DeteX: A highly accurate software for detecting SNV and InDel in single and paired NGS data in cancer research

Background: Genetic testing is becoming more and more accepted in the auxiliary diagnosis and treatment of tumors. Due to the different performance of the existing bioinformatics software and the different analysis results, the needs of clinical diagnosis and treatment cannot be met. To this end, we combined Bayesian classification model (BC) and fisher exact test (FET), and develop an efficient software DeteX to detect SNV and InDel mutations. It can detect the somatic mutations in tumor-normal paired samples as well as mutations in a single sample.Methods: Combination of Bayesian classification model (BC) and fisher exact test (FET).Results: We detected SNVs and InDels in 11 TCGA glioma samples, 28 clinically targeted capture samples and 2 NCCL-EQA standard samples with DeteX, VarDict, Mutect, VarScan and GatkSNV. The results show that, among the three groups of samples, DeteX has higher sensitivity and precision whether it detects SNVs or InDels than other callers and the F1 value of DeteX is the highest. Especially in the detection of substitution and complex mutations, only DeteX can accurately detect these two kinds of mutations. In terms of single-sample mutation detection, DeteX is much more sensitive than the HaplotypeCaller program in Gatk. In addition, although DeteX has higher mutation detection capabilities, its running time is only .609 of VarDict, which is .704 and .343 longer than VarScan and MuTect, respectively.Conclusion: In this study, we developed DeteX to detect SNV and InDel mutations in single and paired samples. DeteX has high sensitivity and precision especially in the detection of substitution and complex mutations. In summary, DeteX from NGS data is a good SNV and InDel caller

Effects of Low-Salinity Stress on Histology and Metabolomics in the Intestine of <i>Fenneropenaeus chinensis</i>

Metabolomics has been used extensively to identify crucial molecules and biochemical effects induced by environmental factors. To understand the effects of acute low-salinity stress on Fenneropenaeus chinensis, intestinal histological examination and untargeted metabonomic analysis of F. chinensis were performed after exposure to a salinity of 15 ppt for 3, 7, and 14 d. The histological examination revealed that acute stress resulted in most epithelial cells rupturing, leading to the dispersion of nuclei in the intestinal lumen after 14 days. Metabolomics analysis identified numerous differentially expressed metabolites (DEMs) at different time points after exposure to low-salinity stress, in which some DEMs were steadily downregulated at the early stage of stress and then gradually upregulated. We further screened 14 overlapping DEMs, in which other DEMs decreased significantly during low-salinity stress, apart from L-palmitoylcarnitine and vitamin A, with enrichments in phenylalanine, tyrosine and tryptophan biosynthesis, fatty acid and retinol metabolism, and ABC transporters. ABC transporters exhibit significant abnormalities and play a vital role in low-salinity stress. This study provides valuable insights into the molecular mechanisms underlying the responses of F. chinensis to acute salinity stress

Thin Films with Low Zn Content Prepared by Chemical Bath Deposition

Chemical bath deposition (CBD) was used for the growth of thin films with low Zn content. The influence of preparation conditions, such as pH, temperature, and concentration, on film properties was investigated. The chemical growth mechanism of thin films was analyzed, and optimized growth conditions for the thin films were established. The fill factor and short-circuit current were improved while was used to replace CdS as the window layer in CdTe solar cells

Genome-wide identification of ATG genes and their expression profiles under biotic and abiotic stresses in Fenneropenaeus chinensis

Abstract Background Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. Extensive research has shown that autophagy plays a pivotal role in both viral infection and replication processes. Despite the increasing research dedicated to autophagy, investigations into shrimp autophagy are relatively scarce. Results Based on three different methods, a total of 20 members of the ATGs were identified from F. chinensis, all of which contained an autophagy domain. These genes were divided into 18 subfamilies based on their different C-terminal domains, and were found to be located on 16 chromosomes. Quantitative real-time PCR (qRT-PCR) results showed that ATG genes were extensively distributed in all the tested tissues, with the highest expression levels were detected in muscle and eyestalk. To clarify the comprehensive roles of ATG genes upon biotic and abiotic stresses, we examined their expression patterns. The expression levels of multiple ATGs showed an initial increase followed by a decrease, with the highest expression levels observed at 6 h and/or 24 h after WSSV injection. The expression levels of three genes (ATG1, ATG3, and ATG4B) gradually increased until 60 h after injection. Under low-salt conditions, 12 ATG genes were significantly induced, and their transcription abundance peaked at 96 h after treatment. Conclusions These results suggested that ATG genes may have significant roles in responding to various environmental stressors. Overall, this study provides a thorough characterization and expression analysis of ATG genes in F. chinensis, laying a strong foundation for further functional studies and promising potential in innate immunity

