MgCl2 Enhances Cluster Formation by Nanoscale Toroidal DNA Condensates

Multivalent cations can cause DNA to condense from its extended state in solution into high-density toroid-shaped particles. Developing methods to control the size and size distribution of DNA toroids is an important goal for the development of artificial gene delivery systems. Here we demonstrate that changes in salt conditions, prior to condensation by multivalent cations, can significantly affect DNA condensation. Specifically, millimolar concentrations of MgCl₂ are shown to cause the formation of toroid clusters, whereas NaCl at the same ionic strength does not.     

Polyethylenimine （PEI）-g-comb-poly（ethylene glycol）-transferrin（Ⅰ）： Tumor-targeted Vector for Gene Delivery In.vitro

The work described the synthesis and evaluation of PEI-g-comb-PEG-transferrin as a potential system for gene therapy in vitro. The MW of PEG was 10KDa, and PEI was 2KDa. Its structure was identified by NMR, FT-IR and TGA spectroscopy. MTT assay found that at concentration up to 4000 n mol/L of the polymer, cell viability was over 85%. The bio-character of polymer/DNA complex was characterized by agarose gel electrophoresis, ethidium bromide exclusion and zeta-potential assay. The polymer could retardate DNA at N/P ratio 3.0-3.5 （mol/mol）. The particle size of the polymer/DNA complex was less than 300 nm. Transfection efficiency of the complex was studied in COS7 and NT2 cell lines.     

L-histidine decarboxylase as a probe in studies on histamine

Because the Falck-Hillarp formaldehyde fluorescence method, which was superbly applied to identify catecholaminergic and serotonergic neurons, is not applicable to histamine, the first author (T.W.) developed an antibody to L-histidine decarboxylase (HDC) for identification of the histaminergic neuron system in the brain. The anti-HDC antibody was of great use for mapping the location and distribution of this histaminergic neuron system. (S)-alpha-fluoromethylhistidine, a specific and potent irreversible inhibitor of HDC, was also very useful in studies on functions of the neuron system. The activity of HDC is increased by various agents, treatments, and physiological conditions. We found new compounds that increased HDC activity (i.e., tetradecanoylphobol acetate (TPA), other tumor promoters, and staphylococcal enterotoxin A); and using mast cell-deficient mutant (W/W(v)) mice, we obtained evidence that this increase occurred in macrophages. To further characterize the mechanism of increases in HDC activity, the second author (H.O.) cloned human HDC cDNA and a human HDC gene. In studies on the regulation mechanism of the HDC gene, which is expressed only in limited types of cells such as mast cells, enterochromaffin-like cells in the stomach, cells in the tuberomammillary nucleus of the brain, and macrophages, CpG islands in the promoter region of the HDC gene were found to be demethylated in cells expressing the gene, whereas they are methylated in other cells that do not express the HDC gene. In collaboration with many other researchers, we developed HDC knockout mice. The resulting research is producing a lot of interesting findings in our laboratory as well as in others. In summary, HDC has been and will be useful in studies on functions of histamine.     

ALTERATION IN CHROMATIN CONFORMATION OF PROLIFERATING AND DIFFERENTIATING ENZYME GENES IN NORMAL MOUSE LIVER AND ASCITES HEPATOMA CELLS AND ITS RELATION TO THE GENE EXPRESSION OF ENZYMES

Nuclei from the normal mouse liver were partially digested with micrococcal nuclease, followed by DNA extraction, agarose gel clectrophoresis and dot blot hybridization with ~(32)P-labeled cDNA probes of CPS_1 and ACT complex, It was clearly shown that the CPS_1 genes were distributed on the monomer, dimer. and trimer of nucleosomes, while the genes coding for ACT complex were distributed on the condensed oligonucleosomes. An opposite manner of distribution of CPS_1 and ACT complex genes was, however, noted in the case of ascites hepatoma cells, in which the specific activity of ACT was 13 times higher than that in the normal liver, while that of CPS_1 was remarkably reduced. Similar patterns of change in mRNA level of CPS_1 and ACT complex were observed in the normal mouse liver and ascites hepatoma cells, indicating a close relationship between chromatin structure and gene expression of these enzymes.     

