MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block.

DNA N6-methyladenine (6mA) is produced by the N6 position of the adenine being methylated, which occurs at the molecular level, and is involved in numerous vital biological processes in the rice genome. Given the shortcomings of biological experiments, researchers have developed many computational methods to predict 6mA sites and achieved good performance. However, the existing methods do not consider the occurrence mechanism of 6mA to extract features from the molecular structure. In this paper, a novel deep learning method is proposed by devising DNA molecular graph feature and residual block structure for 6mA sites prediction in rice, named MGF6mARice. Firstly, the DNA sequence is changed into a simplified molecular input line entry system (SMILES) format, which reflects chemical molecular structure. Secondly, for the molecular structure data, we construct the DNA molecular graph feature based on the principle of graph convolutional network. Then, the residual block is designed to extract higher level, distinguishable features from molecular graph features. Finally, the prediction module is used to obtain the result of whether it is a 6mA site. By means of 10-fold cross-validation, MGF6mARice outperforms the state-of-the-art approaches. Multiple experiments have shown that the molecular graph feature and residual block can promote the performance of MGF6mARice in 6mA prediction. To the best of our knowledge, it is the first time to derive a feature of DNA sequence by considering the chemical molecular structure. We hope that MGF6mARice will be helpful for researchers to analyze 6mA sites in rice.

Elevated preoptic brain activity in zebrafish glial glycine transporter mutants is linked to lethargy-like behaviors and delayed emergence from anesthesia.

Delayed emergence from anesthesia was previously reported in a case study of a child with Glycine Encephalopathy. To investigate the neural basis of this delayed emergence, we developed a zebrafish glial glycine transporter (glyt1 - / -) mutant model. We compared locomotor behaviors; dose-response curves for tricaine, ketamine, and 2,6-diisopropylphenol (propofol); time to emergence from these anesthetics; and time to emergence from propofol after craniotomy in glyt1-/- mutants and their siblings. To identify differentially active brain regions in glyt1-/- mutants, we used pERK immunohistochemistry as a proxy for brain-wide neuronal activity. We show that glyt1-/- mutants initiated normal bouts of movement less frequently indicating lethargy-like behaviors. Despite similar anesthesia dose-response curves, glyt1-/- mutants took over twice as long as their siblings to emerge from ketamine or propofol, mimicking findings from the human case study. Reducing glycine levels rescued timely emergence in glyt1-/- mutants, pointing to a causal role for elevated glycine. Brain-wide pERK staining showed elevated activity in hypnotic brain regions in glyt1-/- mutants under baseline conditions and a delay in sensorimotor integration during emergence from anesthesia. Our study links elevated activity in preoptic brain regions and reduced sensorimotor integration to lethargy-like behaviors and delayed emergence from propofol in glyt1-/- mutants.

Dopamine D1 receptor in the NAc shell is involved in delayed emergence from isoflurane anesthesia in aged mice.

BACKGROUND: Delayed emergence after general anesthesia tends to occur in the elderly population, but the mechanism remains unclear. Apart from age-related pharmacokinetic changes, the aging-induced structural and functional alterations in the arousal-promoting neural substrates should be considered. The nucleus accumbens (NAc) is a crucial arousal-related nucleus, in which activating medium spiny neurons (MSNs) expressing dopamine D1 receptor (D1R) could facilitate the arousal from natural sleep. Meanwhile, the dopaminergic systems decline with aging in multiple brain regions. However, whether the age-related decline in D1R in the NAc shell attenuates its arousal-promoting capacity from general anesthesia remains to be elucidated. METHODS: We first verified the delayed emergence from isoflurane anesthesia and examined the corresponding changes of electroencephalogram (EEG) power in aged mice. In turn, the arousal-modulating capacity of D1R was characterized in the young and aged cohorts by microinjection of D1R agonist/antagonist into the NAc shell. Furthermore, to address the possible mechanism responsible for the attenuated arousal-modulating capacity of the aged NAc, the expression of D1R in the NAc shell was measured and compared between young and aged mice. RESULTS: Our data indicated that compared with young mice, the emergence time in aged mice was notably longer, while EEG power in δ band (1-4Hz) was significantly higher and power in ß band (12-25Hz) was lower. Activating or inhibiting D1R in the NAc shell by microinjection D1R agonist/antagonist promoted or delayed the emergence process in young mice. Nevertheless, this modulation capacity of D1R in the NAc shell declined in aged mice, respectively. Meanwhile, downregulation of D1R expression in the NAc shell was detected in the aged brain. CONCLUSION: Together, these results suggest that aging attenuates the arousal-modulating capacity of D1R in the NAc shell probably through downregulation of D1R expression therein, which may provide a potential explanation and a therapeutic target for increased sensitivity to anesthetics in the elderly patients.

A Case of Delayed Emergence After Propofol Anesthesia: Genetic Analysis.

This case report describes a 71-year-old woman who experienced unusual delayed emergence from propofol, which lasted for 3 hours and resulted in admission to the intensive care unit. Because genetic variations of propofol-metabolizing enzymes are proposed to be causal factors, we explored genetic polymorphisms of cytochrome P450 2B6 (CYP2B6) and uridine 5'-diphospho-glucuronosyltransferase 1A9 (UGT1A9). Suggested high-risk factors (advanced age, CYP2B6 516 G/T, and UGT1A9 I399 C/C) were observed in this case of delayed propofol metabolism. Therefore, genetic variants involved in propofol metabolism should be considered in unexplained delayed emergence.