Silencing of transgene expression in mammalian cells by DNA methylation and histone modifications in gene therapy perspective

DNA methylation and histone modifications are vital in maintaining genomic stability and modulating cellular functions in mammalian cells. These two epigenetic modifications are the most common gene regulatory systems known to spatially control gene expression. Transgene silencing by these two mechanisms is a major challenge to achieving effective gene therapy for many genetic conditions. The implications of transgene silencing caused by epigenetic modifications have been extensively studied and reported in numerous gene delivery studies. This review highlights instances of transgene silencing by DNA methylation and histone modification with specific focus on the role of these two epigenetic effects on the repression of transgene expression in mammalian cells from integrative and non-integrative based gene delivery systems in the context of gene therapy. It also discusses the prospects of achieving an effective and sustained transgene expression for future gene therapy applications.     

NTDB: Thermodynamic Database for Nucleic Acids,Version 2.0

The second release of Thermodynamic Database for Nucleic Acids, NTDB 2.0, includes more than 4600 entries (250% increase over release 1.0). It contains sequence types and details of several thermodynamic parameters (enthalpy, DeltaH; entropy, DeltaS; Gibbs free energy, DeltaG; melting temperature, T(m)), experimental models and methods for extracting thermodynamic parameters, buffer conditions as well as all relevant literature information. In addition, the database statistics and references related to NTDB are included. Information on normal and modified nucleobases and nucleosides are collected in a new section 'Nucleoside' whereby data collected thus far will be release in NTDB 2.0. The NTDB is freely available at http://ntdb.chem.cuhk.edu.hk.     

Ca2+- and calmodulin-dependent stimulation of smooth muscle actomyosin Mg2+-ATPase by fodrin

Fodrin, a spectrin-like actin and calmodulin binding protein, was purified to electrophoretic homogeneity from a membrane fraction of bovine brain. The effect of fodrin on smooth muscle actomyosin Mg2+-ATPase activity was examined by using a system reconstituted from skeletal muscle actin and smooth muscle myosin and regulatory proteins. The simulation of actomyosin Mg2+-ATPase by fodrin showed a biphasic dependence on fodrin concentration and on the time of actin and myosin preincubation at 30 degrees C. Maximal stimulation (50-70%) was obtained at 3 nM fodrin following 10 min of preincubation of actin and myosin. This stimulation was also dependent on the presence of tropomyosin. In the absence of myosin light chain kinase, the fodrin stimulation of Mg2+-ATPase could not be demonstrated with normal actomyosin but could be demonstrated with acto-thiophosphorylated myosin, suggesting that fodrin stimulation depends on the phosphorylation of myosin. Fodrin stimulation was shown to require the presence of both Ca2+ and calmodulin when acto-thiophosphorylated myosin was used. These observations suggest a possible functional role of fodrin in the regulation of smooth muscle contraction and demonstrate an effect on Ca2+ and calmodulin on fodrin function.     

Enzymes of the beta-ketoadipate pathway in Pseudomonas putida: kinetic and magnetic resonance studies of the cis,cis-muconate cycloisomerase catalyzed reaction

Steady-state kinetic analysis of the divalent metal ion requiring cis,cis-muconate cycloisomerase catalyzed interconversion of cis,cis-muconate and (+)-muconolactone obeys Michaelis-Menten kinetics and the Haldane relationship from pH 6.2 to 8.3. The pH vs. kcat/Km profiles suggest free-enzyme apparent pKa values of 6.2 and 7.4: the reciprocal behavior of the data with respect to the latter pKa value is consistent with base-acid catalysis by the enzyme involving proton removal from the lactone and protonation of cis,cis-muconate, respectively. This catalysis by the enzyme of proton transfer is consistent with the stereospecific incorporation of solvent deuterium into the pro-5R position of (+)-muconolactone in the enzyme-catalyzed reaction: in reverse, the departure of the carboxylic oxygen atom and proton from the C(4) and C(5) carbon atoms follows a syn (cis) route [Avigad, G., & Englard, S. (1969) Fed. Proc., Fed. Am. Soc. Exp. Biol. 28, 345, Abstr. 486]. The titration of enzyme freed of divalent metal ion with manganous ion, monitored by electron paramagnetic resonance spectroscopy and steady-state kinetic measurements, indicates a single binding site per subunit characterized by KdissE X Mn = [E] [Mn2+]/[E X Mn2+] = 4.5 and 3.0 microM, respectively, the latter value analyzed via a rapid equilibrium mechanism. The paramagnetic effects of Mn2+ on the 1/T1 and 1/T2 values for the H-5S proton of (+)-muconolactone in the E X ML X Mn ternary complex provide an estimate of the correlation time, tau c, at 5 X 10(-9) s from the T1/T2 ratio, indicating that the condition of rapid exchange of (+)-muconolactone in solution with the ternary complex obtains.(ABSTRACT TRUNCATED AT 250 WORDS)     

