In silico prediction of drug-induced myelotoxicity by using Naïve Bayes method.

Drug-induced myelotoxicity usually leads to decrease the production of platelets, red cells, and white cells. Thus, early identification and characterization of myelotoxicity hazard in drug development is very necessary. The purpose of this investigation was to develop a prediction model of drug-induced myelotoxicity by using a Naïve Bayes classifier. For comparison, other prediction models based on support vector machine and single-hidden-layer feed-forward neural network  methods were also established. Among all the prediction models, the Naïve Bayes classification model showed the best prediction performance, which offered an average overall prediction accuracy of [Formula: see text] for the training set and [Formula: see text] for the external test set. The significant contributions of this study are that we first developed a Naïve Bayes classification model of drug-induced myelotoxicity adverse effect using a larger scale dataset, which could be employed for the prediction of drug-induced myelotoxicity. In addition, several important molecular descriptors and substructures of myelotoxic compounds have been identified, which should be taken into consideration in the design of new candidate compounds to produce safer and more effective drugs, ultimately reducing the attrition rate in later stages of drug development.

Target of rapamycin coordinates auxin are involved in exogenous melatonin regulated low temperature tolerance in cucumber seedlings.

Low temperature (LT) is an important environmental factor affecting the growth and yield of plants. Melatonin (MT) can effectively enhance the LT tolerance of cucumber. This study found that LT stress induced the expression of Comt1 (caffeic acid O-methyltransferase 1), with the highest expression being about 2-times that of the control. Meanwhile, the content of MT was found to be roughly 63.16% of that in the control samples. Compared with LT treatment alone, exogenous MT pretreatment upregulated the expression levels of TOR (Target of rapamycin), PIN1 (Pin-formed 1), and YUC4 (YUCCA 4), with maximum upregulations reaching approximately 66.67%, 79.32%, and 42.86%, respectively. These results suggest that MT may modulate the tolerance of cucumber seedlings to LT stress by regulating the expression of TOR, PIN1, and YUC4. In addition, co-treatment with AZD-8055 (a TOR inhibitor) or NPA (N-1-naphthylphthalamic acid, an auxin polar transport inhibitor) and MT attenuated MT-induced resistance to LT stress, leading to higher levels of reactive oxygen species (ROS), reduced antioxidant defense capacity, and increased damage to the membrane system in cucumber seedlings. Concurrently, the content of osmoregulatory substances and the photosynthesis decreased. These results demonstrate that both TOR and auxin were required for MT to alleviate LT-induced damage in cucumber. In summary, the present study demonstrates that TOR and auxin signaling synergistically contribute to alleviating LT damage in cucumber seedlings by exogenous MT. These findings help us understand the function of MT and provide insights into the regulatory network of MT that regulates the LT tolerance of plants.

Melatonin-mediated low-temperature tolerance of cucumber seedlings requires Ca2+/CPKs signaling pathway.

Melatonin (Mel) is recognized as a prominent plant growth regulator. This study investigated the alleviating effect of Mel pretreatment on growth inhibition caused by low-temperature (LT) stress (10 °C/6 °C) in cucumber seedlings and explored the role of the Ca2+/Calcium-dependent protein kinases (CPKs) signaling pathway in Mel-regulated LT tolerance. The main results are as follows: compared to LT treatment alone, 100 µM Mel increased both the content of Ca2+ (highest about 42.01%) and the expression levels of Ca2+ transporter and cyclic nucleotide-gated channel (CNGC) genes under LT. Similarly, Mel enhanced the content of CPKs (highest about 27.49%) and the expression levels of CPKs family genes in cucumber leaves under LT. Additionally, pretreatment with 100 µM Mel for three days strengthened the antioxidant defense and photosynthesis of seedlings under LT. Genes in the ICE-CBF-COR pathway and the MAPK cascade were upregulated by Mel, with maximum upregulations reaching approximately 2.5-fold and 1.9-fold, respectively, thus conferring LT tolerance to cucumber seedlings. However, the above beneficial effects of Mel were weakened by co-treatment with calcium signaling blockers (LaCl3 or EGTA) or CPKs inhibitors (TFP or W-7), suggesting that the Ca2+/CPKs pathway is involved in the Mel-mediated regulation of LT tolerance. In conclusion, this study revealed that Mel can alleviate growth inhibition in cucumber seedlings under LT stress and demonstrated that the Ca2+/CPKs signaling pathway is crucial for the Mel-mediated enhancement of LT tolerance. The findings hold promise for providing theoretical insights into the application of Mel in agricultural production and for investigating its underlying mechanisms of action.

