Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA.

The experiments described here examined the effects of reaction conditions, various additives, and local sequence on the formation and stability interstrand cross-links (ICLs) derived from the reaction of an apurinic/apyrimidinic (AP) site with the exocyclic amino group of an adenine residue on the opposing strand in duplex DNA. Cross-link formation was observed in a range of different buffers, with faster formation rates observed at pH 5. Inclusion of the base excision repair enzyme alkyladenine DNA glycosylase (hAAG) which binds tightly to AP-containing duplexes decreased, but did not completely prevent, formation of the dA-AP ICL. Formation of the dA-AP ICL was not altered by the presence of the biological metal ion Mg2+ or the biological thiol, glutathione. Several organocatalysts of imine formation did not enhance the rate of dA-AP ICL formation. Duplex length did not have a large effect on dA-AP yield, so long as the melting temperature of the duplex was not significantly below the reaction temperature (the duplex must remain hybridized for efficient ICL formation). Formation of the dA-AP ICL was examined in over 40 different sequences that varied the neighboring and opposing bases at the cross-linking site. The results indicate that ICL formation can occur in a wide variety of sequence contexts under physiological conditions. Formation of the dA-AP ICL was strongly inhibited by the aldehyde-trapping agents methoxyamine and hydralazine, by NaBH3CN, by the intercalator ethidium bromide, and by the minor groove-binding agent netropsin. ICL formation was inhibited to some extent in bicarbonate and Tris buffers. The dA-AP ICL showed substantial inherent stability under a variety of conditions and was not a substrate for AP-processing enzymes APE1 or Endo IV. Finally, we characterized cross-link formation in a small (11 bp) stem-loop (hairpin) structure and in DNA-RNA hybrid duplexes.

Liver Segmentation in MRI Images using an Adaptive Water Flow Model.

BACKGROUND: Identification and precise localization of the liver surface and its segments are essential for any surgical treatment. An algorithm of accurate liver segmentation simplifies the treatment planning for different types of liver diseases. Although liver segmentation turns researcher's attention, it still has some challenging problems in computer-aided diagnosis. OBJECTIVE: This study aimed to extract the potential liver regions by an adaptive water flow model and perform the final segmentation by the classification algorithm. MATERIAL AND METHODS: In this experimental study, an automatic liver segmentation algorithm was introduced. The proposed method designed the image by a transfer function based on the probability distribution function of the liver pixels to enhance the liver area. The enhanced image is then segmented using an adaptive water flow model in which the rainfall process is controlled by the liver location in the training images and the gray levels of pixels. The candidate liver segments are classified by a Multi-Layer Perception (MLP) neural network considering some texture, area, and gray level features. RESULTS: The proposed algorithm efficiently distinguishes the liver region from its surrounding organs, resulting in perfect liver segmentation over 250 Magnetic Resonance Imaging (MRI) test images. The accuracy of 97% was obtained by quantitative evaluation over test images, which revealed the superiority of the proposed algorithm compared to some evaluated algorithms. CONCLUSION: Liver segmentation using an adaptive water flow algorithm and classifying the segmented area in MRI images yields more robust and reliable results in comparison with the classification of pixels.

Catalytic activation of Bacillus laccase after temperature treatment: Structural & biochemical characterization.

Laccases belong to a family of multicopper oxidases that have strong oxidation ability towards phenolic compounds. Here, more detailed investigations were carried out on a Bacillus laccase with remarkable behavior of activation after thermal treatment. The kcat of the enzyme was increased 2.5 fold after 50 min incubation at 70 °C. Copper content determination revealed a molar copper to protein ratio of 3.2 in the both sample. The present paper concerns the differences which are induced in enzyme structure after thermal treatment using common biochemical methods Intrinsic fluorescence of the enzyme was increased after incubation at 70 °C indicating higher compactness of the structure in comparison to untreated molecules. Quenching analysis did not show any significant changes in flexibility of the enzyme structure. The local changes in secondary structures were also obvious by far-UV circular dichroism when non-incubated and incubated laccase were compared. Oligomerization studies of the enzyme using gas-phase electrophoretic mobility macromolecule analysis (GEMMA) did not prove any oligomerization.