Clustered tree regression to learn protein energy change with mutated amino acid.

Accurate and effective prediction of mutation-induced protein energy change remains a great challenge and of great interest in computational biology. However, high resource consumption and insufficient structural information of proteins severely limit the experimental techniques and structure-based prediction methods. Here, we design a structure-independent protocol to accurately and effectively predict the mutation-induced protein folding free energy change with only sequence, physicochemical and evolutionary features. The proposed clustered tree regression protocol is capable of effectively exploiting the inherent data patterns by integrating unsupervised feature clustering by K-means and supervised tree regression using XGBoost, and thus enabling fast and accurate protein predictions with different mutations, with an average Pearson correlation coefficient of 0.83 and an average root-mean-square error of 0.94kcal/mol. The proposed sequence-based method not only eliminates the dependence on protein structures, but also has potential applications in protein predictions with rare structural information.

The role of ambra1 in Pb-induced developmental neurotoxicity in zebrafish.

Lead is a highly toxic metal that displays developmental neurotoxicity. Ambra1 plays a crucial role in embryonic neural development. At present, the role of Ambra1 in lead-induced developmental neurotoxicity remains unknown. In this study, we investigated the mechanism of Ambra1 concerning its role in lead-induced neurotoxicity. Zebrafish (Danio rerio) embryos were exposed to 0.1, 1, or 10 µM Pb until 5 days post-fertilization, and their locomotor activity was significantly impaired by the 10 µM treatment. Meanwhile, Pb reduced the expression of ambra1a and ambra1b in the brain at 48 and 72 h post-fertilization. Overexpression of ambra1a or ambra1b reversed Pb-induced alterations in locomotor activity, and decreased the apoptotic cell numbers in the brains of Pb-treated zebrafish. Our data reveal a novel protective role of Ambra1 against Pb-induced neural damage in the developing zebrafish.

[Analysis of cytochrome P450 2E1 RsaI/PstI and DraI polymorphisms in workers exposed to benzene].

OBJECTIVE: To investigate the cytochrome P450 2E1 (CYP2E1) RsaI/PstI and DraI polymorphisms in workers exposed to benzene. METHODS: A cross-sectional survey was carried out. A total of 71 workers exposed to benzene were included in observation group and the same number of people without occupational benzene exposure were included in control group. Blood samples from the two groups were collected and genotyping for CYP2E1 RsaI/PstI and DraI were conducted using the polymerase chain reaction-restriction fragment length polymorphism. RESULTS: There were no significant differences in CYP2E1 DraI genotype and allele distributions between the observation group and the control group (χ² = 2.374, P > 0.05; χ² = 2.113, P > 0.05). Significant differences in CYP2E1 RsaI/PstI genotype and allele distributions between the two groups were observed (χ² = 9.129, P < 0.01; χ² = 6.028, P < 0.05). CONCLUSION: Mutations at CYP2E1 RsaI/PstI can enhance the expression of CYP2E1 and this suggests individuals with the mutated gene have increased susceptibility to chronic benzene poisoning.

RotNet: A Rotationally Invariant Graph Neural Network for Quantum Mechanical Calculations.

Deep learning has proven promising in biological and chemical applications, aiding in accurate predictions of properties such as atomic forces, energies, and material band gaps. Traditional methods with rotational invariance, one of the most crucial physical laws for predictions made by machine learning, have relied on Fourier transforms or specialized convolution filters, leading to complex model design and reduced accuracy and efficiency. However, models without rotational invariance exhibit poor generalization ability across datasets. Addressing this contradiction, this work proposes a rotationally invariant graph neural network, named RotNet, for accurate and accelerated quantum mechanical calculations that can overcome the generalization deficiency caused by rotations of molecules. RotNet ensures rotational invariance through an effective transformation and learns distance and angular information from atomic coordinates. Benchmark experiments on three datasets (protein fragments, electronic materials, and QM9) demonstrate that the proposed RotNet framework outperforms popular baselines and generalizes well to spatial data with varying rotations. The high accuracy, efficiency, and fast convergence of RotNet suggest that it has tremendous potential to significantly facilitate studies of protein dynamics simulation and materials engineering while maintaining physical plausibility.

Triphenyl phosphate induces clastogenic effects potently in mammalian cells, human CYP1A2 and 2E1 being major activating enzymes.

