Abstract:Folding of some proteins in prokaryote, eukaryote and virus is contrary to Anfinsen’s dogma: Their structure is not determined by the protein’s amino acid sequence. However, the proper folding of them requires the assistance of intramolecular chaperone (IMC). On the basis of different mechanism, IMC can be classified into two categories. The type Ⅰ IMC assists the tertiary structure formation, and the type Ⅱ IMC guides the assembly of quaternary structure to form the functional protein complex. IMC guides the protein folding more effectively than molecular chaperone. This mechanism is a better strategy for protein folding. Study on IMC mechanism not only can determine the essential residues on the guidance of mature peptide folding, but also can modify these residues to change mature peptide. This is a novel approach of protein engineering.

Abstract:Gastric cancer (GC) is one of the most common malignant tumors with high incidence and mortality in the world. Currently, the alterations of protein glycosylation has been extensively reported during gastric carcinogenesis and cancer progression. In the initial steps of the process of gastric carcinogenesis, Helicobacter pylori (H. pylori) uses glycan to adhere the host mucosa, which leads to the increase of sialyl-Lewis^x level. Further up-regulation of the H. pylori colonization induces sustained inflammation in stomach. In the process of chronic atrophic gastritis and intestinal metaplasia, sialyl-Tn antigen showed a significant up-regulation. Moreover, in GC, the abnormal protein glycosylation emerges in serum and tissue from GC patients as well as GC cell lines, such as down-regulation of core fucosylated N-glycan and up-regulation of β1, 6-GlcNAc branched N-glycan were discovered. It also shows that the altered glycosylation of adhesin contributes to the development of GC. This review summarizes the recent progress of protein glycosylation in GC and the important functions of glycosylation in the carcinogenesis and development. Finally, the application values of the alterations of glycosylation, such as potential biomarker for early diagnosis and drug target designing were discussed.

Abstract:Long noncoding RNAs (lncRNA) are non-protein coding transcripts longer than 200 nucleotides. The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years as its large number and important biological functions. Genomic imprinting is an epigenetic phenomenon. The lncRNAs play a critical role in important biological functions by establishing genomic imprinting of target genes. Genomic imprinting has been a great resource for studying transcriptional and post-transcriptional-based gene regulation by lncRNAs. This review will focus on the mechanisms of imprinting in six of the most well-studied imprinted gene clusters: Kcnq1/Cdkn1c, Igf2r/Airn, Prader-Willi (PWS)/Angelman (AS), Snurf/Snrpn, Dlk1-Dio3, H19/Igf2, and overview the functional role of antisense lncRNAs (Kcnq1ot1t1, Airn and Ube3a-ATS), intergenic lncRNAs (H19, IPW and MEG3), and enhancer lncRNAs (IG-DMR eRNAs) to understand the diverse mechanisms being employed by them in cis and (/or) trans to regulate the parent-of-origin-specific expression of target genes. A better understanding of these downstream mechanisms will help to improve our general understanding of the function of ncRNAs throughout the genome.

Abstract:The rapid accumulation of biomedical data provided unprecedented opportunities for biology and clinical research, while it also made traditional data analysis technology face enormous challenges. In this paper, we reviewed recent studies on biomedical data using deep learning. We introduced several recommended deep learning models and summarized current applications of biological and medical data analysis using deep learning, including the general procedure, model construction and training process. Finally, we made a discussion on some issues in deep learning applications.

Abstract:Rad9, Rad1 and Hus1 are critical for the cell cycle checkpoint and can form a heterotrimer complex called 9-1-1 complex which was supposed to play important roles in the cell cycle checkpoint and other activities required for the maintenance of genome integrity. However, lack of high quality anti-Rad1 antibodies has seriously hindered the research on Rad1 as well as working mechanisms of the 9-1-1 complex at molecular level. In this study, a mouse anti-Rad1 monoclonal antibody (mAb) was successfully generated. The mAb possesses high affinity and specificity, and recognizes both endogenous mouse Rad1 (mRad1) and human Rad1 (hRad1) proteins and was successfully used in ELISA, Western blot analysis, immunoprecipitation and immunofluorescence assays. Using this mAb, we found that mRad1 protein expression was increased in Rad9^+/+ mouse embryonic stem (MES) cells after hydroxyurea (HU, a genotoxic agent) treatment while not in Rad9^-/- MES cells, suggesting that mRad1 expression is under Rad9 regulation. Furthermore, endogenous mRad1 was distributed mainly in the cytoplasm and did not migrate to the nucleus after HU treatment, contradicting the generally accepted hypothesis that Rad9, Rad1 and Hus1 form the 9-1-1 complex in the nucleus in response to genotoxic stresses. In summary, the exact molecular roles of Rad1 and the 9-1-1 complex are likely more complicated than previously expected and this anti-Rad1 mAb is a powerful tool for the future investigation on Rad1 as well as the 9-1-1 complex.

