Abstract:The aging of adult stem cells has been researched by the traditional theories and methods of the aging of somatic cells and the unique role of the self-renew and the stem genes of adult stem cells has been ignored by now in the aging of adult stem cells. The down-regulation of stem genes may be the major cause of the aging of stem cells. By analysis of the relevant information, we found that the expression levels of the stem genes and aging-related genes are associated with mutual antagonism which can be reflected in the following four aspects: The aging of stem cells is accompanied by down-regulation of the stem genes; The aging of cells is inhibited by the expression of the stem genes; The stem genes inhibits the expression of aging-related genes; The knockdown of an aging-related gene enhances the expression of the stem genes. The conclusion in this review that the expression levels of the stem genes and aging-related genes are associated with mutual antagonism provides a solid molecular basis of the viewpoint that the aging of adult stem cells may originate from the decline of stemness.

Abstract:The epithelial mesenchymal transition(EMT)confers mesenchymal properties, migration and invasion on epithelial cells which normally is polarized and interacts with basement membrane via its basal surface. Cancer stem cell is a small subset of stem-like cells which have the capacity for self-renewal and asymmetric cell division. They play an important role in cancer initiation and progression. In rencent years, some researches reveal that EMT, which is closely related tumor metastasis, can generate tumour cells with propreties of stem cells. We review here recent observations correlated with the mechanism of it and its significance to clinical therapy.

Abstract:In the post-genomic era after human whole-genome sequencing has been completed, accurate functional annotation of genomic sequences, especially the DNA regulatory elements, has become an urgent need of further in-depth understanding of the complex mechanisms of human genome. Recent large-scale chromatin states mapping efforts have revealed characteristic chromatin modification signatures for various types of functional DNA elements. The conclusions drew in these studies have promoted the emergence of a series of supervised and unsupervised methods of DNA elements identification, some of which have been successfully applied to identify functional DNA elements in a number of genomes and have become the regular tools to decode an unknown genome. These methods are adept at different aspects of genomic studies, varied by the embedded algorithms and the identification strategies. In most cases users should consider joint application of different types of methods to obtain a balance between identification sensitivity and specificity. Despite the successful applications of current methods, each type of methods has its own disadvantages which users should scrupulously avoid. In this paper, we not only reviewed the main types of previous and current DNA elements identification methods, and comprehensively analyzed the advantages and disadvantages of each type of methods, but also pointed out the next possible directions of method improvement. We anticipated the analysis and views put forward in this review could help readers to deepen the understanding of principles of DNA elements identification methods, thus better applied them in their own studies.

Abstract:Immunoassay based on antigen-antibody interaction plays an important role in the screening of low molecular mass organic contaminations such as pesticides, veterinary drugs and biological toxins. However, due to the lack of epitope groups of haptens, the production of antibodies with high affinity is still one of the bottlenecks of immunoassay for small molecules. Dendrimers, as a new type polymer, exhibit many excellent structural properties and histocompatibility, such as clear molecular composition, regular, highly branched and nanometer-sized structure, monodisperse property and presenting dense functional groups on its surface. Previous studies had revealed that dendrimers are potential in the improving performance of immunoassay, such as to produce antibodies with higher affinity, produce antibodies with broad-specificity and improve assay sensitivity. In this work, therefore, the application of dendrimers as carrier to prepare immunogens and coating antigens, as adjuvant to improve immunogenicity, as carrier to amplify signal were reviewed. The potential of application of dendrimers on the development of immunoassays for small molecules was also discussed.

Abstract:Human N-Myc Interactor (Nmi), an interferon (IFN)-induced protein, participates in downstream JAK-STAT pathway and inhibits proliferation of cancer cells．Nmi can bind Interferon-Induced Protein 35 (IFP35) and protect the latter from degradation．Previous research showed that these two proteins associated through their C-terminal domains．In this study, we constructed full length clones and N-terminal truncates of both Nmi and IFP35．Co-expression and GST pull down experiments showed that N-terminal domains of Nmi and IFP 35 are respectively sufficient for their association．We overexpressed and purified recombinant protein complexes afterward．Through immune fluorescence, we found that Nmi and IFP35 co-localized in nucleus in RAW264.7 cells．We also noticed that Nmi localized in nucleus and enriched on surface in normal 293A cells．Although Nmi granularly aggregated in cytoplasm after 24 h induction by interferon as reported, it came back to nucleolus by adding low concentration hydrogen peroxide (H₂O₂)．That result indicated that subcellular localization of Nmi can be affected by the oxidation environment of cells.

Abstract:Filia is one of the components of maternal Subcortical Maternal Complex(SCMC). The N-terminal of Filia is similar to KH domain of type I family, which play roles in transcription regulation in oogenesis and embryo development by binding RNA. Additionally, maternal Filia plays essential role in maintaining euploidy. The absence of maternal Filia appears to delay embryonic progression, which can decrease the number of offspring rather than sterile. During oocyte maturation stage, the concentration of GSH varied to keep balance of oxidation-reduction. Our crystallographic studies successfully reveal the structure of Filia N-terminal protein grown in solution with GSH. In contrast with the structure of Filia N-terminal protein grown in condition free of GSH, protein grown in GSH have five pairs of dimer in an asymmetry unit. Domain swapping occurs in the α3-helix of Filia (N1-124) molecules. A special decamer structure is formed by ionic interaction, H-bond and hydrophobic interaction. The Filia N-terminal structure provides a structural foundation for further researches on the structure and function of Filia in diversity physiological environment.

