Determination of internal controls for quantitative gene expression of Spodoptera litura under microbial pesticide stress.

Quantitative real-time polymerase chain reaction (qRT-PCR) has become a commonly used method for the quantification of gene expression. However, accurate qRT-PCR analysis requires a valid internal reference for data normalization. To determine the valid reference characterized with low expression variability among Spodoptera litura samples after microbial pesticide treatments, nine housekeeping genes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), arginine kinase, ubiquitin C, actin-5C (ACT5C), actin, ribosomal protein S13 (RPS13), tubulin, acidic ribosomal protein P0 (RPLP0) and ubiquinol-cytochrome c reductase, were evaluated for their suitability using geNorm, Normfinder, BestKeeper, RefFinder and the comparative delta CT methods in this study. S. litura larvae after direct treatment (larvae were immersed in biopesticides), indirect treatment (larvae were fed with biopesticide immersed artificial diets) and comprehensive treatment (larvae were treated with the first two treatments in sequence), respectively with Metarhizium anisopliae, Empedobacter brevis and Bacillus thuringiensis, were investigated. The results indicated that the best sets of internal references were as follows: RPLP0 and ACT5C for direct treatment conditions; RPLP0 and RPS13 for indirect treatment conditions; RPS13 and GAPDH for comprehensive treatment conditions; RPS13 and RPLP0 for all the samples. These results provide valuable bases for further genetic researches in S. litura.

Prediction of TTF-1 expression in non-small-cell lung cancer using machine learning-based radiomics.

PURPOSE: To explore the feasibility and performance of machine learning-based radiomics models in predicting thyroid transcription factor-1 (TTF-1) expression in non-small cell lung cancer (NSCLC). METHODS: A total of 227 NSCLC patients were included in this retrospective study and divided into the training set and test set with a ratio of 8:2 randomly. Lung tumors on CT images were semi-automatic segmented utilizing 3D Slicer. Radiomic features quantifying tumor intensity, shape, texture, and transformed wavelet were extracted using a Python toolkit. Variance threshold (VT), principal component analysis (PCA), and least absolute shrinkage selection operator (LASSO) were used to reduce features; logistic regression (LR), random forest (RF), and support vector machine (SVM) were used to develop classifier, respectively. The performance of the models was evaluated by areas under the curves (AUC) of receiver operating characteristic (ROC) curves. Different models were compared by the Delong test to determine the optimal algorithms. RESULTS: Total 1968 radiomic features were extracted from the lung tumors images, and then 13, 15, and 13 stable features were selected by VT, PCA, and LASSO, respectively. Each classifier could discriminate against the TTF-1-positive groups with average AUC ranging from 0.601 to 0.784 in the training set. Among the models, three models constructed by the LASSO method showed satisfactory performance in the test set with AUC ranging from 0.715 to 0.787. The Delong test showed no significant difference between the LASSO models (P > 0.05). CONCLUSION: Machine learning-based radiomics model could predict the expression of TTF-1 in NSCLC patients.

Expression of cotton PLATZ1 in transgenic Arabidopsis reduces sensitivity to osmotic and salt stress for germination and seedling establishment associated with modification of the abscisic acid, gibberellin, and ethylene signalling pathways.

BACKGROUND: Zinc-finger transcription factors play central roles in plant growth, development and abiotic stress responses. PLATZ encodes a class of plant-specific zinc-finger transcription factor. However, biological functions or physiological mechanism controlled by PLATZ are currently limited. RESULTS: GhPLATZ1 transcripts were considerably up-regulated by NaCl, mannitol, abscisic acid (ABA) and gibberellin (GA) treatments. Transgenic Arabidopsis by ectopic expression of GhPLATZ1 exhibited faster seed germination and higher seedling establishment under salt and mannitol stresses than those of wild type (WT), indicating enhanced osmotic insensitivity in GhPLATZ1 transgenic Arabidopsis. The ABA content in dry seeds of GhPLATZ1 transgenic Arabidopsis was lower than that of WT whereas the ABA content was not changed in germinating seeds under salt stress. Seed germination was faster than but the seedling establishment of transgenic Arabidopsis was similar to WT. Besides, GhPLATZ1 transgenic and WT Arabidopsis exhibited insensitivity to paclobutrazol (PAC), a GA biosynthesis inhibitor, whereas exogenous GA could eliminate the growth difference between GhPLATZ1 transgenic and WT Arabidopsis under salt stress. Moreover, exogenous 1-aminocyclopropane-1-carboxylic acid (ACC), an ethylene precursor, exerted similar effects to GA. Furthermore, ABI4 and ETO1 transcripts were significantly down-regulated, whereas ACS8 was up-regulated in GhPLATZ1 transgenic Arabidopsis under salt stress. CONCLUSIONS: In conclusion, GhPLATZ1 had broad influence in responses to salt and mannitol stresses in transgenic Arabidopsis during seed germination and seedling establishment. The effect of GhPLATZ1 expression in transgenic Arabidopsis might be mediated by the ABA, GA, and ethylene pathways. Thus, this study provided new insights into the regulatory network in response to abiotic stresses in plants.

