Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure

Molecular beacons are hairpin-shaped, single-stranded oligonucleotides constituting sensitive fluorescent DNA probes widely used to report the presence of specific nucleic acids. In its closed form the stem of the hairpin holds the fluorophore covalently attached to one end, close to the quencher, which is covalently attached to the other end. Here we report that in the closed form the fluorophore and the quencher form a ground state intramolecular heterodimer whose spectral properties can be described by exciton theory. Formation of the heterodimers was found to be poorly sensitive to the stem sequence, the respective positions of the dyes and the nature of the nucleic acid (DNA or RNA). The heterodimer allows strong coupling between the transition dipoles of the two chromophores, leading to dramatic changes in the absorption spectrum that are not compatible with a Förster-type fluorescence resonance energy transfer (FRET) mechanism. The excitonic heterodimer and its associated absorption spectrum are extremely sensitive to the orientation of and distance between the dyes. Accordingly, the application of molecular beacons can be extended to monitoring short range modifications of the stem structure. Moreover, the excitonic interaction was also found to operate for doubly end-labeled duplexes.     

Functional Interaction between Fluorodeoxyuridine-Induced Cellular Alterations and Replication of a Ribonucleotide Reductase-Negative Herpes Simplex Virus

G207 is an oncolytic herpes simplex virus (HSV) which is attenuated by inactivation of viral ribonucleotide reductase (RR) and deletion of both gamma(1)34.5 genes. The cellular counterparts that can functionally substitute for viral RR and the carboxyl-terminal domain of ICP34.5 are cellular RR and the corresponding homologous domain of the growth arrest and DNA damage protein 34 (GADD34), respectively. Because the thymidylate synthetase (TS) inhibitor fluorodeoxyuridine (FUdR) can alter expression of cellular RR and GADD34, we examined the effect of FUdR on G207 bioactivity with the hypothesis that FUdR-induced cellular changes will alter viral proliferation and cytotoxicity. Replication of wild-type HSV-1 was impaired in the presence of 10 nM FUdR, whereas G207 demonstrated increased replication under the same conditions. Combined use of FUdR and G207 resulted in synergistic cytotoxicity. FUdR exposure caused elevation of RR activity at 10 and 100 nM, whereas GADD34 was induced only at 100 nM. The effect of enhanced viral replication by FUdR was suppressed by hydroxyurea, a known inhibitor of RR. These results demonstrate that the growth advantage of G207 in FUdR-treated cells is primarily based on an RR-dependent mechanism. Although our findings show that TS inhibition impairs viral replication, the FUdR-induced RR elevation may overcome this disadvantage, resulting in enhanced replication of G207. These data provide the cellular basis for the combined use of RR-negative HSV mutants and TS inhibitors in the treatment of cancer.     

PKCdelta-dependent deubiquitination and stabilization of Gadd45 in A431 cells overexposed to EGF.

Epidermal growth factor (EGF) receptor-overexpressing p53-deficient A431 cells response to toxic dose of EGF by G1 arrest and apoptosis was studied. We previously reported an increased expression of growth arrest and DNA-damage-inducible gene, Gadd45, in EGF-overexposed A431 cells. The mechanism for this induction was increased half-lives of mRNA and protein. In this study, using phorbol ester (a PKC activator) and specific inhibitors of PKC isoforms, we showed that protein kinase C-delta (PKCdelta) was involved in the increase of Gadd45 protein stability. We further demonstrated that Gadd45 is ubiquitinated and is regulated by proteolysis. While EGF induced ubiquitination of total cellular proteins, there was a decrease in Gadd45 ubiquitination, which could be inhibited by Rottlerin, a PKCdelta-specific inhibitor. These results suggest that an increase in Gadd45 stability may involve PKCdelta-dependent ubiquitin-proteasome pathway.     

Melphalan-induced DNA damage in p53(+/-) and wild type mice analysed by the comet assay

Melphalan is an alkylating substance used as a therapeutic agent; its mutagenicity is related to its ability to produce monoadducts and to form DNA cross-links. The alkaline comet assay is a useful test for the detection of DNA lesions. However, cross-links are not easily detected under standard conditions. Recently, modifications to the test have been introduced to measure cross-links by evaluating the reduction in induced DNA migration.

In this work, the standard comet assay and an assay modified by prolonging the electrophoresis time have been applied to evaluate DNA lesions induced by single, 4 or 26 weekly oral administrations of melphalan to p53^+/− knockout and to isotype parental mice. Cells were analysed from the liver, bone marrow, peripheral blood and the distal intestine. Moreover, a further protocol in which the presence of cross-links was inferred by the reduction in X-ray-induced DNA migration was applied to bone marrow cells and the sensitivity of the different methods was compared.

The majority of groups examined by the standard protocol showed no difference compared to controls, while the modified protocol (prolonged electrophoresis time) could detect a retarded DNA migration in cells from all the organs analysed with the exception of bone marrow cells.

Only the protocol based on X-ray in vitro irradiation showed the presence of melphalan-induced cross-links in bone marrow cells exposed to 2 mg/kg for 4 weeks, demonstrating that this was the most sensitive approach for detecting this type of lesion.

DNA lesions were evident in all the organs analysed. However, results suggest that the kinetics of cross-link repair could be different in bone marrow cells compared to other organs tested. After comparison between genotype-matched treated and control groups, a significant effect was shown more frequently in p53^+/− than in wild type groups.     