As a new-type flame retardant and toxic substance, triphenyl phosphate (TPP) is a ubiquitous pollutant present even in human blood. TPP is transformed by human CYP enzymes to oxidized/dealkylated metabolites. The impact of TPP metabolism on its toxicity, however, remains unclear. In this study, the genotoxicity of TPP in several mammalian cell lines and its relevance to CYP/sulfortransferase (SULT) activities were investigated. The results indicated that TPP induced micronucleus formation at ≥1 µM concentrations in a human hepatoma (C3A, endogenous CYPs being substantial) cell line, which was abolished by 1-aminobenzotriazole (CYPs inhibitor). In cell line HepG2 (parental to C3A with lower CYP expression) TPP was inactive up to 10 µM, while pretreatment with ethanol (CYP2E1 inducer), PCB 126 (CYP1A inducer), or rifampicin (CYP3A inducer) led to micronucleus formation by TPP. In V79-Mz and V79-derived cells expressing human CYP1A1 TPP was inactive (up to 32 µM), and in cells expressing human CYP1B1, 2B6 and 3A4 it induced micronucleus weakly (positive only at 32 µM). However, TPP induced micronucleus potently in V79-derived cells expressing human CYP1A2, while this effect was drastically reduced by human SULT1A1 co-expression; likewise, TPP was inactive in cells expressing both human CYP2E1 and SULT1A1, but became positive with pentachlorophenol (inhibitor of SULT1) co-exposure. Moreover, in C3A cells TPP selectively induced centromere-free micronucleus (immunofluorescent assay), and TPP increased γ-H2AX (by Western blot, indicating double-strand DNA breaks). In conclusion, this study suggests that TPP is potently clastogenic, human CYP1A2 and 2E1 being major activating enzymes while SULT1A1 involved in detoxification.

Association analysis of gut microbiota and efficacy of SSRIs antidepressants in patients with major depressive disorder.

BACKGROUND: Relevant studies have shown that gut microbiome plays an important role in the occurrence, development and treatment of major depressive disorder (MDD). Many studies have also shown that, selective serotonin reuptake inhibitors (SSRIs) antidepressants can improve the symptoms of depression by changing the distribution of gut microbiome, Here we investigated whether a distinct gut microbiome was associated with Major depressive disorder (MDD), and how it was modulated by SSRIs antidepressants. METHOD: In this study, we analyzed the gut microbiome composition of 62 patients with first-episode MDD and 41 matched healthy controls, before SSRIs antidepressants treatment, using 16S rRNA gene sequencing. MDD patients characterized as treatment-resistant (TR) or responders (R) to antidepressants by score reduction rate were ≥50 % after SSRIs antidepressants treatment for eight weeks. RESULTS: LDA effect size (LEfSe) analysis found that there were 50 different bacterial groups among the three groups, of which 19 genera were mainly at the genus level. The relative abundance of 12 genera increased in the HCs group, 5 genera in the R group increased in relative abundance, and 2 genera in the TR group increased in relative abundance. The correlation analysis of 19 bacterial genera and the score reduction rate showed that Blautia, Bifidobacterium and Coprococcus with higher relative abundance in the treatment effective group were related to the efficacy of SSRIs antidepressants. CONCLUSIONS: Patients with MDD have a distinct gut microbiome that changes after SSRIs antidepressants treatment. Dysbiosis could be a new therapeutic target and prognostic tool for the treatment of patients with MDD.

Phenylalanine Residues in the Active Site of CYP2E1 Participate in Determining the Binding Orientation and Metabolism-Dependent Genotoxicity of Aromatic Compounds.

The composition of amino acids forming the active site of a CYP enzyme is impactful in its substrate selectivity. For CYP2E1, the role of PHE residues in the formation of effective binding orientations for its aromatic substrates remains unclear. In this study, molecular docking and molecular dynamics analysis were performed to reflect the interactions between PHEs in the active site of human CYP2E1 and various aromatic compounds known as its substrates. The results indicated that the orientation of 1-methylpyrene (1-MP) in the active site was highly determined by the presence of PHEs, PHE478 contributing to the binding free energy most significantly. Moreover, by building a random forest model the relationship between each of 19 molecular descriptors of polychlorinated biphenyl (PCB) compounds (from molecular docking, quantum mechanics, and physicochemical properties) and their human CYP2E1-dependent mutagenicityas established mostly in our lab, was investigated. The presence of PHEs did not appear to significantly modify the electronic or structural feature of each bound ligand (PCB), instead, the flexibility of the conformation of PHEs contributed substantially to the effective binding energy and orientation. It is supposed that PHE residues adjust their own conformation to permit a suitablly shaped cavity for holding the ligand and forming its orientation as favorable for a biochemical reaction. This study has provided some insights into the role of PHEs in guiding the interactive adaptation of the active site of human CYP2E1 for the binding and metabolism of aromatic substrates.