Abstract:Oncolytic adenovirus could target and kill cancer stem cells and recognized as a promising anticancer agent. Our previous studies showed that oncolytic adenovirus ZD55 was developed to target liver cancer and exhibited obvious cytotoxicity effect. However, it still remained to be confirmed that whether ZD55 could also effectively eliminate liver cancer stem cells. We first utilized the suspension culture to enrich the liver cancer stem-like cells and validate the properties of acquired liver cancer stem cells. Further, we use MTT, Hoechst staining, Western blot, flow cytometry assay to detect cell viability, apoptotic effect and cytopathic effect in liver cancer stem-like cells after treatment with ZD55. The results indicated that liver cancer stem-like cells had the features of self-renewal, differentiation, high expression of cancer stem cell-related transcription factors (eg.NANOG and OCT4), quiescence, chemo-resistance. Oncolytic virus ZD55 resulted in obvious cytotoxicity and killing effect (the minimum cell viability for Huh7 sphere is 26.7%) on liver cancer stem-like cells, and induced significant cell apoptosis (the maximum apoptosis rate for Huh7 sphere is 60%). Thus, ZD55 might virtually represent an attractive therapeutic agent for targeting liver cancer stem cells to achieve better clinical outcome for HCC patients.

Abstract:Hepatic stellate cell(HSC), an important interstitial cell in the liver, is the main source of extracellular matrix. Epimorphin (EPM, also called syntaxin2), a mesenchymal cell surface-associated molecule expressed in HSC, has been reported that the dysfunction is related to the development, regeneration and carcinogenesis of the liver. We found that the expression of EPM was up-regulated in hepatic stellate cells in the process of hepatic fibrosis. We studied the mechanism of EPM expression changes, found that the demethylation of promoter region promoted the expression of EPM. Stable EPM-overexpression transgenic cell lines were generated by transfecting human hepatic stellate cells with plasmids. Reverse transcriptase polymerase chain reaction(PCR) analyses and Westen blot indicated that the mRNA and protein levels of EPM in the transgenic cell lines were significantly up-regulated than that in control. By MTT assay and transwell motility assay, we further confirmed that EPM induced HSC proliferation and invasion. In conclusion, the high expression of EPM in activated hepatic stellate cells is caused by DNA demethylation, and EPM can promote the proliferation and migration of hepatic stellate cells, it may be involved in hepatic fibrogenesis.

Abstract:Enoyl-ACP reductase (ENR) is one of the key enzymes in bacterial fatty acids biosynthesis. Through sequence alignment, gene XC_0119, annotated as trans-2-enoyl CoA reductase, was found in the genome of Xanthomonas campestris pv. campestris (Xcc) 8004. However, the protein encoded by XC_0119 shows 59% identity with fabV, the ENR from Pseudomonas aeruginosa, and contains the same catalytic triad Tyr-(Xaa)₈-Lys. Expression of XccfabV restored the growth of the E. coli fabI temperature sensitive mutant JP1111 under non-permissive condition. In vitro assay identified that XccFabV catalysed enoyl-ACP with viarable chain lengths to acy-ACP, and the activity was not inhibited by triclosan. Furthermore, genetic research proved that XccfabV is an essential gene, and none of XccfabV deletion mutants was obtained. However, XccfabV in the chromosome could be deleted when plasmid expressing E. coli fabI was introduced into Xcc8004. And the fabI replaced mutant showed similar growth characteristic and fatty acid compositions with wild type, but changed to be sensitive to triclosan. These results domonstrated XccfabV is essential for growth, encodes ENR involved in fatty acid de novo biosynthesis, and FabV confers triclosan resistance on Xcc.

Abstract:In order to further understand the growth of abdominal aortic aneurysm (AAA) and to provide a reference for clinical AAA surgery, we put forward a model based on the characteristic of the growth of AAA and creep mechanics. We establish a simplified model of AAA and use finite element analysis to simulate its growth. Our results show that the proposed model can simulate the morphological change of AAA during its growth and the optimized model has a good result of AAA growth process which compliance with clinical data. We also discussed the influence of parameters of the abdominal aorta on the model itself and suggest the future research direction.