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Objective To compare the three different methods for direct transfection of small exogenous nicotinamide adenine dinucleotide phosphate(NADPH) into cells by a non-metabolic pathway. Methods Three different transfection reagents (X-tremeGENETM HP DNA, LipofectamineTM RNAiMAX and LipofectamineTM 2000) were used to find the transfection efficiency of NADPH into human osteosarcoma cell line U2OS and mouse embryonic fibroblast cell line 3T3L1. Their effects on adipocyte differentiation were compared by Oil Red O staining. Results Transfection of NADPH with X-tremeGENE HP DNA transfection reagent effectively increased intracellular NADPH level(P＜0.001). With the increase of NADPH transfection concentration (10 μmol/L NADPH and 10 μL transfection reagent), the level of NADPH in cells increased in a dose-dependent manner. In addition, three transfection reagents were used to transfect NADPH in 3T3L1 preadipocytes. Only cells transfected with NADPH using X-tremeGENE HP DNA transfection reagent contained more lipids than control cells (P＜0.001). Conclusions Transfection of NADPH with X-tremeGENE HP DNA transfection reagent effectively increases the level of NADPH in cells.

Objective To study the expression of Xklp2 target protein (targeting protein for Xenopus kinesin-like protein2, TPX2) in pancreatic carcinoma and its potential value in predicting prognosis. Methods Based on 200 genes related to glycolysis, the information of pancreatic patients was obtained from TCGA and GEO databases, and the characteristics of glycolysis metabolism of the latter were evaluated. At the same time, the metabolic characteristics and differential genes of the patients were evaluated, the risk model was established by Cox regression and Lasso regression analysis, and the key glycolysis related gene TPX2 was obtained. The prognostic validity of the model was verified by GEO database based on the expression of prognostic genes, the overall survival (OS) of patients with pancreatic cancer, the difference in the expression of prognostic genes between normal pancreatic tissue and pancreatic cancer was analyzed and finally the function of prognostic genes was verified at the cellular level. Results The case cohort was divided into three characteristic groups: high, medium and low glycolysis metabolism. Patients with low-rate glycolysis metabolism had certain survival advantages. TPX2 was the key gene of this model. Pancreatic cancer patients showed high expression of TPX2 and had poor prognosis. Knocking down TPX2 at cellular level can inhibit the proliferation and colony formation of pancreatic cancer cells. Conclusions The model based on glycolysis metabolism can effectively predict the prognosis of patients with pancreatic cancer. TPX2 is expected to become a potential marker gene for predicting the prognosis of pancreatic cancer.

Objective To screen out a transcriptional target gene of p53 regulation, and to analyze the role of this gene in colon adenocarcinoma(COAD) by bioinformatics.Methods RNA-seq data of colon cancer cell line HCT116 treated with p53 protein stabilizer Nutlin were analyzed for differential gene expression (DEGs) and GO, KEGG and GSEA enrichment analysis. Nutlin was treated to stabilize p53 or transfected siRNA to knock down p53 expression in HCT116 and HCT8 cells. Quantitative real-time PCR was used to detect the mRNA expression of the predicted target gene. Dual luciferase reporter assay was used to verify the transcriptional regulation of p53 on the target gene. The expression of the target gene and the prognosis of patients was analyzed by TCGA-COAD database. Results After Nutlin treatment, the genes coding for cell cycle, DNA replication and chromosome segregation etc were changed. The p53 signaling pathway was also activated. The mRNA level of GGT6 was positively correlated with the protein expression of p53 in HCT116 and HCT8 cells. Dual luciferase reporter assay identified GGT6 as a target gene of p53 transcriptional regulation. The TCGA-COAD data analysis showed that the expression of GGT6 in COAD tissues was higher than that in the adjacent tissues(P＜0.001), and the overall survival(OS) time of patients with high GGT6 expression was longer than that of patients with low GGT6 expression(P＜0.01), suggesting GGT6 as a tumor suppressor in COAD. Conclusions GGT6 is a new transcriptional target gene of p53 and a potential tumor suppressor for colon adenocarcinoma development.

In this information era, there is an urgent need for tighter integration of bioinformatics and experimental biology. The enormous amount of data generated by biological experiments calls for extensive computational analysis. Many bioinformatics textbooks at present mainly focus on theories, which hinders the vigorous development of scientific research. As a result, most students are simply familiar with the bioinformatics theories but lack the opportunity to put them into practice. Here, we present our bioinformatics docking project conducted during the self-isolation period of the COVID-19 pandemic. Five students used the RBD-ACE2 complex as a benchmark to conduct a systematic comparison of several open-source online molecular docking programs. The virus surface spike protein mediates the entry of the SARS-CoV-2 virus into human cells by binding to its receptor, angiotensin-converting enzyme 2 (ACE2), through its receptor-binding domain (RBD). Through docking and comparing predicted structures to the crystal structure, students gained the opportunity to practice different bioinformatics tools independently and conduct research collaboratively. It opens a window for students to reach out to the state-of-the-art bioinformatics techniques and to keep up with the research trends. The online workshop has also proven to be an innovative method for bioinformatics teaching. We hope our work can inspire other educators to develop strategies to expose undergraduate students to modern bioinformatics and turn every temporary difficulty into a possible learning opportunity.