DNA as a ‘Nanomaterial’

DNA is recognized as a nanomaterial, not as a biological material, in the research field of nanotechnology. This article reviews recent research on nanowires, nanoarchitectures, computing, aptamers, biocatalysts, devices, and machines using DNA. In these works, the characteristics of DNA including facile synthesis by the solid-phase method, self-assembly, electro-conductivity, information elements, amplification, switching, molecular recognition, and catalytic functions, were appropriately applied. Multiple functions of DNA could be used simultaneously, and activated independently, by molecular switching. Therefore, the combinations of functional sequences of DNA can produce unique materials. It is obvious that the DNA molecule is one of the most promising functional nanomaterials. However, the application of DNA molecules is still under study because of the big gap that exists between theory and practice. We eagerly anticipate a ‘coming out’ of DNA due to breakthroughs in nanobiotechnology.     

Identification of adherens junction-associated GTPase activating proteins by the fluorescence localization-based expression cloning

The junctional complex, including tight junctions (TJs), adherens junctions (AJs), and desmosomes, plays crucial roles in the structure and functions of epithelial cellular sheets. In this study, we evaluated the fluorescence localization-based retrovirus-mediated expression cloning (FL-REX) method as an approach to identify novel molecular components of TJs and AJs. Using an expression library of cDNA-GFP-fusions derived from mRNA of a mouse epithelial cell line, we confirmed that cDNAs for various known TJ- and AJ-components could be cloned in the FL-REX. Furthermore, cDNAs for ARHGAP12 and SPAL3, two putative GTPase activating proteins (GAPs) for small G proteins, were cloned as novel components of the junctional complex. Immunofluorescence staining using antibodies generated in-house demonstrated that these GAPs were localized at epithelial cell-cell junctions in various mouse tissues, and were specific to AJs when observed under confocal laser-scanning microscopy. These data suggest that FL-REX is a powerful tool to identify novel proteins localized at TJs and AJs.     

mRNA expression of lysyl oxidase and matrix metalloproteinase-12 in mouse skin

Elastic fibers in the dermis play an important role in skin elasticity. The desmosine crosslinking structure constructed of lysyl oxidase (LOX) in elastic fibers contributes to elasticity, while elastic fibers are primarily degraded by one of the matrix metalloproteinases (MMPs), MMP-12. We investigated the gender differences and diurnal variation of these enzymes. Gender-based differences in LOX mRNA expression were detected, and were significantly lower in females. In contrast, higher MMP-12 mRNA expression was observed in the light period, suggesting that elastic fibers might be degraded in the light rather than the dark period.     

Uncoupling Sonic hedgehog control of pattern and expansion of the developing limb bud

Sonic hedgehog (Shh), which regulates proliferation in many contexts, functions as a limb morphogen to specify a distinct pattern of digits. How Shh's effects on cell number relate to its role in specifying digit identity is unclear. Deleting the mouse Shh gene at different times using a conditional Cre line, we find that Shh functions to control limb development in two phases: a very transient, early patterning phase regulating digit identity, and an extended growth-promoting phase during which the digit precursor mesenchyme expands and becomes recruited into condensing digit primordia. Our analysis reveals an unexpected alternating anterior-posterior sequence of normal mammalian digit formation. The progressive loss of digits upon successively earlier Shh removal mirrors this alternating sequence and highlights Shh's role in cell expansion to produce the normal digit complement.     

Metabolic profiling of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> metamorphosis: a new insight into the central metabolic pathways

Introduction

Metamorphosis is a complicated process in which cell proliferation, differentiation, and death are orchestrated to form the mature structures of insects. In Drosophila, this process is controlled by ecdysone, a steroid hormone responsible for tissue remodeling and organogenesis that gives rise to the adult fly.

Objective

By using a metabolomics approach, this study aimed to elucidate global changes in the central metabolic pathways in Drosophila throughout metamorphosis and then further examine the effects of temperature and origin on metabolic profiles.

Methods

Targeted and non-targeted metabolic profiling of time-course samples from Drosophila were constructed to cover a wide range of cellular metabolites during metamorphosis.

Results

This was the first wide-scale metabolomics study of Drosophila metamorphosis focusing on central metabolism. The abundance of detected metabolites changed drastically and correlated strongly with the development of Drosophila pupae. In non-stress conditions, temperature affected the developmental time, but the metabolic state at a certain stage of metamorphosis remained stable. Between D. melanogaster Canton S and Oregon R, similar metabolic profiles throughout metamorphosis was observed. However, there were still differences in purine and pyrimidine metabolism at an early stage in the pupal period, which was matched by differences in ecdysteroid levels.

Conclusion

This study supported the strength of metabolomics in the field of developmental biology. The results provided a general view on the metabolic profile of Drosophila during metamorphosis, which provides basic 3 knowledge for future metabolomics studies using Drosophila.

     

Rough sets and genetic algorithms in learning cellular neural networks cloning template for decision making system

We purpose to find a new beneficial method for accelerating the Decision-Making and classifier support applied on imprecise data. This acceleration can be done by integration between Rough Sets theory, which gives us the minimal set of decision rules, and the Cellular Neural Networks. Our method depends on Genetic Algorithms for designing the cloning template for more accuracy. Some illustrative examples are given to demonstrate the effectiveness of the proposed method, whose advantages and limitations are also discussed.     

Reverse genetic studies of the DNA damage response in the chicken B lymphocyte line DT40

In the 'post-genome' era, reverse genetics is one of the most informative and powerful means to investigate protein function. The chicken B lymphocyte line DT40 is widely used for reverse genetics because the cells have a number of advantages, including efficient gene targeting as well as a remarkably stable phenotype. Furthermore, the absence of functional p53 in DT40 cells enables identification of DNA damage using chromosome analysis by suppressing damage-induced apoptosis during interphase. This review summarizes the contribution of DT40 cells to reverse genetic studies of DNA damage response pathways in higher eukaryotic cells.