Single-nucleotide polymorphism analysis using fluorescence resonance energy transfer between DNA-labeling fluorophore,fluorescein isothiocyanate,and DNA intercalator,POPO-3, on bacterial magnetic particles

To develop an analytical system for single-nucleotide polymorphisms (SNPs), the fluorescence resonance energy transfer (FRET) technique was employed on a bacterial magnetic particle (BMP) surface. A combination of fluorescein isothiocyanate (FITC; excitation 490 nm/emission 520 nm) labeled at the 5' end of DNA and an intercalating compound (POPO-3, excitation 534 nm/emission 570 nm) was used to avoid the interference from light scattering caused by nanoparticles. After hybridization between target DNA immobilized onto BMPs and FITC-labeled probes, fluorescence from POPO-3, which was excited by the energy from the FITC, was detected. The major homozygous (ALDH2*1), heterozygous (ALDH2*1/*2), and minor homozygous (ALDH2*2) genotypes in the blood samples were discriminated by this method. The assay described herein allows for a simple and rapid SNP analysis using a fully automated system.     

Estimation of dispersal distance by mark-recapture experiments using traps: correction of bias caused by the artificial removal by traps

Although in mark-recapture experiments traps are useful to estimate the dispersal distance of organisms, they cause a dilemma that may be called a kind of Heisenberg effect: a large number of traps should be placed to yield a precise estimate of mean dispersal distance, while these traps shorten the mean dispersal distance itself by intercepting organisms that should have dispersed for further distances. We propose a procedure to solve this dilemma by placing traps uniformly in a lattice pattern, and by assuming a random movement and a constant rate of settlement for organisms. We applied this procedure to estimate the dispersal distance of the sugarcane wireworm Melanotus okinawensis Ohira (Coleoptera: Elateridae). The estimated mean dispersal distance was 143.8 m. Through the use of a conventional method of estimation, the mean dispersal distance was estimated to be 118.1 m. Thus, it was shown that the conventional estimate of dispersal distance was 18% smaller than the corrected estimate in our experiment.     

Prevention and induction of autoimmune exocrinopathy is dependent on pathogenic autoantigen cleavage in murine Sjögren's syndrome

The in vivo role of autoantigen cleavage during apoptosis in autoimmune diseases remains unclear. Previously, we found a cleavage product of 120-kDa alpha-fodrin as an important autoantigen in the pathogenesis of primary Sj?gren's syndrome (SS). In the murine primary SS model, tissue-infiltrating CD4(+) T cells purified from the salivary glands bear a large proportion of Fas ligand, and the salivary gland duct cells constitutively possess Fas. Infiltrating CD4(+) T cells, but not CD8(+) T cells, identified significant (51)Cr release against mouse salivary gland cells. In vitro studies demonstrated that apoptotic mouse salivary gland cells result in a specific alpha-fodrin cleavage into 120 kDa and that preincubation with caspase inhibitor peptides blocked alpha-fodrin cleavage. In vivo treatment with caspase inhibitors N-benzyloxycarbonyl-Val-Ala-Asp fluoromethyl ketone and N-acetyl-Asp-Glu-Val-Asp-al-CHO into the murine model results in dramatic inhibitory effects on the development of autoimmune lesions and in restoration of sicca syndrome. Furthermore, we found that immunization with recombinant alpha-fodrin protein identical with an autoantigen into normal recipients induced autoimmune lesions similar to SS. These data indicate that prevention and induction of autoimmune exocrinopathy is dependent on autoantigen cleavage via caspase cascade and that caspase inhibitors might provide a new therapeutic option directed at reducing tissue damage in the murine model for SS.     

Wolbachia-mediated parthenogenesis in the predatory thrips Franklinothrips vespiformis (Thysanoptera: Insecta)

Wolbachia are bacterial endosymbionts in arthropods and filarial nematodes. They cause thelytoky, which is a form of parthenogenesis in which females produce females without males, in hymenopteran insects. Infection of this parthenogenesis-inducing Wolbachia has been restricted to the order Hymenoptera, but was found in another insect order, Thysanoptera. A parthenogenetic colony of a predatory thrips Franklinothrips vespiformis (Aeolothripidae) possessed B-group Wolbachia. Male progeny were produced from this thrips by heat and tetracycline treatments. Males produced motile sperm, which were transferred to the female spermatheca by mating. However, the mating did not affect the sex ratios of the next generation, suggesting that the sperm do not fertilize the eggs.     