Learning chronobiology by improving wikipedia

Although chronobiology is of growing interest to scientists, physicians, and the general public, access to recent discoveries and historical perspectives is limited. Wikipedia is an online, user-written encyclopedia that could enhance public access to current understanding in chronobiology. However, Wikipedia is lacking important information and is not universally trusted. Here, 46 students in a university course edited Wikipedia to enhance public access to important discoveries in chronobiology. Students worked for an average of 9 h each to evaluate the primary literature and available Wikipedia information, nominated sites for editing, and, after voting, edited the 15 Wikipedia pages they determined to be highest priorities. This assignment (http://www.nslc.wustl.edu/courses/Bio4030/wikipedia_project.html) was easy to implement, required relatively short time commitments from the professor and students, and had measurable impacts on Wikipedia and the students. Students created 3 new Wikipedia sites, edited 12 additional sites, and cited 347 peer-reviewed articles. The targeted sites all became top hits in online search engines. Because their writing was and will be read by a worldwide audience, students found the experience rewarding. Students reported significantly increased comfort with reading, critiquing, and summarizing primary literature and benefited from seeing their work edited by other scientists and editors of Wikipedia. We conclude that, in a short project, students can assist in making chronobiology widely accessible and learn from the editorial process.     

Optimal production of polyhydroxyalkanoates (PHA) in activated sludge fed by volatile fatty acids (VFAs) generated from alkaline excess sludge fermentation

To reduce the production cost of polyhydroxyalkanoates (PHA) and disposal amount of excess sludge simultaneously, the feasibility of using fermentative volatile fatty acids (VFAs) as carbon sources to synthesize PHA by activated sludge was examined. At pH 11.0, 60 degrees C and fermentative time of 7d, the VFAs yield was 258.65 mgTOC/gVSS. To restrain cell growth during PHA production, the released phosphorus and residual ammonium in the fermentative VFAs was recovered by the formation of struvite precipitation. Acetic acid was the predominant composition of the fermentative VFAs. PHA accumulation in excess sludge occurred feeding by fermentative VFAs with aerobic dynamic feeding process. The maximum PHA content accounted for 56.5% of the dry cell. It can be concluded from this study that the VFAs generated from excess sludge fermentation were a suitable carbon source for PHA production by activated sludge.     

Complement 3 deficiency impairs early pregnancy in mice

Human oviductal cells produce complement‐3 (C3) and its derivative, iC3b. These molecules are important in immune responses. Our recent study suggested that iC3b also possessed embryotrophic activity and it stimulates the blastulation and hatching rates of in vitro cultured mouse embryos. The objective is to study the impact of C3 deficiency on early pregnancy in vivo using homozygous C3‐deficient (C3KO) and wild‐type (C3WT) mice. C3 protein was undetectable in the reproductive tissues of C3KO mice. Deficiency in C3 is associated with significantly longer estrous cycle (P = 0.037). No significant difference was found in the ovulation rate, total cell count in blastocysts and implantation rate between the wild‐type and the C3KO mice, though C3KO mice tended to have lower values in the latter two parameters. On day 15 of pregnancy, C3KO mice had fewer conceptus (P < 0.001) and higher resorption rate (P < 0.001) than that of C3WT mice. The fetal and placental weights (P < 0.001) were lower in the C3KO mice. The placenta of C3KO mice had smaller spongiotrophoblast (P = 0.001) and labyrinth (P = 0.037). Deficiency in C3 is associated with mild impairment in early pregnancy including longer estrous cycle and higher resorption rates after implantation. The impairment may be related to compromised placental development leading to under‐developed fetuses. Mol. Reprod. Dev. 76: 647–655, 2009. © 2009 Wiley‐Liss, Inc.     

Folic acid consumption reduces resistin level and restores blunted acetylcholine-induced aortic relaxation in obese/diabetic mice

Folic acid supplementation provides beneficial effects on endothelial functions in patients with hyperhomocysteinemia. However, its effects on vascular functions under diabetic conditions are largely unknown. Therefore, the effect(s) of folic acid (5.7 and 71 μg/kg/day for 4 weeks) on aortic relaxation was investigated using obese/diabetic (+db/+db) mice and lean littermate (+db/+m) mice. Acetylcholine-induced relaxation in +db/+db mice was less than that observed in +db/+m mice. The reduced relaxation in +db/+db mice was restored by consumption of 71 μg/kg folic acid. Acetylcholine-induced relaxation (with and without folic acid treatment) was sensitive to N^G-nitro-l-arginine methyl ester, 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one, geldanamycin and triciribine. In addition, acetylcholine-induced relaxation was attenuated by resistin. The plasma level of resistin in +db/+db mice was sevenfold higher than that measured in +db/+m mice, and the elevated plasma level of resistin in +db/+db mice was reduced by 25% after treatment with 71 μg/kg folic acid. Folic acid slightly increased the ratio of reduced glutathione to oxidized glutathione in +db/+db mice. Moreover, folic acid caused a reduction in PTEN (phosphatase and tensin homolog deleted on chromosome 10) expression, an increase in the phosphorylation of endothelial nitric oxide synthase (eNOS^Ser1177) and Akt^Ser473, and an enhanced interaction of heat shock protein 90 (HSP90) with eNOS in both strains, with greater magnitude observed in +db/+db mice. In conclusion, folic acid consumption improved blunted acetylcholine-induced relaxation in +db/+db mice. The mechanism may be, at least partly, attributed to enhancement of PI3K/HSP90/eNOS/Akt cascade, reduction in plasma resistin level, down-regulation of PTEN and slight modification of oxidative state.