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BMC Bioinformatics Nov 2023Messenger RNA (mRNA) has an essential role in the protein production process. Predicting mRNA expression levels accurately is crucial for understanding gene regulation,...
Messenger RNA (mRNA) has an essential role in the protein production process. Predicting mRNA expression levels accurately is crucial for understanding gene regulation, and various models (statistical and neural network-based) have been developed for this purpose. A few models predict mRNA expression levels from the DNA sequence, exploiting the DNA sequence and gene features (e.g., number of exons/introns, gene length). Other models include information about long-range interaction molecules (i.e., enhancers/silencers) and transcriptional regulators as predictive features, such as transcription factors (TFs) and small RNAs (e.g., microRNAs - miRNAs). Recently, a convolutional neural network (CNN) model, called Xpresso, has been proposed for mRNA expression level prediction leveraging the promoter sequence and mRNAs' half-life features (gene features). To push forward the mRNA level prediction, we present miREx, a CNN-based tool that includes information about miRNA targets and expression levels in the model. Indeed, each miRNA can target specific genes, and the model exploits this information to guide the learning process. In detail, not all miRNAs are included, only a selected subset with the highest impact on the model. MiREx has been evaluated on four cancer primary sites from the genomics data commons (GDC) database: lung, kidney, breast, and corpus uteri. Results show that mRNA level prediction benefits from selected miRNA targets and expression information. Future model developments could include other transcriptional regulators or be trained with proteomics data to infer protein levels.
Topics: MicroRNAs; RNA, Messenger; Mirex; Gene Expression Regulation; Transcription Factors; Gene Expression Profiling
PubMed: 37993778
DOI: 10.1186/s12859-023-05560-1 -
Environmental Research Jan 2024Organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCB), they have contributed to the exposure of women to persistent organic pollutants (POPs). These...
Placental concentrations of xenoestrogenic organochlorine pesticides and polychlorinated biphenyls and assessment of their xenoestrogenicity in the PA-MAMI mother-child cohort.
BACKGROUND
Organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCB), they have contributed to the exposure of women to persistent organic pollutants (POPs). These compounds can cross the placental barrier and interfere with the hormonal system of newborns.
AIM
To determine concentrations of OCPs and PCBs and their xenoestrogenic activity in placentas of women from the PA-MAMI cohort of Panama.
METHODS
Thirty-nine placenta samples from women in the Azuero peninsula (Panama) were analyzed. Five OCPs [p-p'-dichlorodiphenyldichloroethylene (p-p'-DDE), beta-hexachlorohexane (β-HCH), γ-hexachlorohexane (lindane), hexachlorobenzene (HCB) and mirex] and three PCB congeners (PCB-138, PCB-153 and PCB-180) were quantified in placenta extracts. The xenoestrogenic activity of extracts was assessed with the E-Screen bioassay to estimate the total effective xenoestrogen burden (TEXB).
RESULTS
All placental samples were positive for at least three POP residues and >70% for at least six. The frequencies of quantified OCPs ranged from 100% for p,p'-DDE and HCB to 30.8% for β-HCH. The highest median concentration was for lindane (380.0 pg/g placenta), followed by p,p'-DDE (280.0 pg/g placenta), and HCB (90.0 pg/g placenta). Exposure to p,p'-DDE was associated with greater meat consumption, suggesting that animal fat is a major source of exposure to DDT metabolites. The frequency of detected PCBs ranged between 70 and 90%; the highest median concentration was for PCB 138 (17.0 pg/g placenta), followed by PCB 153 (16.0 pg/g placenta). All placentas were positive in the estrogenicity bioassay with a median TEXB-α of 0.91 pM Eeq/g of placenta. Exposure to lindane was positively associated with the xenoestrogenicity of TEXB- α, whereas this association was negative in the case of exposure to PCB 153.
CONCLUSIONS
To our best knowledge, this study contributes the first evidence on the presence of POPs and xenoestrogenic burden in placentas from Latin-American women. Given concerns about the consequences of prenatal exposure to these compounds on children's health, preventive measures are highly recommended to eliminate or minimize the risk of OCP exposure during pregnancy.
Topics: Infant, Newborn; Animals; Female; Humans; Pregnancy; Polychlorinated Biphenyls; Hexachlorocyclohexane; Dichlorodiphenyl Dichloroethylene; Hexachlorobenzene; DDT; Placenta; Hydrocarbons, Chlorinated; Pesticides; Environmental Pollutants; Mother-Child Relations
PubMed: 37977273
DOI: 10.1016/j.envres.2023.117622 -
Molecules (Basel, Switzerland) Jul 2023A subcritical water degradation and extraction method was developed to remediate environmental soils contaminated by highly recalcitrant organochlorine pollutants....
