On the computational power of insertion-deletion systems

Gene insertion and deletion are basic phenomena found in DNA processing or RNA editing in molecular biology. The genetic mechanism and development based on these evolutionary transformations have been formulated as a formal system with two operations of insertion and deletion, called insertion-deletion systems (Kari and Thierrin, 1996; Kari et al., 1997).We investigate the generative power of insertion-deletion systems (InsDel systems), and show that the family INS ¹ ₁ DEL ¹ ₁ is equal to the family of recursively enumerable languages. This gives a positive answer to an open problem posed in Kari et al. (1997) where it was conjectured contrary. This revised version was published online in June 2006 with corrections to the Cover Date.     

The fluorescence behavior from SAM of dendron with rhodamine B as a center

We studied energy transfer between rhodamine B molecules centered in each corn-shaped dendrons that forms self-assembled monolayer (SAM) film on an Au substrate. A SAM film using dendron moiety as a spacer can change the distance between rhodamines depending on the size, so that the energy transfer from an initially photo-excited rhodamine to its surrounding molecules can be controlled. The absorption spectrum of a SAM film for each generation of dendron was measured to ascertain a linear correlation between the generation and the distance. Picosecond time-resolved fluorescence spectra showed clear differences in the fluorescence decay dynamics between third-generation (G3) and fourth-generation (G4) dendron SAM films. In addition, we found that “dry” or “wet” dendron SAM considerably influenced fluorescence behavior. As a result, the use of “wet” G4 SAM is suitable in preserving photo-excitation energy. This is because it gave almost equal dynamics to G4 dendron in the dilute solution and prevented deactivation by energy dissipation.     

Sar1 Affects the Localization of Perilipin 2 to Lipid Droplets

Lipid droplets (LDs) are intracellular organelles that are ubiquitous in many types of cells. The LD core consists of triacylglycerols (TGs) surrounded by a phospholipid monolayer and surface proteins such as perilipin 2 (PLIN2). Although TGs accumulate in the phospholipid bilayer of the endoplasmic reticulum (ER) and subsequently nascent LDs buds from ER, the mechanism by which LD proteins are transported to LD particles is not fully understood. Sar1 is a GTPase known as a regulator of coat protein complex Ⅱ (COPⅡ) vesicle budding, and its role in LD formation was investigated in this study. HuH7 human hepatoma cells were infected with adenoviral particles containing genes coding GFP fused with wild-type Sar1 (Sar1 WT) or a GTPase mutant form (Sar1 H79G). When HuH7 cells were treated with oleic acid, Sar1 WT formed a ring-like structure around the LDs. The transient expression of Sar1 did not significantly alter the levels of TG and PLIN2 in the cells. However, the localization of PLIN2 to the LDs decreased in the cells expressing Sar1 H79G. Furthermore, the effects of Sar1 on PLIN2 localization to the LDs were verified by the suppression of endogenous Sar1 using the short hairpin RNA technique. In conclusion, it was found that Sar1 has some roles in the intracellular distribution of PLIN2 to LDs in liver cells.     

Uterine Deletion of Bmal1 Impairs Placental Vascularization and Induces Intrauterine Fetal Death in Mice

Recently, it was demonstrated that the expression of BMAL1 was decreased in the endometrium of women suffering from recurrent spontaneous abortion. To investigate the pathological roles of uterine clock genes during pregnancy, we produced conditional deletion of uterine Bmal1 (cKO) mice and found that cKO mice could receive embryo implantation but not sustain pregnancy. Gene ontology analysis of microarray suggested that uterine NK (uNK) cell function was suppressed in cKO mice. Histological examination revealed the poor formation of maternal vascular spaces in the placenta. In contrast to WT mice, uNK cells in the spongiotrophoblast layer, where maternal uNK cells are directly in contact with fetal trophoblast, hardly expressed an immunosuppressive NK marker, CD161, in cKO mice. By progesterone supplementation, pregnancy could be sustained until the end of pregnancy in some cKO mice. Although this treatment did not improve the structural abnormalities of the placenta, it recruited CD161-positive NK cells into the spongiotrophoblast layer in cKO mice. These findings indicate that the uterine clock system may be critical for pregnancy maintenance after embryo implantation.     

