Deep learning models incorporating endogenous factors beyond DNA sequences improve the prediction accuracy of base editing outcomes.

Adenine base editors (ABEs) and cytosine base editors (CBEs) enable the single nucleotide editing of targeted DNA sites avoiding generation of double strand breaks, however, the genomic features that influence the outcomes of base editing in vivo still remain to be characterized. High-throughput datasets from lentiviral integrated libraries were used to investigate the sequence features affecting base editing outcomes, but the effects of endogenous factors beyond the DNA sequences are still largely unknown. Here the base editing outcomes of ABE and CBE were evaluated in mammalian cells for 5012 endogenous genomic sites and 11,868 genome-integrated target sequences, with 4654 genomic sites sharing the same target sequences. The comparative analyses revealed that the editing outcomes of ABE and CBE at endogenous sites were substantially different from those obtained using genome-integrated sequences. We found that the base editing efficiency at endogenous target sites of both ABE and CBE was influenced by endogenous factors, including epigenetic modifications and transcriptional activity. A deep-learning algorithm referred as BE_Endo, was developed based on the endogenous factors and sequence information from our genomic datasets, and it yielded unprecedented accuracy in predicting the base editing outcomes. These findings along with the developed computational algorithms may facilitate future application of BEs for scientific research and clinical gene therapy.

Formation of nitrogen-containing disinfection by-products during the chloramination treatment of an emerging pollutant.

Chloramination was commonly used as disinfectant for killing pathogens in water. However, in this process, nitrogen-containing disinfection by-products (N-DBPs) would accidently form and subsequently rise toxicity. Here, we investigated acute toxicity variation and by-products formation during chloramination treatment on UV filter 2-hydroxy-4-methoxy-5-sulfonic acid benzophenone (BP-4). Under alkaline conditions, the acute toxicity of this system had significant increase. A total of 17 transformation products were tentatively identified, and for them, plausible transformation pathways were proposed. Noticeably, numerous aniline and nitrosobenzene analogs were detected, and the dramatic increase of acute toxicity in this system might be primarily attributed to the formation of benzoquinone and aniline analogs. Besides, bromophenol, iodophenol and iodobenzoquinone analogs exhibiting high toxicity were generated in the presence of bromine and iodide ions. This study indicates that chloramination treatment may significantly increase potential health risk, further management on disinfection system is reasonable.

The role of vitamin D through SphK1/S1P in the regulation of MS progression.

Sphingosine-1-phosphate (S1P) is biologically active lipid, leading to neuroinflammation and macrophage invasion in central nervous system, plays an important role in the development of multiple sclerosis (MS) model in experimental allergic encephalomyelitis (EAE) rats. Vitamin D is observed to be a key factor in regulating cell S1P levels. We detected vitamin D can alleviate the symptoms of EAE rats, but the exact mechanism is unclear. In PC12 cells, vitamin D can reverse S1P-induced cell death, but the signaling pathway unclear. This study was aimed to investigate S1P regulation mechanism or signaling pathway mediated by vitamin D in EAE and PC12 model. In our experiments, S1P and Sphingosine kinase type 1 (SphK1) mRNA and protein expression in EAE rats group, control group, vitamin D feeding group were detected by HPLC, ELISA, RT-PCR and western blot. PC12 cell death was detected by Propidium (PI) staining. VDR plasmid overexpression and RNA interference, immunofluorescence, real-time cell analysis, protein immunoblotting was used to detect SphK1 transcriptional regulation, cell-substrate attachment quality, the signaling pathway of cell apoptosis and inflammation related gene expression (Bax/Bcl-2, Casepase-3, Il-6, TGF-ß, TNF-α). Our study showed vitamin D can reverse the elevation of S1P level in EAE rats, reduce the severity and shorten the course of EAE. 1,25-(OH) 2D3 coupled with vitamin D receptor (VDR) inhibited SphK1 transcription. 1,25-(OH)2D3 significantly reduced PC12 cell death rate induced by S1P, in addition improved the cell substrate attachment quality. 1,25-(OH) 2D3 can block S1P-induced p-ERK activation and PI3K /Akt signaling pathway reduced Il-6, TGF-ß, TNF-α cytokine release and Bax/Bcl-2, Casepase-3 apoptosis protein expression. On the other hand, immunofluorescence staining showed 1,25-(OH) 2D3 can increase the expression of neuronal perinuclear protein MAP2 in PC12 cells probably protect nerve cells further. In summary, the ameliorative effect of vitamin D was derived from its ability to reduce S1P levels, provides an idea for vitamin D as a combination therapy for disease.

Source and composition analysis of petroleum hydrocarbons in the refinery circulating water.

Oil leakage from water coolers in refinery circulating water occurs from time to time, which affects the long-term and stable operation of refinery units. So far, workers in the refineries still adopt manual check methods, opening water coolers one by one and checking the water's smell and color to find out the spilled water coolers. In this study, a more rapid method of source appointment of oil spill in the circulating water by combining chemical fingerprinting with model recognition was developed. Firstly, chemical fingerprints including benzene/naphthalene series, and light hydrocarbon (C3-C5) in oil samples from all water coolers in the refinery fluid catalytic cracking (FCC) unit were analyzed by gas chromatography-mass spectrometry (GC/MS). Gasoline, diesel, and poor oil could be distinguished in terms of benzene and naphthalene distribution. The three similar types of gasolines could be distinguished by the volatile hydrocarbons especially C3-C4. The classification model for the spill of gasoline, diesel, and poor oil in circulating water was constructed by the partial least squares discriminant analysis algorithm with a 100% correct classification rate at the concentration more than 10 ppm. The gasoline spills in the circulating backwater of the refinery were successfully recognized by the classification model. This method enables the rapid prediction of oil spill type in refinery circulating water, and a similar method by installing online instrument and software potentially can be used for monitoring the circulating water in real time.