Identification and expression analysis of MAPK cascade gene family in foxtail millet (Setaria italica).

The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including Arabidopsis thaliana, Oryza sativa, and Triticum aestivum, but have not been identified in foxtail millet (Setaria italica). In this study, a total of 93 MAPK cascade genes, including 15 SiMAPKs, 10 SiMAPKKs and 68 SiMAPKKKs genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the SiMAPKs and SiMAPKKs into four subgroups, respectively, and the SiMAPKKKs into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most SiMAPKs and SiMAPKKs were changed under both exogenous hormone and abiotic stress treatments, with SiMAPK3 and SiMAPKK4-2 being induced under almost all treatments, while the expression of SiMAPKK5 was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet (Setaria italica).

GR24-mediated enhancement of salt tolerance and roles of H2O2 and Ca2+ in regulating this enhancement in cucumber.

This study investigated the regulation of the exogenous strigolactone (SL) analog GR24 in enhancing the salt tolerance and the effects of calcium ion (Ca2+) and hydrogen peroxide (H2O2) on GR24's regulation effects in cucumber. The seedlings were sprayed with (1) distilled water (CK), (2) NaCl, (3) GR24, then NaCl, (4) GR24, then H2O2 scavenger, then NaCl, and (5) GR24, then Ca2+ blocker, then NaCl. The second true leaf was selected for biochemical assays. Under the salt stress, the exogenous GR24 maintained the ion balance, increased the activity of antioxidant enzymes, reduced the membrane lipid peroxidation, and increased the activities of catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX), accompanied by a decrease in relative conductivity, an increase in the proline content, and elevated gene expression levels of antioxidant enzymes, nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, calcium-dependent protein kinases (CDPKs), salt overly sensitive SOS1, CBL-interacting protein kinase 2 (CIPK2), and calcineurin B-like protein 3 (CBL3). Such protective effects triggered by GR24 were attenuated or almost abolished by ethylene glycol tetraacetic acid (EGTA), lanthanum chloride (LaCl3, Ca2+ channel blocker), diphenyleneiodonium (DPI, NADPH oxidase inhibitor), and dimethylthiourea (DMTU, hydroxyl radical scavenger). Our data suggest that exogenous GR24 is highly effective in alleviating salt-induced damages via modulating antioxidant capabilities and improving ionic homeostasis and osmotic balance and that H2O2 and Ca2+ are required for GR24-mediated enhancement of salt tolerance.

Involvement of NO and Ca2+ in the enhancement of cold tolerance induced by melatonin in winter turnip rape (Brassica rapa L.).

As a multifunctional phytohormone, melatonin (Mel) plays pivotal roles in plant responses to multiple stresses. However, its mechanism of action remains elusive. In the present study, we evaluated the role of NO and Ca2+ signaling in Mel enhanced cold tolerance in winter turnip rape. The results showed that the NO content and concentration of intracellular free Ca2+ ([Ca2+]cyt) increased by 35.42% and 30.87%, respectively, in the leaves of rape seedlings exposed to cold stress. Compared with those of the seedlings in cold stress alone, the NO content and concentration of [Ca2+]cyt in rape seedlings pretreated with Mel increased further. In addition, the Mel-mediated improvement of cold tolerance was inhibited by L-NAME (a NO synthase inhibitor), tungstate (a nitrate reductase inhibitor), LaCl3 (a Ca2+ channel blocker), and EGTA (a Ca2+ chelator), and this finding was mainly reflected in the increase in ROS content and the decrease in osmoregulatory capacity, photosynthetic efficiency and antioxidant enzyme activities, and expression levels of antioxidant enzyme genes. These findings suggest that NO and Ca2+ are necessary for Mel to improve cold tolerance and function synergistically downstream of Mel. Notably, the co-treatment of Mel with L-NAME, tungstate, LaCl3, or EGTA also inhibited the Mel-induced expression of MAPK3/6 under cold stress. In conclusion, NO and Ca2+ are involved in the enhancement of cold tolerance induced by Mel through activating the MAPK cascades in rape seedlings, and a crosstalk may exist between NO and Ca2+ signaling.

