A pipeline for improved QSAR analysis of peptides: physiochemical property parameter selection via BMSF, near-neighbor sample selection via semivariogram, and weighted SVR regression and prediction

In this paper, we present a pipeline to perform improved QSAR analysis of peptides. The modeling involves a double selection procedure that first performs feature selection and then conducts sample selection before the final regression analysis. Five hundred and thirty-one physicochemical property parameters of amino acids were used as descriptors to characterize the structure of peptides. These high-dimensional descriptors then go through a feature selection process given by the Binary Matrix Shuffling Filter (BMSF) to obtain a set of important low dimensional features. Each descriptor that passed the BMSF filtering also receives a weight defined through its contribution to reduce the estimation error. These selected features were served as the predictors for subsequent sample selection and modeling. Based on the weighted Euclidean distances between samples, a common range was determined with high-dimensional semivariogram and then used as a threshold to select the near-neighbor samples from the training set. For each sample to be predicted, the QSAR model was established using SVR with the weighted, selected features based on the exclusive set of near-neighbor training samples. Prediction was conducted for each test sample accordingly. The performances of this pipeline are tested with the QSAR analysis of angiotensin-converting enzyme (ACE) inhibitors and HLA-A*0201 data sets. Improved prediction accuracy was obtained in both applications. This pipeline can optimize the QSAR modeling from both the feature selection and sample selection perspectives. This leads to improved accuracy over single selection methods. We expect this pipeline to have extensive application prospect in the field of regression prediction

Photocatalytic Degradation of Dimethoate in Bok Choy Using Cerium-Doped Nano Titanium Dioxide

Dimethoate, a systemic insecticide, has been used extensively in vegetable production. Insecticide residues in treated vegetables, however, pose a potential risk to consumers. Photocatalytic degradation is a new alternative to managing pesticide residues. In this study, the degradation of dimethoate in Bok choy was investigated under the field conditions using cerium-doped nano titanium dioxide (TiO2/Ce) hydrosol as a photocatalyst. The results show that TiO2/Ce hydrosol can accelerate the degradation of dimethoate in Bok choy. Specifically, the application of TiO2/Ce hydrosol significantly increased the reactive oxygen species (ROS) contents in the treated Bok choy, which speeds up the degradation of dimethoate. Ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) analysis detected three major degradation products, including omethoate, O,O,S-trimethyl thiophosphorothioate, and 1,2-Bis (acetyl-N-methyl-) methane disulfide. Two potential photodegradation pathways have been proposed based on the intermediate products. To understand the relationship between photodegradation and the molecular structure of target insecticides, we investigated the bond length, Mulliken atomic charge and frontier electron density of dimethoate using ab initio quantum analysis. These results suggest the P = S, P-S and S-C of dimethoate are the initiation sites for the photocatalytic reaction in Bok choy, which is consistent with our empirical data

Metabolomic and transcriptomic analyses of rice plant interaction with invasive weed Leptochloa chinensis

IntroductionLeptochloa chinensis is an annual weed in paddy fields, which can engage in competition with rice, leading to a severe yield reduction. However, theunderlying mechanism governing this interaction remain unknown.MethodsIn this study, we investigated the mutual inhibition between rice and the weed undermono-culture and co-culture conditions. We found that the root exudates of both species played essential roles in mediating the mutual inhibition. Further metabolomic analysis identified a significant number of differential metabolites. These metabolites were predominantly enriched in the phenylpropanoid and flavonoid biosynthesis pathways in weed and rice. Transcriptomic analysis revealed that the differentially expressed genes responding to the interaction were also enriched in these pathways.ResultsPhenylpropanoid and flavonoid biosynthesis pathways are associated with allelopathy, indicating their pivotal role in the response of rice-weed mutual inhibition.DiscussionOur findings shed light on the conserved molecular responses of rice and L. chinensis during theirinteraction, provide evidence to dissect the mechanisms underlying the allelopathic interaction and offer potential strategies for weed management in rice paddies

Weed genomics : yielding insights into the genetics of weedy traits for crop improvement

Weeds cause tremendous economic and ecological damage worldwide. The number of genomes established for weed species has sharply increased during the recent decade, with some 26 weed species having been sequenced and de novo genomes assembled. These genomes range from 270 Mb (Barbarea vulgaris) to almost 4.4 Gb (Aegilops tauschii). Importantly, chromosome-level assemblies are now available for 17 of these 26 species, and genomic investigations on weed populations have been conducted in at least 12 species. The resulting genomic data have greatly facilitated studies of weed management and biology, especially origin and evolution. Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement. In this review, we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field

Photocatalytic Degradation of Profenofos and Triazophos Residues in the Chinese Cabbage, \u3cem\u3eBrassica chinensis\u3c/em\u3e, Using Ce-Doped TiO\u3csub\u3e2\u3c/sub\u3e

Pesticides have revolutionized the modern day of agriculture and substantially reduced crop losses. Synthetic pesticides pose a potential risk to the ecosystem and to the non-target organisms due to their persistency and bioaccumulation in the environment. In recent years, a light-mediated advanced oxidation processes (AOPs) has been adopted to resolve pesticide residue issues in the field. Among the current available semiconductors, titanium dioxide (TiO2) is one of the most promising photocatalysts. In this study, we investigated the photocatalytic degradation of profenofos and triazophos residues in Chinese cabbage, Brassica chinensis, using a Cerium-doped nano semiconductor TiO2 (TiO2/Ce) under the field conditions. The results showed that the degradation efficiency of these organophosphate pesticides in B. chinensis was significantly enhanced in the presence of TiO2/Ce. Specifically, the reactive oxygen species (ROS) contents were significantly increased in B. chinensis with TiO2/Ce treatment, accelerating the degradation of profenofos and triazophos. Ultra-performance liquid chromatography–mass spectroscopy (UPLC-MS) analysis detected 4-bromo-2-chlorophenol and 1-phenyl-3-hydroxy-1,2,4-triazole, the major photodegradation byproducts of profenofos and triazophos, respectively. To better understand the relationship between photodegradation and the molecular structure of these organophosphate pesticides, we investigated the spatial configuration, the bond length and Mulliken atomic charge using quantum chemistry. Ab initio analysis suggests that the bonds connected by P atom of profenofos/triazophos are the initiation cleavage site for photocatalytic degradation in B. chinensis