Cooperative Competition Clustering for Gene Selection

Clustering analysis of data from DNA microarray hybridization studies is an essential task for identifying biologically relevant groups of genes. Attribute cluster algorithm (ACA) has provided an attractive way to group and select meaningful genes. However, ACA needs much prior knowledge about the genes to set the number of clusters. In practical applications, if the number of clusters is misspecified, the performance of the ACA will deteriorate rapidly. We propose the Cooperative Competition Cluster Algorithm (CCCA) in this paper. In the algorithm, we assume that both cooperation and competition exist simultaneously between clusters in the process of clustering. By using this principle of Cooperative Competition, the number of clusters can be found in the process of clustering. Experimental results on a synthetic and gene expression data are demonstrated. The results show that CCCA can choose the number of clusters automatically and get excellent performance with respect to other competing methods.     

Studies of poly-<Emphasis Type="Italic">L</Emphasis>-lysine-starch nanoparticle preparation and its application as gene carrier

Anion starch nanoparticle (StNP) with a diameter of 50 nm was prepared in water-in-oil microemulsion, with soluble starch as raw materials and POCl₃ as crosslinking agent. PLL-StNP was prepared by linking poly-L-lysine (PLL) on the surface of StNP. At the same time, the size of PLL-StNP and its stability in aqueous solution were checked by AFM. The analysis of plasmid DNA binding, DNase I enzymatic degradation, toxicity and transfection were done. We discovered that PLL-StNP may be used as non-virus nanoparticle gene carrier. And we developed the method of preparing PLL-StNP gene carrier and used it in cell transfection. As non-virus gene carrier, PLL-StNP has some advantages, such as large load of DNA, high transfection efficiency, low cell toxicity and biodegradability.     

Development of a systems analysis approach for resolving the structure of biodegrading soil systems

An experimental and mathematical method is developed for the microbial systems analysis of polyaromatic hydrocarbon (PAH)-degrading mixed cultures in PAH-contaminated “town gas” soil systems. Frequency response is the primary experimental and data analysis tool used to probe the structure of these complicated systems. The objective is to provide a fundamental protocol for evaluating the performance of specific mixed microbial cultures on specific soil systems by elucidating the salient system variables and their interactions. Two well-described reactor systems, a constant volume stirred tank reactor (CSTR) and a plug flow differential volume reactor, are used in order to remove performance effects that are related to reactor type as opposed to system structure. These two reactor systems are well-defined systems that can be described mathematically and represent the two extremes of one potentially important system variable, macroscopic mass transfer. The experimental and mathematical structure of the protocol is described, experimental data is presented, and data analysis is demonstrated for the stripping, sorption, and biodegradation of napththalene.     

CLONING, EXPRESSION AND CHARACTERIZATION OF Pro3 GENE OF YEAST Saccharomyces cerevisiae

The proline biosynthetic pathway and Pro genes in Saccharomyces cerevisiae have just begun to be studied recently. In our laboratory, Pro2 gene of S. cerevisiae had been cloned in yeast. As described in this paper, yeast Pro3 gene was also cloned, which can complement yeast Pro3 mutants, and be expressed efficiently in E. coli. The high activities of this gene product, L-pyrroline-5-carboxylate (P5C) reductase, can be detected in both organisms. The activity of the Pro3 gene product in multiple copy plasmids is not higher than that of single copy genes in chromosomes in both yeast and E. coll. The preliminary characterization of the gene is also reported.     

Novel amphiphilic fluorescent graft copolymers: synthesis,characterization, and potential as gene carriers

Amphiphilic fluorescent graft copolymer (PVP‐PyATAm) was successfully synthesized by the free radical copolymerizations of hydrophobic monomer N‐acryloyl‐thioureylene‐4‐(1‐pyrene)‐butyryl amide (PyATAm) with hydrophilic precursor polymers of vinyl‐functionalized poly (N‐vinylpyrrolidone) (Acryloyl‐PVP) in DMF. FT‐IR, ¹H NMR, TEM, gel permeation chromatography‐multi‐angle laser light scattering, UV‐vis spectroscopy, viscometric measurement, and fluorescence spectroscopy were used to characterize this copolymer. The TEM observation showed that the copolymer PVP‐ PyATAm formed spherical micelles in an aqueous solution and the size of micelles was between 50 and 70 nm in diameter. The interaction of PVP‐PyATAm copolymer and plasmid DNA was examined by agarose gel electrophoresis and TEM. Results indicated that the copolymer–DNA complexes were self‐assembled and the size of complexes was between 90 and 120 nm in diameter. Cytotoxity studies using MTT colorimetric assays suggested good biocompatibility of PVP‐PyATAm in vitro. These results suggested the potential of this graft copolymer as gene delivery carrier. Copyright © 2007 John Wiley & Sons, Ltd.