control the oxidation-reduction potential of the fermentation broth. However, the molecular and biochemical basis underlying EF are still largely unknown. This review provides a comprehensive overview of recent literature studies including both AEF and CEF examples using pure or mixed microbial cultures. A critical analysis of biochemical, microbiological, and engineering aspects which presently hamper the transition of the EF technology from the laboratory to the market is also presented.

A recurrent neomorphic mutation in MYOD1 defines a clinically aggressive subset of embryonal rhabdomyosarcoma associated with PI3K-AKT pathway mutations.

Rhabdomyosarcoma, a cancer of skeletal muscle lineage, is the most common soft-tissue sarcoma in children. Major subtypes of rhabdomyosarcoma include alveolar (ARMS) and embryonal (ERMS) tumors. Whereas ARMS tumors typically contain translocations generating PAX3-FOXO1 or PAX7-FOXO1 fusions that block terminal myogenic differentiation, no functionally comparable genetic event has been found in ERMS tumors. Here we report the discovery, through whole-exome sequencing, of a recurrent somatic mutation encoding p.Leu122Arg in the myogenic transcription factor MYOD1 in a distinct subset of ERMS tumors with poor outcomes that also often contain mutations altering PI3K-AKT pathway components. Previous mutagenesis studies had shown that MYOD1 with a p.Leu122Arg substitution can block wild-type MYOD1 function and bind to MYC consensus sequences, suggesting a possible switch from differentiation to proliferation. Our functional data now confirm this prediction. Thus, MYOD1 p.Leu122Arg defines a subset of rhabdomyosarcomas eligible for high-risk protocols and the development of targeted therapeutics.

Oncogene mutation profiling of pediatric solid tumors reveals significant subsets of embryonal rhabdomyosarcoma and neuroblastoma with mutated genes in growth signaling pathways.

PURPOSE: In contrast to the numerous broad screens for oncogene mutations in adult cancers, few such screens have been conducted in pediatric solid tumors. To identify novel mutations and potential therapeutic targets in pediatric cancers, we conducted a high-throughput Sequenom-based analysis in large sets of several major pediatric solid cancers, including neuroblastoma, Ewing sarcoma, rhabdomyosarcoma (RMS), and desmoplastic small round cell tumor (DSRCT). EXPERIMENTAL DESIGN: We designed a highly multiplexed Sequenom-based assay to interrogate 275 recurrent mutations across 29 genes. Genomic DNA was extracted from 192 neuroblastoma, 75 Ewing sarcoma, 89 RMS, and 24 DSRCT samples. All mutations were verified by Sanger sequencing. RESULTS: Mutations were identified in 13% of neuroblastoma samples, 4% of Ewing sarcoma samples, 21.1% of RMS samples, and no DSRCT samples. ALK mutations were present in 10.4% of neuroblastoma samples. The remainder of neuroblastoma mutations involved the BRAF, RAS, and MAP2K1 genes and were absent in samples harboring ALK mutations. Mutations were more common in embryonal RMS (ERMS) samples (28.3%) than alveolar RMS (3.5%). In addition to previously identified RAS and FGFR4 mutations, we report for the first time PIK3CA and CTNNB1 (ß-catenin) mutations in 5% and 3.3% of ERMS, respectively. CONCLUSIONS: In ERMS, Ewing sarcoma, and neuroblastoma, we identified novel occurrences of several oncogene mutations recognized as drivers in other cancers. Overall, neuroblastoma and ERMS contain significant subsets of cases with nonoverlapping mutated genes in growth signaling pathways. Tumor profiling can identify a subset of pediatric solid tumor patients as candidates for kinase inhibitors or RAS-targeted therapies.

Real time PCR detection of the PI*Z and PI*S mutations associated with alpha-1 antitrypsin deficiency.

Alpha-1 antitrypsin (A1AT or AAT) is a serine protease inhibitor (PI) which, when present at low levels, can cause chronic obstructive pulmonary disease (COPD) and liver disease in both children and adults. Several mutations within the SERPINA1 gene have been found to cause this deficiency. The most common variants are PI*Z and PI*S, each caused by a single nucleotide polymorphism (SNP). We describe a real time polymerase chain reaction (PCR) assay for the rapid genotyping of these polymorphisms. DNA was extracted from fourteen EDTA-anticoagulated whole blood samples using the Qiagen EZ1 blood extraction kit. SNP genotyping was performed using primer/probe sets purchased from Applied Biosystems. These were evaluated for performance and assay conditions on the Applied Biosystems 7500 FAST System. The genotypes of these samples were compared with their phenotype results from isoelectric focusing assays, which were performed by an independent reference laboratory. In addition, twenty samples that were previously genotyped at another laboratory were obtained for accuracy studies. Thirty-four samples were tested; five genotypes were represented and the assay was able to discriminate these successfully. Only one genotype could not be correlated with its phenotype result, as the phenotype was reported as an "unidentified allele". All other genotyping results were concordant with previously determined genotypes and phenotypes. We describe a rapid real time PCR assay that is suitable for clinical use in genotyping AAT alleles and which can be used as the initial step in A1AT testing algorithms.