A subcritical water degradation and extraction method was developed to remediate environmental soils contaminated by highly recalcitrant organochlorine pollutants. Hydrogen peroxide was used to effectively decompose organochlorine pollutants under subcritical water conditions. As a method optimization study, the static wet oxidation of chlorophenols was first performed in subcritical water with and without added hydrogen peroxide. Complete oxidation was achieved using an added oxidant, and thus, the oxidation and extraction of chlorophenols from a sand matrix was then attempted. Complete oxidation and extraction with added oxidant were achieved within 30 min at 100 °C. We then investigated the subcritical water degradation and extraction of dieldrin, mirex, and p,p'-DDD. These organochlorine pesticides were not as easily oxidized as the chlorophenols, and the benefit of adding hydrogen peroxide was only clearly observed at 200 °C. Approximately a 20% increase in degradation was noted for each pesticide and insecticide at this temperature. Unfortunately, this difference was not observed with an increase in temperature to 250 °C, except in some cases, where the amount of degradation byproducts was reduced. Dieldrin and p,p'-DDD were essentially destroyed at 250 °C, while all the pesticides and the insecticides were completely removed from the sand at this temperature. The proposed method was then used to remediate a soil sample highly contaminated with DDT. The soil was obtained from the grounds of an old DDT mixing facility in Virginia and has been aging for several decades. Not only was 100% removal of DDT from this soil achieved using the proposed method at 250 °C, but also, the extracted DDT was completely destroyed during the process. The proposed remediation method, therefore, demonstrates a high potential as an efficient and environmentally sound technique for the detoxification of soils.
PubMed: 37513317
DOI: 10.3390/molecules28145445 -
Journal of Chromatography. A May 2024Birds are excellent bioindicators of environmental pollution, and blood provides information on contaminant exposure, although its analysis is challenging because of the...
Optimization and uncertainty assessment of a gas chromatography coupled to Orbitrap mass spectrometry method to determine organic contaminants in blood: A case study of an endangered seabird.
Birds are excellent bioindicators of environmental pollution, and blood provides information on contaminant exposure, although its analysis is challenging because of the low volumes that can be sampled. The objective of the present study was to optimize and validate a miniaturized and functional extraction and analytical method based on gas chromatography coupled to Orbitrap mass spectrometry (GCOrbitrap-MS) for the trace analysis of contaminants in avian blood. Studied compounds included 25 organochlorine pesticides (OCPs), 6 polychlorinated biphenyls (PCBs), 8 polybrominated diphenyl ethers (PBDEs) and 15 polycyclic aromatic hydrocarbons (PAHs). Four extraction and clean-up conditions were optimized and compared in terms of efficiency, accuracy, and uncertainty assessment. Extraction with hexane:dichloromethane and miniaturized Florisil pipette clean-up was the most adequate considering precision and accuracy, time, and costs, and was thereafter used to analyse 20 blood samples of a pelagic seabird, namely the Bermuda petrel (Pterodroma cahow). This species, endemic to the Northwest Atlantic, is among the most endangered seabirds of the region that in the '60 faced a decrease in the breeding success likely linked to a consistent exposure to dichloro-diphenyl-trichloroethane (DDT). Indeed, p,p'-DDE, the main DDT metabolite, was detected in all samples and ranged bewteen 1.13 and 6.87 ng/g wet weight. Other ubiquitous compounds were PCBs (ranging from 0.13 to 6.76 ng/g ww), hexachlorobenzene, and mirex, while PAHs were sporadically detected at low concentrations, and PBDEs were not present. Overall, the extraction method herein proposed allowed analysing very small blood volumes (∼ 100 µL), thus respecting ethical principles prioritising the application of less-invasive sampling protocols, fundamental when studying threatened avian species.
Topics: Animals; Gas Chromatography-Mass Spectrometry; Pesticides; Birds; Hydrocarbons, Chlorinated; Polychlorinated Biphenyls; Halogenated Diphenyl Ethers; Polycyclic Aromatic Hydrocarbons; Endangered Species; Environmental Monitoring; Environmental Pollutants
PubMed: 38604058
DOI: 10.1016/j.chroma.2024.464870