Gut microbiota composition in depressive disorder: a systematic review, meta-analysis, and meta-regression.

Studies investigating gut microbiota composition in depressive disorder have yielded mixed results. The aim of our study was to compare gut microbiome between people with depressive disorder and healthy controls. We did a meta-analysis and meta-regression of studies by searching PubMed, Web of Science, Embase, Scopus, Ovid, Cochrane Library, ProQuest, and PsycINFO for articles published from database inception to March 07, 2022. Search strategies were then re-run on 12 March 2023 for an update. We undertook meta-analyses whenever values of alpha diversity and Firmicutes, Bacteroidetes (relative abundance) were available in two or more studies. A random-effects model with restricted maximum-likelihood estimator was used to synthesize the effect size (assessed by standardized mean difference [SMD]) across studies. We identified 44 studies representing 2091 patients and 2792 controls. Our study found that there were no significant differences in patients with depressive disorder on alpha diversity indices, Firmicutes and Bacteroidetes compared with healthy controls. In subgroup analyses with regional variations(east/west) as a predictor, patients who were in the West had a lower Chao1 level (SMD -0.42[-0.74 to -0.10]). Subgroup meta-analysis showed Firmicutes level was decreased in patients with depressive disorder who were medication-free (SMD -1.54[-2.36 to -0.72]), but Bacteroidetes level was increased (SMD -0.90[0.07 to 1.72]). In the meta-regression analysis, six variables cannot explain the 100% heterogeneity of the studies assessing by Chao1, Shannon index, Firmicutes, and Bacteroidetes. Depleted levels of Butyricicoccus, Coprococcus, Faecalibacterium, Fusicatenibacter, Romboutsia, and enriched levels of Eggerthella, Enterococcus, Flavonifractor, Holdemania, Streptococcus were consistently shared in depressive disorder. This systematic review and meta-analysis found that psychotropic medication and dietary habit may influence microbiota. There is reliable evidence for differences in the phylogenetic relationship in depressive disorder compared with controls, however, method of measurement and method of patient classification (symptom vs diagnosis based) may affect findings. Depressive disorder is characterized by an increase of pro-inflammatory bacteria, while anti-inflammatory butyrate-producing genera are depleted.

Influence of aryl hydrocarbon receptor and sulfotransferase 1A1 on bisphenol AF-induced clastogenesis in human hepatoma cells.

Bisphenol compounds (BPs) are ubiquitously existing pollutants. Recent evidence shows that they may be activated by human CYP1A1 for clastogenic effects; however, factors that influence/mediate CYP1A1-activated 4,4'-(hexafluoroisopropylidene)diphenol (BPAF) toxicity, particularly the aryl hydrocarbon receptor (AhR), sulfotransferase (SULT) 1A1 [known to conjugate 2,2-bis(4-hydroxyphenol)-propane (BPA)] and reactive oxygen species (ROS), remain unclear. In this study, a human hepatoma (HepG2) cell line was genetically engineered for the expression of human CYP1A1 and SULT1A1, producing HepG2-hCYP1A1 and HepG2-hSULT1A1, respectively. They were used in the micronucleus test and γ-H2AX analysis (Western blot) (indicating double-strand DNA breaks) with BPAF; the role of AhR in mediating BPAF toxicity was investigated by coexposure of AhR modulators in HepG2 and its derivative C3A (with no genetic modifications but enhanced CYP expression). The results indicated induction of micronuclei by BPAF (≥ 2.5 µM, for 2-cell cycle) in HepG2-hCYP1A1 and C3A, while inactive in HepG2 and HepG2-hSULT1A1; however, BPAF induced micronuclei in HepG2 pretreated with 3,3',4,4',5-pentachlorobiphenyl (PCB126, AhR activator), and BAY-218 (AhR inhibitor) blocked the effect of BPAF in C3A. In HepG2-hCYP1A1 BPAF selectively induced centromere-free micronuclei (immunofluorescent assay) and double-strand DNA breaks. In HepG2 cells receiving conditional medium from BPAF-HepG2-hCYP1A1 incubation micronuclei were formed, while negative in HepG2-hSULT1A1. Finally, the intracellular levels of ROS, superoxide dismutase and reduced glutathione in C3A and HepG2-hCYP1A1 exposed to BPAF were all moderately increased, while unchanged in HepG2 cells. In conclusion, like other BPs BPAF is activated by human CYP1A1 for potent clastogenicity, and this effect is enhanced by AhR while alleviated by SULT1A1.

