GATA3 somatic mutations are associated with clinicopathological features and expression profile in TCGA breast cancer patients

Acknowledgments This work was mainly conducted in a sabbatical period at the Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, Canada (FA), with the financial support from the Mashhad University of Medical Sciences, Mashhad, Iran. Authors gratefully acknowledge the use of data generated by TCGA Research Network (https://www.cancer.gov/tcga). Funding Information: This work was financially supported by Mashhad University of Medical Sciences under grant 931185. Supplementary Information: The online version contains supplementary material available at https://doi. org/10.1038/s41598-020-80680-9.Peer reviewedPublisher PD

De novo Transcriptome Assembly and Differential Expression Analysis of Catharanthus roseus in Response to Salicylic acid

Publication history: Accepted - 12 September 2022; Published online - 24 October 2022The anti-cancer vinblastine and vincristine alkaloids can only be naturally found in periwinkle (Catharanthus roseus). Both of these alkaloids' accumulations are known to be influenced by salicylic acid (SA). The transcriptome data to reveal the induction effect (s) of SA, however, seem restricted at this time. In this study, the de novo approach of transcriptome assembly was performed on the RNA-Sequencing (RNA-Seq) data in C. roseus. The outcome demonstrated that SA treatment boosted the expression of all the genes in the Terpenoid Indole Alkaloids (TIAs) pathway that produces the vinblastine and vincristine alkaloids. These outcomes supported the time-course measurements of vincristine alkaloid, the end product of the TIAs pathway, and demonstrated that SA spray had a positive impact on transcription and alkaloid synthesis. Additionally, the abundance of transcription factor families including bHLH, C3H, C2H2, MYB, MYB-related, AP2/ ERF, NAC, bZIP, and WRKY suggests a role for a variety of transcription families in response to the SA stimuli. Di-nucleotide and tri-nucleotide SSRs were the most prevalent SSR markers in microsatellite analyses, making up 39% and 34% of all SSR markers, respectively, out of the 77,192 total SSRs discovered

An Integrated Bioinformatics Approach to Identify Network Derived Hub Genes in Starving Zebrafish

The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein–protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ2 = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish

The Expression of Terpenoid Indole Alkaloid (TIAs) Pathway Genes in Catharanthus roseus in Response to Salicylic Acid treatment

Publication history: Accepted - 28th August 2020; Published online - 4th September.Vinblastine and vincristine are two important anti-cancer drugs that are synthesized by the Terpenoid Indole Alkaloids (TIAs) pathway in periwinkle (Catharanthus roseus). The major challenge in the pharmaceutical industry is the low production rate of these alkaloids. TIA pathway is affected by elicitors, such as salicylic acid (SA). This study aimed to investigate the expression pattern of some key genes in TIAs pathway under SA treatment. Foliar application of SA (0.01 and 0.1 mM) was used and leaves samples were taken at 0, 12, 18, 24 and 48 hours after the treatment. qRT-PCR was used to investigate the expression pattern of Chorismate mutase (Cm), Tryptophan decarboxylase (Tdc), Geraniol-10-hydroxylase (G10h), Secologanin synthase (Sls), Strictosidine synthase (Str), Desacetoxyvindoline-4-hydroxylase (D4h) and Deacetylvindoline-4-O-acetyltransferase (Dat) genes, following the SA treatment. The results of this experiment showed that transcript levels of Tdc, G10h, Sls, Str, D4h and Dat genes were significantly up-regulated in both SA concentration treatments. Furthermore, the highest transcript levels of Dat was observed after 48 hours of the SA treatments. qRT-PCR results suggests that SA induces transcription of major genes involved in alkaloids biosynthesis in Catharanthus roseus. It can be concluded that up-regulation of Tdc, G10h, Sls, Str, D4h and Dat genes can result in a higher production rate of vinblastine and vincristine alkaloids

Bioinformatics analysis of differentially gene expression profiles related to heat stress in brain, liver, and leg muscle of broiler chickens based on microarray technique

Publication history: Accepted - 5 August 2022; Published online - 23 September 2023.In the poultry industry, the heat stress caused by high environmental temperature has a negative influence on broiler chicken performance and has become a major challenge. Transcriptome profile analysis of the data and identification of patterns of differential gene expression in related tissues can be involved in the discovery of molecular mechanisms resistant to heat stress. The main purpose of this study was to use transcriptome profiles of three tissues brain, liver, and leg muscle of two groups of the control and heat stress broiler chickens to identify candidate genes associated with heat stress. By the analysis of microarray data to express the gene differences, 657 significant genes (P ± 2). Then, by studying the ontology of the relevant genes resulting from data analysis and literature mining as well as the reconstructed protein-protein interaction network, hub genes including NSDHL, DHCR24, LSS, FDPS, PCK1, ACTA1, HSP90AA1, HSPA2, HSPB1, HSF1, CRYAB, APOB, and IL6 were identified. Annotation results of these genes indicated that they have a role in the main process of metabolic and signaling pathways related to the ion transport system, steroid, antibodies, cholesterol biosynthesis, lipid metabolism, immune system function, and various signaling pathways such as MAP kinase, RET, and ERK. Overall, the present study can provide new insights into evidence of the pathways activated by these genes to identify effective genes and a better understanding of biological processes related to heat stress

Digestive function and serum biochemical parameters of juvenile Cyprinus carpio in response to substitution of dietary soybean meal with sesame seed (Sesamum indicum) cake

A feeding trial was designed to evaluate effects of soybean meal replacement (SBM) with sesame seed cake (SSC) at 0 (SSC0), 25 (SSC25), 50 (SSC50), 75 (SSC75), and 100 (SSC100) % in isoproteic (30%) and isolipidic (8%) diets on the growth performance, digestive function and serum and hematological parameters in Cyprinus carpio. Four hundred and fifty common carp juveniles (83.09 g) were randomly distributed into 15 tanks with a flow-through system. Triplicate groups of fish were hand-fed one of the diets to visual satiation thrice daily for 90 days. The survival rate, growth performance and somatic indices did not show significant differences between treatments. Among feed utilization indicators, nitrogen retention efficiency was significantly higher in SSC25 than in other treatments. Lipid retention efficiency significantly increased from SSC50 to SSC100. The number of white blood cells was significantly higher in SSC0 than other treatments. Significantly higher hemoglobin was observed in SSC75 as compared to SS0 and SSC25. Serum biochemical parameters did not significantly differ between dietary treatments. Dietary SSC resulted in significant increase in calcium ADC and activity of digestive trypsin, chymotrypsin, lipase, α-amylase, and alkaline phosphatase. Significantly higher villi height and intestinal muscle layer width were observed in fish fed the SSC75 diet. The villi width in SSC25 and SSC50 was significantly less than in SSC0. Comparable growth performance, feed utilization, apparent digestibility, digestive function, hematological and serum factors indicated the possibility of 75–100% substitution of SBM by SSC in the diet of juvenile C. carpio