Detection of biomolecular interaction between biotin and streptavidin on a self-assembled monolayer using magnetic nanoparticles

For developing a magnetic bioassay system, an investigation to determine the presence of a specific biomolecular interaction between biotin and streptavidin was done using magnetic nanoparticles and a silicon substrate with a self-assembled monolayer. Streptavidin was immobilized on the magnetic particles, and biotin was attached to the monolayer-modified substrate. The reaction of streptavidin-modified magnetic particles on the biotin-modified substrate was clearly observed under an optical microscope. The magnetic signals from the particles were detected using a magnetic force microscope. The results of this study demonstrate that the combination of a monolayer-modified substrate with biomolecule-modified magnetic particles is useful for detecting biomolecular interactions in medical and diagnostic analyses.     

Independent and cooperative roles of N-glycans and molecular chaperones in the folding and disulfide bond formation of the low-density lipoprotein (LDL) receptor-related protein

The low-density lipoprotein receptor-related protein (LRP) is a large receptor that contains extensive glycosylation sites and disulfide bonds. Here we analyzed how N-linked glycosylation and molecular chaperones function during LRP folding. Treatment of cells with a glycosylation inhibitor tunicamycin significantly impaired LRP folding, although binding to receptor-associated protein (RAP), a specialized chaperone for LRP, was not affected. The effects of tunicamycin on LRP folding were not due to an inhibition of RAP glycosylation since a mutant RAP that harbors a mutation at its sole glycosylation site was still capable of promoting LRP folding. The roles of N-linked glycosylation and the lectin chaperone, calnexin, in LRP folding were further dissected using LRP minireceptors that carry mutations at individual glycosylation sites. Interestingly, we found that RAP interacts with oxidoreductase ERp57 and mediates its interaction with LRP. Since previous studies have shown that N-glycan-bound calnexin/calreticulin are also capable of recruiting ERp57, our results suggest that N-linked glycosylation and RAP can independently and cooperatively recruit oxidoreductases to facilitate protein folding and proper disulfide bond formation.     

Sex pheromone and related compounds in the Ishigaki and Okinawa strains of the tussock moth Orgyia postica (Walker) (Lepidoptera: Lymantriidae)

Two distinct electroantennographycally active (EAG-active) components, A and B, and a weakly active component C were found in a solvent extract from virgin females of the Ishigaki strain of the tussock moth, Orgyia postica (Walker). Components A, B, and C were found in the extract of the females at 4.0, 0.5, and 4.0 ng/female respectively. Components A, B, and C were identified as (6Z,9Z,11S,12S)-11,12-epoxyhenicosa-6,9-diene [(11S,12S)-1: posticlure], (6Z)-henicos-6-en-11-one (2), and (6Z,9Z)-henicosa-6,9-diene (3), respectively. Component B was absent in the extract from the Okinawa strain, in which components A and C were present at 2.0 and 1.5 ng/female respectively. (11S,12S)-1 and the racemic mixture showed attractiveness for both the Okinawa and Ishigaki strains, whereas (11R,12R)-1 did not. The addition of 2 significantly reduced the trap catches with (11S,12S)-1 on the Okinawa strain which lacked 2, while there was no significant inhibitory effect on the Ishigaki strain. The addition of 3 to (11S,12S)-1 did not significantly affect trap catches at Ishigaki or Okinawa. This confirmed that the attractant pheromone of O. postica of the Ishigaki strain is also (11S,12S)-1.     

Prediction of physical protein-protein interactions

Many essential cellular processes such as signal transduction, transport, cellular motion and most regulatory mechanisms are mediated by protein-protein interactions. In recent years, new experimental techniques have been developed to discover the protein-protein interaction networks of several organisms. However, the accuracy and coverage of these techniques have proven to be limited, and computational approaches remain essential both to assist in the design and validation of experimental studies and for the prediction of interaction partners and detailed structures of protein complexes. Here, we provide a critical overview of existing structure-independent and structure-based computational methods. Although these techniques have significantly advanced in the past few years, we find that most of them are still in their infancy. We also provide an overview of experimental techniques for the detection of protein-protein interactions. Although the developments are promising, false positive and false negative results are common, and reliable detection is possible only by taking a consensus of different experimental approaches. The shortcomings of experimental techniques affect both the further development and the fair evaluation of computational prediction methods. For an adequate comparative evaluation of prediction and high-throughput experimental methods, an appropriately large benchmark set of biophysically characterized protein complexes would be needed, but is sorely lacking.