scholarly journals Quantitative non-targeted analysis: Bridging the gap between contaminant discovery and risk characterization

2022 ◽  
Vol 158 ◽  
pp. 107011
Author(s):  
James P. McCord ◽  
Louis C. Groff ◽  
Jon R. Sobus
Author(s):  
Adam L. Numis ◽  
Gilberto da Gente ◽  
Elliott H. Sherr ◽  
Hannah C. Glass

Abstract Background The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known. Methods Case–control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches. Results Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy. Conclusions In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy. Impact We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures. Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy. Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis.


Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 142
Author(s):  
Mariella Cuomo ◽  
Luca Borrelli ◽  
Rosa Della Monica ◽  
Lorena Coretti ◽  
Giulia De Riso ◽  
...  

The bidirectional microbiota–gut–brain axis has raised increasing interest over the past years in the context of health and disease, but there is a lack of information on molecular mechanisms underlying this connection. We hypothesized that change in microbiota composition may affect brain epigenetics leading to long-lasting effects on specific brain gene regulation. To test this hypothesis, we used Zebrafish (Danio Rerio) as a model system. As previously shown, treatment with high doses of probiotics can modulate behavior in Zebrafish, causing significant changes in the expression of some brain-relevant genes, such as BDNF and Tph1A. Using an ultra-deep targeted analysis, we investigated the methylation state of the BDNF and Tph1A promoter region in the brain and gut of probiotic-treated and untreated Zebrafishes. Thanks to the high resolution power of our analysis, we evaluated cell-to-cell methylation differences. At this resolution level, we found slight DNA methylation changes in probiotic-treated samples, likely related to a subgroup of brain and gut cells, and that specific DNA methylation signatures significantly correlated with specific behavioral scores.


2021 ◽  
Vol 147 ◽  
pp. 106345
Author(s):  
Haiyang Chen ◽  
Chang Liu ◽  
Yanguo Teng ◽  
Zulin Zhang ◽  
Yihan Chen ◽  
...  

Author(s):  
Varshita Chirumamilla ◽  
Joseph M. Gerard ◽  
Alison E. Sweeney ◽  
Kristin P. Tully ◽  
Alison M. Stuebe ◽  
...  

Assessing hospital environment conditions is necessary for healthcare providers and patients to coordinate safe care. The aims of this research included: a) identifying patterns in hospital visit feedback transcripts regarding bathroom doors and lights in the hospital room and b) interpreting the results to make recommendations for more enabling clinical environments. The methods used by the research team included organizing transcript data, assigning codes, and conducting an interrater reliability test to assess codebook efficacy. Finally, working with maternal and infant mortality experts, recommendations for the hospital were developed. We identified four possible interventions to address barriers: a) implement low-height, dimmable lighting along the base of the patient room, b) provide personal lights, such as penlights, to staff for nighttime assessments, c) install and improve on existing grab bars in patient room bathrooms and d) replace the standard patient room bathroom door with a different kind of auditory/visual privacy barrier.


2021 ◽  
Vol 769 ◽  
pp. 145218
Author(s):  
Xiao Liu ◽  
Minkyu Park ◽  
Shawn C. Beitel ◽  
Israel J. Lopez-Prieto ◽  
Ning-Zheng Zhu ◽  
...  

2021 ◽  
Vol 22 (8) ◽  
pp. 4274
Author(s):  
Dèlia Yubero ◽  
Daniel Natera-de Benito ◽  
Jordi Pijuan ◽  
Judith Armstrong ◽  
Loreto Martorell ◽  
...  

The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Marcin Luzarowski ◽  
Rubén Vicente ◽  
Andrei Kiselev ◽  
Mateusz Wagner ◽  
Dennis Schlossarek ◽  
...  

AbstractProtein–metabolite interactions are of crucial importance for all cellular processes but remain understudied. Here, we applied a biochemical approach named PROMIS, to address the complexity of the protein–small molecule interactome in the model yeast Saccharomyces cerevisiae. By doing so, we provide a unique dataset, which can be queried for interactions between 74 small molecules and 3982 proteins using a user-friendly interface available at https://promis.mpimp-golm.mpg.de/yeastpmi/. By interpolating PROMIS with the list of predicted protein–metabolite interactions, we provided experimental validation for 225 binding events. Remarkably, of the 74 small molecules co-eluting with proteins, 36 were proteogenic dipeptides. Targeted analysis of a representative dipeptide, Ser-Leu, revealed numerous protein interactors comprising chaperones, proteasomal subunits, and metabolic enzymes. We could further demonstrate that Ser-Leu binding increases activity of a glycolytic enzyme phosphoglycerate kinase (Pgk1). Consistent with the binding analysis, Ser-Leu supplementation leads to the acute metabolic changes and delays timing of a diauxic shift. Supported by the dipeptide accumulation analysis our work attests to the role of Ser-Leu as a metabolic regulator at the interface of protein degradation and central metabolism.


Food Control ◽  
2021 ◽  
pp. 107991
Author(s):  
Simranjot Kaur ◽  
Jasbir Singh Bedi ◽  
Pankaj Dhaka ◽  
Deepthi Vijay ◽  
Rabinder Singh Aulakh

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