Dietary exposure of the water flea Daphnia galeata to microcystin-LR.

Harmful substances like the cyanotoxin microcystin-leucine-arginine (MC-LR) are commonly found in eutrophic freshwater environments, posing risks to aquatic organisms. The water flea, Daphnia, is a well-established model organism for environmental toxicology research. Nevertheless, there is currently insufficient research on the genes that respond to MC-LR in Daphnia galeata. This study aimed to gain insights into the notable genes that react significantly to MC-LR. In this study, we generated an extensive RNA-Seq sequences isolated from the D. galeata HK strain, Han River in Korea. This strain was nourished with a diet of the green microalga Chlorella vulgaris and treated with pure MC-LR at a concentration of 36 ug/L. The transcriptome profile in response to the MC-LR treatment was obtained and 336 differentially expressed genes were subjected to Gene Ontology (GO) and euKaryotic Orthologous Groups of proteins analyses. GO enrichment analysis showed that chemical stimulus, amino sugar metabolic and catabolic process, oxidative stress, and detoxification were highly enriched, in reverse, proteolysis and fucosylation were underpresented. Detoxification process related genes such as peroxidase-like, chorion, and thyroid peroxidase-like were enriched for eliminating or neutralizing MC_LR from an organism's body. Furthermore, functional protein classification revealed an upregulation of lipid and inorganic ion transport processes, while amino acid and carbohydrate transport processes were found to be downregulated. These findings offer insights into how organisms respond to ecotoxic stimuli, providing valuable information for understanding adaptation or defense pathways.

Identifying the acute toxicity of contaminated sediments using machine learning models.

Ecological risk assessment of contaminated sediment has become a fundamental component of water quality management programs, supporting decision-making for management actions or prompting additional investigations. In this study, we proposed a machine learning (ML)-based approach to assess the ecological risk of contaminated sediment as an alternative to existing index-based methods and costly toxicity testing. The performance of three widely used index-based methods (the pollution load index, potential ecological risk index, and mean probable effect concentration) and three ML algorithms (random forest, support vector machine, and extreme gradient boosting [XGB]) were compared in their prediction of sediment toxicity using 327 nationwide data sets from Korea consisting of 14 sediment quality parameters and sediment toxicity testing data. We also compared the performances of classifiers and regressors in predicting the toxicity for each of RF, SVM, and XGB algorithms. For all algorithms, the classifiers poorly classified toxic and non-toxic samples due to limited information on the sediment composition and the small training dataset. The regressors with a given classification threshold provided better classification, with the XGB regressor outperforming the other models in the classification. A permutation feature importance analysis revealed that Cr, Cu, Pb, and Zn were major contributors to toxicity prediction. The ML-based approach has the potential to be even more useful in the future with the expected increase in available sediment data.

Water quality assessment of the Sinchun stream based on epilithic diatom communities.

Water quality was assessed 11 sites on the Sinchun Stream, in the region of Daegu City (South Korea), from May 2007 to March 2008 using Diatom Assemblage Index to Organic Water Pollution (DAIpo) and Trophic Diatom Index (TDI). The reference sites were unaffected by effluent from a closed mine or treated sewage and had, epilithic diatom communities that were dominated by saproxenous taxa such as Achnanthes convergens and Cocconeisplacentula var. lineata. The water quality of these sites had DAIpo values ranging between 77.5-93.8 and TDI values between 51.3-67.6, indicating ß-oligosaprobic and mesotrophic environments, respectively. Study sites affected by effluent from the closed mine had epilithic diatom communities that were dominated by acidobiontic diatoms, such as Eunotia exigua and Achnanthidium minutissimum. The water quality of these sites had DAlpo values of 45.9-70.8, indicating ß-mesosaprobic to α-oligosaprobic environments, whereas TDI ranged between 1.7-66.9, indicating an oligotrophic to mesotrophic environment. Downstream sites affected by the influx of mine effluent and treated sewage had many species and a high percentage of saprophilous taxa, including Fragilaria construens var. venter and Nitzschia amphibia. The water quality of these regions had DAIpo values ranging between 21.8-33.1 and TDI values between 67.5-76.7, indicating α-mesosaprobic and eutrophic environments, respectively.

Gene expression changes in a rat model of oxygen-induced retinopathy.

PURPOSE: To identify altered patterns of retinal mRNA expression in a rat model of oxygen-induced retinopathy (OIR). METHODS: Sprague-Dawley rats from P2 to P14 were exposed to hyperoxia (80% oxygen) to induce OIR and then returned to normoxic conditions. Control rats were sustained in room air. Retinal gene expression between the rats of OIR and the controls was compared using cDNA microarray analysis. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to verify the microarray results. RESULTS: Among a total of 12,731 cDNAs analyzed by microarray, 13 genes were strongly up- or down-regulated (>2-fold change over controls) in the OIR rats. We found a significant increase in expression of 10 genes (CaM-kinase II inhibitor; acidic nuclear phosphoprotein 32 family, member A; vascular endothelial growth factor; interferon α-inducible protein 27-like; similar to enthoprotin, epsin 4, clathrin interacting protein; nidogen [entactin]; tubulin, ß5; fibrillin-1; spectrin ß2; and stearoyl-coenzyme A desaturase 2) and a significant decrease in expression of 3 genes (myelin-associated oligodendrocytic basic protein, heat shock protein, and decorin) in OIR rats compared to controls. CONCLUSIONS: We confirmed changes in expressions of various retinal genes in a rat model of OIR by microarray and RT-PCR. This study should contribute to the understanding of genetic indicators associated with OIR.

Treatment with triamcinolone acetonide prevents decreased retinal levels of decorin in a rat model of oxygen-induced retinopathy.

PURPOSE: To investigate the effect of triamcinolone acetonide (TA) on retinal expression of decorin in a rat model of oxygen-induced retinopathy (OIR). MATERIALS AND METHODS: OIR was stimulated by exposing Sprague-Dawley (SD) rats to hyperoxia (80 +/- 1.3% O2) from postnatal day (P) 2 to P14 and then returning them to normoxia (room air, 21 +/- 1.5% O2). Control rats were maintained in normoxia. At P15, TA (40 mg/ml) was injected into the right vitreous of OIR rats and saline into the left vitreous of control rats. All rats were sacrificed at P18. RT-PCR, western blot and immunohistochemistry, TUNEL assay were performed to detect the effects of TA on molecular and morphological changes in retinal decorin levels in P18 OIR rats. RESULTS: In P18 OIR rats, mRNA and protein of retinal levels and immunoreactivity of retinal decorin were significantly less (p-value = 0.0000000012, 0.0007, 0.000003; n = 5; respectively) than in control rats. In addition, neuronal cell death was increased in P18 OIR rats (p-value = 0.0028; n = 5) relative to controls. However, treatment with TA prevented the decrease of mRNA, protein levels, and immunoreactivity in retinal decorin in P18 OIR rats (p-value = 0.00023, 0.003, 0.000079; n = 5, respectively), and restored neuronal cell death in P18 OIR rats (p-value = 0.0022, n = 5). CONCLUSION: Our results suggest that decorin is involved in hypoxic retinal damage and that TA protects retinal neurons damaged by relative hypoxia from decreased decorin levels.