Brain functional alterations in MDD patients with somatic symptoms: A resting-state fMRI study.

OBJECTIVE: It has been established that major depressive disorder (MDD) is accompanied by various somatic symptoms that are related to the clinical course and severity of depression. However, the mechanisms of somatic symptoms in MDD have rarely been studied. In this study, we sought to investigate the functional neurological changes in MDD patients with somatic symptoms based off the regional homogeneity (ReHo) and the amplitude of low-frequency fluctuation (ALFF). METHOD: Study participants included 74 first-episode, drug naïve MDD patients as well as 70 healthy subjects (HCs). Patients diagnosed with MDD were separated into two groups based on the presence (n=50) or absence (n=24) of somatic symptoms. Functional images were obtained and analyzed. Alterations in ReHo/ALFF and the severity of clinical symptoms were investigated using correlation analysis. RESULTS: More severe depressive symptoms were observed in the somatic depression group than that of the pure depression group (P< 0.001). Furthermore, there was a significant reduction in ReHo and ALFF in the bilateral precentral gyrus, bilateral postcentral gyrus, and left paracentral gyrus in the somatic MDD group as compared to the pure depression group (GRF correction, voxel-P< 0.001, cluster-P < 0.01). Pearson correlation analysis revealed a negative correlation between ReHo and ALFF values in these abnomal regions with the severity of somatic and depressive symptoms (P< 0.01). CONCLUSION: Somatic depression is more severe than pure depression. The ReHo and ALFF changes in the precentral gyrus, postcentral gyrus, and paracentral gyrus may serve a significant role in the pathophysiology of somatic symptoms in MDD.

Gut Microbiome Composition Linked to Inflammatory Factors and Cognitive Functions in First-Episode, Drug-Naive Major Depressive Disorder Patients.

OBJECTIVE: The microbiota-gut-brain axis, especially the inflammatory pathway, may play a critical role in the pathogenesis of cognitive impairment in major depressive disorder (MDD). However, studies on the microbiota-inflammatory-cognitive function axis in MDD are lacking. The aim of the present study was to analyze the gut microbiota composition and explore the correlation between gut microbiota and inflammatory factors, cognitive function in MDD patients. METHOD: Study participants included 66 first-episode, drug naïve MDD patients as well as 43 healthy subjects (HCs). The composition of fecal microbiota was evaluated using16S rRNA sequencing and bioinformatics analysis. The cytokines such as hs-CRP, IL-1ß, IL-6, IL-10, and TNF-α in peripheral blood were detected via enzyme linked immunosorbent assay (ELISA); assessment of cognitive functions was performed using the Color Trail Test (CTT), The Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and the Stroop Color-Word Test (SCWT). RESULTS: We found that compared with HCs, MDD patients had cognitive impairments and showed different α-diversity and ß-diversity of gut microbiota composition. LDA effect size (LEfSe) analysis found MDD have higher Deinococcaceae and lower Bacteroidaceae, Turicibacteraceae, Clostridiaceae and Barnesiellaceae at family level. Deinococcus and Odoribacter was higher in the MDD group, however, Bacteroides, Alistipes, Turicibacter, Clostridium, Roseburia, and Enterobacter were lower at genus level. Furthermore, In MDD patients, the Bacteroidaceae and Bacteroides were both positively correlated with hsCRP, CCT1, CCT2. Alistipes was positively correlated with IL-6, Word time, Color time, Word-Color time, Color-Word time and negatively correlated with Delayed Memory, Total score and Standardized score. Turicibacteraceae and Turicibacter were both negatively correlated with IL-1ß and IL-6. CONCLUSION: The present findings confirm that the gut microbiota in MDD patients have altered gut microbes that are closely associated with inflammatory factors and cognitive function in MDD patients.

A protective role of autophagy in Pb-induced developmental neurotoxicity in zebrafish.