Reference Gene Selection for qRT-PCR Analysis in the Sweetpotato Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae)

BACKGROUND: Accurate evaluation of gene expression requires normalization relative to the expression of reliable reference genes. Expression levels of classical reference genes can differ, however, across experimental conditions. Although quantitative real-time PCR (qRT-PCR) has been used extensively to decipher gene function in the sweetpotato whitefly Bemisia tabaci, a world-wide pest in many agricultural systems, the stability of its reference genes has rarely been validated. RESULTS: In this study, 15 candidate reference genes from B. tabaci were evaluated using two Excel-based algorithms geNorm and Normfinder under a diverse set of biotic and abiotic conditions. At least two reference genes were selected to normalize gene expressions in B. tabaci under experimental conditions. Specifically, for biotic conditions including host plant, acquisition of a plant virus, developmental stage, tissue (body region of the adult), and whitefly biotype, ribosomal protein L29 was the most stable reference gene. In contrast, the expression of elongation factor 1 alpha, peptidylprolyl isomerase A, NADH dehydrogenase, succinate dehydrogenase complex subunit A and heat shock protein 40 were consistently stable across various abiotic conditions including photoperiod, temperature, and insecticide susceptibility. CONCLUSION: Our finding is the first step toward establishing a standardized quantitative real-time PCR procedure following the MIQE (Minimum Information for publication of Quantitative real time PCR Experiments) guideline in an agriculturally important insect pest, and provides a solid foundation for future RNA interference based functional study in B. tabaci

High-accuracy splice sites prediction based on sequence component and position features

Identification of splice sites plays a key role in annotation of genes and hence, the improvement of computational prediction of splice sites with high accuracy has great significance. In this article, we first quantitatively determined the length of window and the number and position of the consensus bases by a Chi-square test, and then extracted the sequence multi-scale component (MSC) features and the position (Pos) and adjacent positions relationship (APR) features of consensus sites. Then we constructed a novel classification model using SVM with above features and applied it to the HS³D dataset. Compared with the results in current literatures, our method produces a great improvement in the 10-fold cross validation accuracies for training sets with true and spurious splice sites of both equal and different-proportions. This method was also applied to the NN269 dataset for further evaluation and independent test. The obtained results are superior to those in literature, which demonstrates the stability and superiority of this method. Satisfying results show that our method has high accuracy for prediction of splice sites

The Pro-197-Thr mutation in the ALS gene confers novel resistance patterns to ALS-inhibiting herbicides in Bromus japonicus in China

IntroductionBromus japonicus is one of the most notorious agricultural weeds in China. The long-term use of ALS-inhibiting herbicides has led to rapid evolution of herbicide resistance in B. japonicus. B. japonicus population (BJ-R) surviving mesosulfuron-methyl treatment was collected from wheatland. Here, we aimed to confirm the resistance mechanisms in this putative resistant population.MethodsThe dose-reponse tests were used to test the resistance level of the B. japonicus to ALS-inhibiting herbicides. Pretreatment with P450 and GST inhibitors and GST activity assays were used to determine whether P450 or GST was involved in the resistance of the BJ-R population. Sanger sequencing was used to analyse the ALS mutation of the BJ-R population. RT-qPCR was used to confirm the the expression levels of the ALS gene in mesosulfuron-methyl -resistant (BJ-R) and-susceptible (BJ-S) B. japonicus. An in vitro ALS activity assay was used to determine the ALS activity of the BJ-R and BJ-S populations. Homology modelling and docking were used to determine the binding energy of the BJ-R and BJ-S populations with ALS-inhibiting herbicides.ResultsB. japonicus population (BJ-R) was confirmed to be 454- and 2.7-fold resistant to the SU herbicides mesosulfuron-methyl and nicosulfuron, and 7.3-, 2.3-, 1.1- and 10.8-fold resistant to the IMI herbicide imazamox, the TP herbicide penoxsulam, the PTB herbicide pyribenzoxim and the SCT herbicide flucarbazone-sodium, respectively, compared with its susceptible counterpart (BJ-S). Neither a P450 inhibitor nor a GST inhibitor could reverse the level of resistance to mesosulfuron-methyl in BJ-R. In addition, no significant differences in GST activity were found between the BJ-R and BJ-S. ALS gene sequencing revealed a Pro-197-Thr mutation in BJ-R, and the gene expression had no significant differences between the BJ-R and BJ-S. The ALS activity of BJ-R was 106-fold more tolerant to mesosulfuron-methyl than that of BJ-S. Molecular docking showed that the binding energy of the ALS active site and mesosulfuron-methyl was changed from -6.67 to -4.57 kcal mol-1 due to the mutation at position 197.DiscussionThese results suggested that the Pro-197-Thr mutation was the main reason for the high resistance level of BJ-R to mesosulfuron-methyl. Unlike previous reports of the cross-resistance pattern conferred by this mutation, we firstly documented that the Pro-197-Thr mutation confers broad cross-resistance spectrums to ALS-inhibiting herbicides in B. japonicus