Abstract:Increased plasminogen activator inhibitor-1 (PAI-1) level is the risk of thrombotic disease and atherosclerosis (As). Our research aims to study the effect and mechanism of PPARδ antagonist GW501516 on the expression of PAI-1. Firstly, human umbilical vein endothelial cells (HUVECs) were incubated with DMEM, and then treated with siRNA and TGFβ-Smad3 inhibitor, respectively. The protein and mRNA expression were examined by Western blotting assays and Real-time quantitative PCR, respectively. The result showed that GW501516 induced PAI-1 mRNA and protein expression in HUVECs compared with control groups (P < 0.05). According to PPARδ gene, the designed PPARδ siRNA primer silenced the PPARδ expression and depressed the induction of GW501516 on PAI-1 expression. Then, the HUVECs were treated by SB431542 or SIS3, which is the TGFβ-Smad3 signaling pathway blocker, and found that PAI-1 expression of cells were down-regulated.At last, we found that SB431542, SIS3 and GW501516 inhibited the expressions of pSmad3 protein. These results suggested that TGF beta-Smad3 signaling pathway involved in the regulation of GW501516-induced PAI-1 expression in HUVECs.

Abstract:WRKY is one of the largest families of transcription factors in plants. In this paper, transcriptional analysis revealed that the transcription of rice WRKY42 gene was occurred at seedling stage and anther, while the expression of WRKY42 protein was detected in the leaf blade at all growth stages. In the process of Xa21- mediated resistance to bacterial blight, the induction of WRKY42 protein was apparent in the late stage after inoculation; further comparison among incompatible (R), compatible (S) and mock control (M) reactions revealed similar expression pattern between R and S interactions, and the abundance of WRKY42 in both R and S interactions was significantly greater than that in mock control reaction. This evidence suggested that WRKY42 protein may play a role in the interactions between rice and Xoo. Next, the WRKY42 protein was expressed in E. coli. The purified WRKY42 protein was used to investigate its binding capacity with cis-elements in the promoter region of downstream genes using microscale thermophoresis (MST) technique. It was found that the WRKY42 protein binds to W-box-containing oligonucleotide derived from the promoter region of PR1a and PR1b specifically, and their dissociation constant (K_d) were 73.3 μmol/L and 58.3 μmol/L, respectively. Taken together, the data provide direct evidences for the function of WRKY42 to regulate downstream pathogenesis-related genes, and further support that WRKY42 play a role in the process of rice resistance to Xoo. In the last, a working model of WRKY transcription factors in rice-Xoo interactions was proposed.

Abstract:Simple sequence repeats(SSR), whose biological significance causes people's increasing attention, are widely distributed in genomes of many organisms. Many of them can be elongated easily and abnormal extension can directly result in certain hereditary diseases in some cases. In this research, sixty kinds of tetranucleotide repetitive sequences (TRS) and six kinds of dinucleotide repetitive sequences (DRS) of 20 nt single strands were used for isothermal amplification by thermophilic DNA polymerase. The electrophoresis results demonstrated that most of single-strand repeats, even the sequences with no complementary bases inside like AGGA, can be elongated. The results of quantitative analysis demonstrated: palindromic sequences were amplified most easily; DRS could be amplified at a broader range of temperature than TRS; DNA with more G and C, were more suitable for amplification under higher temperature; Most strands whose repetitive unit contains two same pyrimidines were amplified more easily than their complimentary ones; the concentration of products exhibited linear relationship with time. The results of restriction endonuclease digestion indicated that the products had the same repetitive unit with their original repetitive sequences. Finally, an two-stage amplification model, including amplification by intra-chain slide and mediated by hairpin-contained structure, was proposed to provide information for the study of nonspecific amplification of repetitive sequences and pathogenetic mechanisms of relevant diseases.

Abstract:The disease caused by the opportunistic pathogen Vibrio harveyi is a serious infection which brings a heavy damage to aquaculture. Accurate and rapid detection of the microorganism is the first and necessary step to control the disease. Aptamers have a good potential application in the detection and identification of microorganisms because of their strong affinity, high specificity and good stability. In the present paper, aptamers targeting to V. harveyi were selected by the technique of systematic evolution of ligands by exponential enrichment (SELEX), and their affinities and specificities to V. harveyi were also evaluated. After 15 rounds of selection, the affinity of the aptamers in the enriched pool increased to 58.95, which was 16.8 times of that (3.51) in the original pool. After cloning and sequencing, 52 supposed aptamers were obtained from the enriched pool. These aptamers were divided into 8 families based on the homology analysis. Over 50% of these aptamers in the first and the second families shared higher homology, suggesting the selection was convergent and efficient. Six high-frequency aptamers were also found to have significant affinities and specificities to V. harveyi (P < 0.01). Five of them (S1,S25, S26, S27, S35) were proved to have higher affinities, and their affinity constants (K_d) were as followed: (32.6±7.1), (45.3±10.1), (24.7±5.8), (34.8±5.6) and (12.9±4.0) nmol/L, respectively. The production mechanism and the application values of high-frequency aptamers were also discussed. The present paper was the first report of aptamers with high affinity and specificity to the target V. harveyi, which would lay the foundation for the detection of the pathogenic microorganism based on aptamers.

Abstract:Protein folding problem is a classical non-deterministic polynomial(NP) hard problem in bioinformatics. The energy landscape paving (ELP) method is a class of heuristic global optimization algorithm. This paper applies the ELP method to simulate protein folding conformations for the hydrophobic-polar (HP) model on the face-centered-cube (FCC) lattice. By putting forward a new update mechanism of the histogram function in ELP and incorporating the generation of initial conformation based on the greedy strategy and the neighborhood search strategy based on pull-moves into ELP, an improved energy landscape paving (ELP+) method is put forward for the protein folding problem on the FCC lattice model. We test the method on nine benchmark sequences. The lowest energies by ELP are as good as or better than those of other methods in the literature for all instances. Computational results show that ELP is an effective method for protein folding problem on FCC lattice model.