Lead (Pb) is one of the most toxic heavy metals and has aroused widespread concern as it can cause severe impairments in the developing nervous system. Autophagy has been proposed as an injury factor in Pb-induced neurotoxicity. In this study, we used zebrafish embryo as a model, measured the general toxic effects of Pb, and investigated the effect of Pb exposure on autophagy, and its role in Pb-induced developmental neurotoxicity. Zebrafish embryos were exposed to Pb at concentrations of 0, 0.1, 1 or 10 µM until 4 days post-fertilization. Our data showed that exposure to 10 µM Pb significantly reduced survival rates and impaired locomotor activity. Uptake of Pb was enhanced as the concentration and duration of exposure increased. Inhibition of lysosomal degradation with bafilomycin A1 treatment abolished the suppression of Lc3-II protein expression by Pb. Furthermore, autophagosome formation was inhibited by Pb in the brain. In addition, mRNA expression of beclin1, one of the critical genes in autophagy, were decreased in Pb exposure groups at 72 h post-fertilization. Whole-mount in situ hybridization assay showed that beclin1 gene expression in the brain was reduced by Pb. Rapamycin, an autophagy inducer, partly resolved developmental neurotoxicity induced by Pb exposure. Our results suggest that autophagy plays a protective role in the developmental neurotoxicity of Pb in zebrafish embryos and larvae.

Role of neurexin2a in lead-induced locomotor defect in developing zebrafish.

Low-dose chronic lead (Pb) exposure interferes with the development of the nervous system, which may lead to learning disabilities, behavioral abnormalities, and mental retardation. Neurexins (Nrxns) are synaptic cell-adhesion molecules associated with neurological disorders. We hypothesized that Pb can affect the expression of nrxns during synapse formation and alter the phenotype behavior. Here, apoptosis, nrxns mRNA expression, and alterations of locomotion were examined after exposure to Pb in zebrafish embryos/larvae. To confirm the function of nrxn2a, rescue experiments were performed using ß-nrxn2a mRNA microinjection. Pb exposure increased apoptosis and altered locomotor behavior in zebrafish larvae. Quantitative PCR showed that among several synaptic adhesion molecules, only nrxn2a were affected by Pb exposure. Moreover, exposure to Pb at 10µmol/L upregulated mRNA expression of nrxn1a and nrxn3a at 24h post fertilization (hpf) and downregulated expression at 48 hpf, whereas the expression remained unchanged at 72 hpf. Only the two isoforms of nrxn2a were downregulated by Pb at 10µmol/L at all three time points. Rescue experiments showed that ß-nrxn2a mRNA injection recovered the decreased locomotor activity and the increased apoptosis induced by Pb. In addition, overexpression of ß-nrxn2a mRNA upregulated α-nrxn2a. These data indicated that Pb inhibited the expression of nrxn2a genes, which play a critical role in neural development, and further altered the behavior of zebrafish embryos/larvae.

Effects of cadmium, manganese, and lead on locomotor activity and neurexin 2a expression in zebrafish.

The synaptic adhesion protein Neurexin 2a (Nrxn2a) plays a key role in neuronal development and is associated with cognitive functioning and locomotor behavior. Although low-level metal exposure poses a potential risk to the human nervous system, especially during the developmental stages, little is known about the effects of metal exposures on nrxn2a expression during embryonic development. We therefore exposed wild-type zebrafish embryos/larvae to cadmium (CdCl2 ), manganese (MnCl2 ), and lead ([CH3 COO]2 Pb), to determine their effect on mortality, malformation, and hatching rate. Concentrations of these metals in zebrafish were detected by inductively coupled plasma mass spectrometry analysis. Locomotor activity of zebrafish larvae was analyzed using a video-track tracking system. Expression of nrxn2a was assessed by in situ hybridization and quantitative polymerase chain reaction. The results showed that mortality, malformation, and bioaccumulation increased as the exposure dosages and duration increased. Developmental exposure to these metals significantly reduced larval swim distance and velocity. The nrxn2aa and nrxn2ab genes were expressed in the central nervous system and downregulated by almost all of the 3 metals, especially Pb. These data demonstrate that exposure to metals downregulates nrxn2a in the zebrafish model system, and this is likely linked to concurrent developmental processes. Environ Toxicol Chem 2017;36:2147-2154. © 2017 SETAC.