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1.  Helix control in polymers 
Artificial DNA, PNA & XNA  2012;3(2):31-44.
The helix is a critical conformation exhibited by biological macromolecules and plays a key role in fundamental biological processes. Biological helical polymers exist in a single helical sense arising from the chiral effect of their primary units—for example, DNA and proteins adopt predominantly a right-handed helix conformation in response to the asymmetric conformational propensity of D-sugars and L-amino acids, respectively. In using these homochiral systems, nature blocks our observations of some fascinating aspects of the cooperativity in helical systems, although when useful for a specific purpose, “wrong” enantiomers may be incorporated in specific places. In synthetic helical systems, on the contrary, incorporation of non-racemic chirality is an additional burden, and the findings discussed in this review show that this burden may be considerably alleviated by taking advantage of the amplification of chirality, in which small chiral influences lead to large consequences. Peptide nucleic acid (PNA), which is a non-chiral synthetic DNA mimic, shows a cooperative response to a small chiral effect induced by a chiral amino acid, which is limited, however, due to the highly flexible nature of this oligomeric chimera. The lack of internal stereochemical bias is an important factor which makes PNA an ideal system to understand some cooperative features that are not directly accessible from DNA.
doi:10.4161/adna.20572
PMCID: PMC3429529  PMID: 22772039
helix control; chiral amplification; cooperativity; helical polymers; PNA
2.  Hubs in biological interaction networks exhibit low changes in expression in experimental asthma 
Asthma is a complex polygenic disease involving the interaction of many genes. In this study, we investigated the allergic response in experimental asthma. First, we constructed a biological interaction network using the BOND (Biomolecular Object Network Databank) database of literature curated molecular interactions. Second, we mapped differentially expressed genes from microarray data onto the network. Third, we analyzed the topological characteristics of the modulated genes. Fourth, we analyzed the correlation between the topology and biological function using the Gene Ontology classifications. Our results demonstrate that nodes with high connectivity (hubs and superhubs) tend to have low levels of change in gene expression. The significance of our observations was confirmed by permutation testing. Furthermore, our analysis indicates that hubs and superhubs have significantly different biological functions compared with peripheral nodes based on Gene Ontology classification. Our observations have important ramifications for interpreting gene expression data and understanding biological responses. Thus, our analysis suggests that a combination of differential gene expression plus topological characteristics of the interaction network provides enhanced understanding of the biology in our model of experimental asthma.
doi:10.1038/msb4100138
PMCID: PMC1865580  PMID: 17437023
allergic asthma; biological network; Gene Ontology; microarray
3.  Immunomodulatory Effects of CpG Oligodeoxynucleotides on Established Th2 Responses 
CpG oligodeoxynucleotides (CpG ODNs) are known to induce type 1 T-helper-cell (Th1) responses. We have previously demonstrated that CpG ODNs administered during sensitization prevent Th2-mediated eosinophilic airway inflammation in vivo. We also reported that key Th1 cytokines, gamma interferon (IFN-γ) and interleukin 12 (IL-12), are not necessary for this protection. Recent in vivo data suggest that CpG ODNs might also reverse established pulmonary eosinophilia. In order to clarify how CpG ODNs can inhibit established Th2 responses, we evaluated the cytokine production from splenocytes from antigen- and alum-immunized mice. Restimulation with antigen induced IL-5, which was clearly inhibited by coculture with CpG ODNs in a concentration-dependent manner. CpG ODNs also induced IFN-γ, but in a concentration-independent manner. The inhibition of IL-5 production was not mediated through natural killer cells or via CD8+ T lymphocytes. Although IFN-γ plays an important role in inhibition of antigen-induced IL-5 production by CpG ODNs, IFN-γ was not the sole factor in IL-5 inhibition. CpG ODNs also induced IL-10, and this induction correlated well with IL-5 inhibition. Elimination of IL-10 reduced the anti-IL-5 effect of CpG ODNs, although incompletely. This may be because IFN-γ, induced by CpG ODNs, is also inhibited by IL-10, serving as a homeostatic mechanism for the Th1-Th2 balance. Overproduction of IFN-γ was downregulated by CpG ODN-induced IL-10 via modulation of IL-12 production. These data suggest that CpG ODNs may inhibit established Th2 immune responses through IFN-γ and IL-10 production, the latter serving to regulate excessive Th1 bias. These properties of CpG ODNs might be a useful feature in the development of immunotherapy adjuvants against allergic diseases such as asthma.
doi:10.1128/CDLI.9.6.1260-1269.2002
PMCID: PMC130087  PMID: 12414759

Results 1-3 (3)