Delayed germination of Arabidopsis seeds under chilling stress by overexpressing an abiotic stress inducible GhTPS11.

Trehalose-6-phosphate synthase (TPS) plays an important role in metabolic regulation and stress responses in a variety of organisms. However information about cotton TPS is poor. Here a cotton TPS gene GhTPS11 was isolated and characterized. Expression analysis revealed that GhTPS11 was induced in 20-day old cotton seedlings by heat drought and high salt stresses as well as GA and ABA. Moreover GhTPS11 was induced by chilling stress and mannitol while was depressed by sucrose. Tissue expression analysis indicated that GhTPS11 expressed higher in leaves than in stems and roots of 20-day old cotton seedlings. The GhTPS11 overexpressing Arabidopsis seeds germinated slower than the wild-type (WT) under chilling stress. Trehalose-6-phosphate (T6P) and trehalose contents were evidently higher in GhTPS11 overexpressing lines 3, 5, and 22 than in WT under normal germination condition as well as chilling stress. Further analysis demonstrated that the expression of ICE1 CBF3 and RCI2A was induced lower whereas that of CBF1 and CBF2 was induced higher under chilling stress in the GhTPS11 overexpressing seeds than WT respectively. These results suggested that GhTPS11 encoded a stress-responsive TPS protein and functioned in chilling stress during seed germination. Perhaps the chilling stress sensitivity of transgenic Arabidopsis seeds was caused by the expression changes of at least some chilling-related genes such as ICE1 CBFs and RCI2A other than HOS1. So this article provided the useful information for GhTPS11 usage for crop molecular breeding.

DJ-1: a promising marker in metastatic uveal melanoma.

PURPOSE: Overexpression of DJ-1 was associated with metastatic uveal melanoma (UM). The purpose of this study was to evaluate the potential of serum DJ-1 as a biomarker for metastasis of uveal melanoma. METHODS: Serum DJ-1 levels were determined by ELISA assays in 27 patients with metastatic UM metastatic uveal melanoma and in 76 patients who were disease free for at least 10 years and 30 age- and sex-matched controls. Receiver operating characteristic (ROC) curve was used to evaluate the feasibility of DJ-1 in detection of metastatic uveal melanoma. RESULTS: Serum DJ-1 levels were significantly higher in patients with metastatic UM compared with patients who were disease free for at least 10 years (P < 0.001) or with controls (P < 0.001). ROC curve for DJ-1 revealed an area under the curve of 86.3%, and when 3.350 ng/mL was used as the cutoff value, a sensitivity of 74.1% and a specificity of 94.3% were achieved. Comparison of DJ-1 and liver function tests (LFTs) ROC curves indicated that DJ-1 was superior to LFTs in detection of metastatic UM. CONCLUSIONS: Our data suggest that DJ-1 might be a promising serum marker for monitoring metastatic uveal melanoma.

Serum YKL-40 independently predicts outcome after transcatheter arterial chemoembolization of hepatocellular carcinoma.

BACKGROUND: Transcatheter arterial chemoembolization (TACE) is the most widely used treatment option for unresectable hepatocellular carcinoma (HCC). Elevated serum YKL-40 level has been shown to predict poor prognosis in HCC patients undergoing resection. This study was designed to validate the prognostic significance of serum YKL-40 in patients with HCC undergoing TACE treatment. METHODS: Serum YKL-40 level was determined by enzyme-linked immunosorbent assay. Overall survival (OS) was evaluated with the Kaplan-Meier method and compared by the log-rank test. Multivariate study with Cox proportional hazard model was used to evaluate independent prognostic variables of OS. RESULTS: The median pretreatment serum YKL-40 in HCC patients with was significantly higher than that in healthy controls (P<0.001). The YKL-40 could predict survival precisely either in a dichotomized or continuous fashion (P<0.001 and P = 0.001, respectively). Multivariate Cox regression analysis indicated that serum YKL-40 was an independent prognostic factor for OS in HCC patients (P = 0.001). In further stratified analyses, YKL-40 could discriminate the outcomes of patients with low and high alpha-fetoprotein (AFP) level (P = 0.006 and 0.016, respectively). Furthermore, the combination of serum YKL-40 and AFP had more capacity to predict patients' outcomes. CONCLUSIONS: Serum YKL-40 was demonstrated to be an independent prognostic biomarker in HCC patients treated with TACE. Our results need confirmation in an independent study.