Effects of salt and drought stresses on antioxidant system and RbohC and RbohF genes expression in Brassica campestris.

To investigate the effects of salt stress and PEG-6000 simulating drought stress on the active oxygen and antioxidant enzyme activities, as well as the expression level of RbohC and RbohF genes, the seedlings of two Brassica campestris, Longyou 6 and Tianyou 2, were treated with U0126 (a MAPKK inhibitor), DMTU (a H2O2 scavenger), as well as DPI and IMD (NADPH oxidase inhibitors). The results showed that under both stresses, H2O2 accumulation as well as antioxidant enzyme (SOD, CAT, APX, GR) activities and the expression of RbohC and RbohF genes increased, while O2-· accumulation decreased. The O2-· accumulation, antioxidant enzyme activity and RbohC and RbohF genes expression in both varieties all significantly decreased. Compared to seedlings with on pretreatment before salt and PEG-6000 simulating drought stress, the accumulation of H2O2 decreased in seedlings pretreated with DMTU, DPI and IMD. However, the accumulation of H2O2 increased in those pretreated with U0126. Those results indicated that the NADPH oxidase, MAP kinase cascade and H2O2 were involved in the regulation of active oxygen production and antioxidant enzyme activity, as well as the expression of RbohC and RbohF under salt stress and drought stress.

[Effects of diverse stresses on gene expression and enzyme activity of glutathione reductase in Brassica campestris.] / é€†å¢ƒèƒè¿«å¯¹æ²¹èœè°·èƒ±ç”˜è‚½è¿˜åŽŸé ¶åŸºå› è¡¨è¾¾åŠå ¶é ¶æ´»æ€§çš„å½±å“.

A novel glutathione reductase gene (GR2) was isolated from Brassica campestris Longyou 6 by rapid isolation of cDNA ends (RACE). The full-length of cDNA of GR2 was 2073 bp, with an open reading frame (ORF) of 1692 bp. GR2 encoded a protein of 563 amino acids with a deduced molecular mass of about 60.7 kDa and an isoelectric point of 7.9. The real-time quantitative PCR results showed that GR2 was expressed in the roots, stems and leaves in B. campestris, among which the expression of GR2 in leaves was the highest. The transcript levels of GR1 and GR2, and the enzyme activity of glutathione reductase (GR) increased in response to cold temperature, high temperature, drought stress, and salt stress. The results suggested that GR played an important role in coping with diverse stresses in B. campestris. When abscisic acid (ABA) pretreatment was applied before cold temperature, high temperature, drought stress, salt stress, the expression levels of GR1and GR2, and the activity level of GR all significantly increased compared with the single stress, which indicated that ABA could induce GR1 and GR2 gene transcription and GR activity. However, when MAPKK inhibitor (U0126) pretreatment was applied before the above stresses, the expression levels of GR1and GR2 and the activity level of GR significantly decreased compared with the single stress suggesting that U0126 inhibited GR1 and GR2 gene transcription and GR activity.

Novel naïve Bayes classification models for predicting the chemical Ames mutagenicity.

Prediction of drug candidates for mutagenicity is a regulatory requirement since mutagenic compounds could pose a toxic risk to humans. The aim of this investigation was to develop a novel prediction model of mutagenicity by using a naïve Bayes classifier. The established model was validated by the internal 5-fold cross validation and external test sets. For comparison, the recursive partitioning classifier prediction model was also established and other various reported prediction models of mutagenicity were collected. Among these methods, the prediction performance of naïve Bayes classifier established here displayed very well and stable, which yielded average overall prediction accuracies for the internal 5-fold cross validation of the training set and external test set I set were 89.1±0.4% and 77.3±1.5%, respectively. The concordance of the external test set II with 446 marketed drugs was 90.9±0.3%. In addition, four simple molecular descriptors (e.g., Apol, No. of H donors, Num-Rings and Wiener) related to mutagenicity and five representative substructures of mutagens (e.g., aromatic nitro, hydroxyl amine, nitroso, aromatic amine and N-methyl-N-methylenemethanaminum) produced by ECFP_14 fingerprints were identified. We hope the established naïve Bayes prediction model can be applied to risk assessment processes; and the obtained important information of mutagenic chemicals can guide the design of chemical libraries for hit and lead optimization.