Detection of Potential Mutated Genes Associated with Common Immunotherapy Biomarkers in Non-Small-Cell Lung Cancer Patients

Microsatellite instability (MSI), high tumor mutation burden (TMB-H) and programmed cell death 1 ligand 1 (PD-L1) expression are hot biomarkers related to the improvement of immunotherapy response. Two cohorts of non-small-cell lung cancer (NSCLC) were collected and sequenced via targeted next-generation sequencing. Drug analysis was then performed on the shared genes using three different databases: Drugbank, DEPO and DRUGSURV. A total of 27 common genes were mutated in at least two groups of TMB-H-, MSI- and PD-L1-positive groups. AKT1, SMAD4, SCRIB and AXIN2 were severally involved in PI3K-activated, transforming growth factor beta (TGF-&beta;)-activated, Hippo-repressed and Wnt-repressed pathways. This study provides an understanding of the mutated genes related to the immunotherapy biomarkers of NSCLC

Effect of cosmic rays irradiation on the phase change characteristics of an on-orbit fixed point

Using the phase change characteristics of fixed points to trace the temperature of a spaceborne calibration blackbody is an important technical means to carry out the high-precision on-orbit calibration of thermal infrared remote sensors. In contrast to an experimental environment on the ground, a fixed point will produce radiation damage in the high-energy cosmic rays environment and may affect the phase change characteristics. This study investigates the effect of radiation damage caused by cosmic rays irradiation on the phase change characteristics of fixed points in a spaceborne calibration blackbody. In this research, the simulation method of molecular dynamics was used to simulate the irradiation damage effect of a strong cosmic rays environment on fixed-point indium (In). The experimental system was established to measure the phase change curves of samples with different irradiation doses, and then, the influence of irradiation on the phase change characteristics of the samples was analyzed. The results showed that most of the energy of irradiation was deposited on the In fixed point, resulting in the migration of 0.3% of the displacement atoms inside the In to the gap position to form the Frenkel pairs (FPs). The overcooling of the irradiated In fixed point was reduced by 0.3 $$^\circ \hbox {C}$$, the phase change temperature was increased by 30 mK, and the phase change plateau was more stable

SmMYB4 Is a R2R3-MYB Transcriptional Repressor Regulating the Biosynthesis of Phenolic Acids and Tanshinones in Salvia miltiorrhiza

Salvia miltiorrhiza Bunge is one of the most famous traditional Chinese medicinal plants. The two most important classes of pharmaceutically relevant compounds in S. miltiorrhiza are phenolic acids and tanshinones. The MYB family of transcription factors may efficiently regulate the secondary metabolism in plants. In this study, a subgroup 4 R2R3MYB transcription factor gene, SmMYB4, was isolated from S. miltiorrhiza and functionally characterized using overexpression and a RNAi-mediated silencing. We achieved a total of six overexpressions and eight RNAi transgenic lines from the Agrobacterium leaf disc method. The content of the total phenolics, rosmarinic acid, and salvianolic acid B markedly decreased in the SmMYB4-overexpressing lines but increased in the SmMYB4-RNAi lines. The content of the total tanshinones, cryptotanshinone, and tanshinone IIA decreased in the SmMYB4-overexpressing transgenic lines but increased in the SmMYB4-RNAi lines. A gene expression analysis demonstrated that SmMYB4 negatively regulated the transcription of the critical enzyme genes involved in the phenolic acid and tanshinone biosynthesis. The genetic control of this transcriptional repressor may be used to improve the content of these bioactive compounds in the cultivated S. miltiorrhiza

Genome-Wide Characterization of B-Box Gene Family in Salvia miltiorrhiza

B-box (BBX) is a type of zinc finger transcription factor that contains a B-box domain. BBX transcription factors play important roles in plant photomorphogenesis, signal transduction, as well as abiotic and biological stress responses. However, the BBX gene family of Salvia miltiorrhiza has not been systematically investigated to date. For this study, based on the genomic data of Salvia miltiorrhiza, 27 SmBBXs genes were identified and clustered into five evolutionary branches according to phylogenetic analysis. The promoter analysis suggested that SmBBXs may be involved in the regulation of the light responses, hormones, stress signals, and tissue-specific development. Based on the transcriptome data, the expression patterns of SmBBXs under different abiotic stresses and plant hormones were analyzed. The results revealed that the expressions of the SmBBXs genes varied under different conditions and may play essential roles in growth and development. The transient expression analysis implied that SmBBX1, SmBBX4, SmBBX9, SmBBX20, and SmBBX27 were in the nucleus. A transcriptional activation assay showed SmBBX1, SmBBX4, SmBBX20, and SmBBX24 had transactivation activities, while SmBBX27 had none. These results provided a basis for further research on the role of SmBBXs in the development of Salvia miltiorrhiza