Zinc finger protein ZFP57 requires its co-factor to recruit DNA methyltransferases and maintains DNA methylation imprint in embryonic stem cells via its transcriptional repression domain

Previously, we discovered that ZFP57 is a maternal-zygotic effect gene, and it maintains DNA methylation genomic imprint at multiple imprinted regions in mouse embryos. Despite these findings, it remains elusive how DNA methyltransferases are targeted to the imprinting control regions to initiate and maintain DNA methylation imprint. To gain insights into these essential processes in genomic imprinting, we examined how ZFP57 maintains genomic DNA methylation imprint in mouse embryonic stem (ES) cells. Here we demonstrate that the loss of ZFP57 in mouse ES cells led to a complete loss of genomic DNA methylation imprint at multiple imprinted regions, similar to its role in mouse embryos. However, reintroduction of ZFP57 into Zfp57-null ES cells did not result in reacquisition of DNA methylation imprint, suggesting that the memory for genomic imprinting had been lost or altered in Zfp57-null ES cells in culture. Interestingly, ZFP57 and DNA methyltransferases could form complexes in the presence of KAP1/TRIM28/TIF1β when co-expressed in COS cells. We also found that the wild-type exogenous ZFP57 but not the mutant ZFP57 lacking the KRAB box that interacts with its co-factor KAP1/TRIM28/TIF1β could substitute for the endogenous ZFP57 in maintaining the DNA methylation imprint in ES cells. These results suggest that ZFP57 may recruit DNA methyltransferases to its target regions to maintain DNA methylation imprint, and this interaction is likely facilitated by KAP1/TRIM28/TIF1β.     

我国一株鹦鹉病毒的鉴定及其生化特性

１９９５ 年作者从湖北濒死鹦鹉体内分离到一株新病毒,经鹦鹉胚成纤维细胞盲传四代过渡到鸡胚成纤维细胞,再传至第五代出现细胞病变。适应细胞的病毒纯化后,经 Ｓ Ｄ Ｓ Ｐ Ａ Ｇ Ｅ 分析,发现病毒粒子结构蛋白由８ 条多肽组成,分子量范围在１４ ．５ ～６０ ｋ Ｄ 之间。病毒的酸碱氨基酸之比为２ ．５１ ,富含 Ａｓｐ 、 Ｃｌｕ 和 Ｌｅｕ ,而 Ａｒｇ 和 Ｍｅｔ 含量较少。病毒核酸为双链 Ｄ Ｎ Ａ,存在超螺旋型、环型和线型三种形态, Ｇ＋ Ｃ 的含量为４５ ％ 。经限制性内切酶分析,核酸的分子量为３ ．３ ×１０６ Ｄ。根据病毒分类的标准确认为澳州长尾小鹦鹉幼雏病病毒,应归属于乳多空病毒科多瘤病毒属。     

Complex Marine Natural Products as Potential Epigenetic and Production Regulators of Antibiotics from a Marine Pseudomonas aeruginosa

Marine microbes are capable of producing secondary metabolites for defense and competition. Factors exerting an impact on secondary metabolite production of microbial communities included bioactive natural products and co-culturing. These external influences may have practical applications such as increased yields or the generation of new metabolites from otherwise silent genes in addition to reducing or limiting the production of undesirable metabolites. In this paper, we discuss the metabolic profiles of a marine Pseudomonas aeruginosa in the presence of a number of potential chemical epigenetic regulators, adjusting carbon sources and co-culturing with other microbes to induce a competitive response. As a result of these stressors certain groups of antibiotics or antimalarial agents were increased most notably when treating P. aeruginosa with sceptrin and co-culturing with another Pseudomonas sp. An interesting cross-talking event between these two Pseudomonas species when cultured together and exposed to sceptrin was observed.     

Glycogen accumulation in adipocyte precursors from elderly and obese subjects triggers inflammation via SIRT1/6 signaling

Dysfunctional adipocyte precursors have emerged as key determinants for obesity‐ and aging‐related inflammation, but the mechanistic basis remains poorly understood. Here, we explored the dysfunctional adipose tissue of elderly and obese individuals focusing on the metabolic and inflammatory state of human adipose‐derived mesenchymal stromal cells (hASCs), and on sirtuins, which link metabolism and inflammation. Both obesity and aging impaired the differentiation potential of hASCs but had a different impact on their proliferative capacity. hASCs from elderly individuals (≥65 years) showed an upregulation of glycolysis‐related genes, which was accompanied by increased lactate secretion and glycogen storage, a phenotype that was exaggerated by obesity. Multiplex protein profiling revealed that the metabolic switch to glycogenesis was associated with a pro‐inflammatory secretome concomitant with a decrease in the protein expression of SIRT1 and SIRT6. siRNA‐mediated knockdown of SIRT1 and SIRT6 in hASCs from lean adults increased the expression of pro‐inflammatory and glycolysis‐related markers, and enforced glycogen deposition by overexpression of protein targeting to glycogen (PTG) led to a downregulation of SIRT1/6 protein levels, mimicking the inflammatory state of hASCs from elderly subjects. Overall, our data point to a glycogen‐SIRT1/6 signaling axis as a driver of age‐related inflammation in adipocyte precursors.