Development and Evaluation of a Robust Sandwich Immunoassay System Detecting Serum WFA-Reactive IgA1 for Diagnosis of IgA Nephropathy

Aberrant glycosylation of IgA1 is involved in the development of IgA nephropathy (IgAN). There are many reports of IgAN markers focusing on the glycoform of IgA1. None have been clinically applied as a routine test. In this study, we established an automated sandwich immunoassay system for detecting aberrant glycosylated IgA1, using Wisteria floribunda agglutinin (WFA) and anti-IgA1 monoclonal antibody. The diagnostic performance as an IgAN marker was evaluated. The usefulness of WFA for immunoassays was investigated by lectin microarray. A reliable standard for quantitative immunoassay measurements was designed by modifying a purified IgA1 substrate. A validation study using multiple serum specimens was performed using the established WFA-antibody sandwich automated immunoassay. Lectin microarray results showed that WFA specifically recognized N-glycans of agglutinated IgA1 in IgAN patients. The constructed IgA1 standard exhibited a wide dynamic range and high reactivity. In the validation study, serum WFA-reactive IgA1 (WFA+-IgA1) differed significantly between healthy control subjects and IgAN patients. The findings indicate that WFA is a suitable lectin that specifically targets abnormal agglutinated IgA1 in serum. We also describe an automated immunoassay system for detecting WFA+-IgA1, focusing on N-glycans.     

Correction and evaluation of the effect due to parasitic motion on primary accelerometer calibration

Primary accelerometer calibration is carried out under the assumption that a vibration exciter gives a rectilinear motion to an accelerometer to be calibrated. However practical vibration given by the vibration exciter includes parasitic motion such as transverse, rocking, and bending motion. Such parasitic motion would give two serious effects on primary calibration results, transverse motion effect and vibration distribution effect. Transverse motion effect is caused by an inner product of the vectors of both transverse motion and transverse sensitivity. On the other hand, the vibration distribution effect is caused by relative motion between a sensing point of accelerometer and a spot sensed by the interferometer. As these effects have close interaction between parasitic motion and measuring instruments, it would be very difficult to evaluate them by measuring independently each component.     

Effects of Sampling Tube Geometry on Soft Clayey Sample Quality Evaluated by Nondestructive Methods

Sample disturbance caused by difference in sampling tube geometry was evaluated by two nondestructive methods: the measurement of the residual effective stress (p_r') by ceramic disc; and the use of the bender element to ascertain the shear wave velocity (V_s), and thus the maximum shear modulus (G_BE). Samples were measured under atmosphere, i.e., not under confined stress conditions. The soil samples were obtained from two sources: reconstituted Kasaoka clay prepared in the laboratory, and at the test site at Takuhoku, Hokkaido, Japan. Samplers with different geometrical designs, referring to the Japanese standard stationary piston sampler, were used for the model ground and field sampling. The geometrical effects of the sampling tube, for example, the thickness of the tube wall, the edge angle, and the existence of a piston were carefully examined. The quality of the samples taken with different samplers was evaluated by p_r' and G_BE, values which were normalized by the in situ vertical effective stress (σ'_vo) and G_f measured by the seismic cone test in the field. It was found from these studies that p_r'/σ'_vo and G_BE/G_f vary considerably due to the geometry of the sampler, with the edge angle of sampling tubes being the most important feature in obtaining high quality samples. The wall thickness, and thus, the area ratio of the sampler is not critical to the sample quality if the edge angle is sharp enough. The existence of the piston does not significantly influence the sample quality in field samples. Furthermore, the correlation between G_BE and p_r' was also investigated, and it was found that the two parameters are strongly dependent.     

GPC Profile Change of Potato Starch with Extrusion Processing

Native potato starch (moisture content 15%) was treated by twin screw extruder under four operating conditions with varying barrel temperatures (110°C–230°C). These modified starch samples were compared to native and drum-dried starch. Starch sample solution for gel chromatography was prepared by the three methods (acidic, alkaline, and neutral methods). They were subjected to gel chromatography on Toyopearl HW-75, and some difference was found among the three gel chromatographic patterns obtained from the same starch solution. This discrepancy among GPC patterns suggests formation of some types of anhydro-bonds between chains of amylopectin and or amylose in the extrusion process. Elevating barrel temperature increases degree of depolymerization. The size of fragments formed with the treatment is bigger than that of oligosaccharides but smaller than that of amylose.