Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2

The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3′ tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3′ tail of UnaL2 RNA contains a stem region with a putative internal loop. Deletion of the putative internal loop region abolishes UnaL2 mobilization, indicating that this putative internal loop is required for UnaL2 retrotransposition; the exact role of the putative internal loop in retrotransposition, however, has not been elucidated. To establish a structure-based foundation on which to address the issue of the putative internal loop function in retrotransposition, we used NMR to determine the solution structure of a 36 nt RNA derived from the 3′ conserved tail of UnaL2. The region forms a compact structure containing a single bulged cytidine and a U–U mismatch. The bulge and mismatch region have conformational flexibility and molecular dynamics simulation indicate that the entire stem of the 3′ conserved tail RNA can anisotropically fluctuate at the bulge and mismatch region. Our structural and mutational analyses suggest that stem flexibility contributes to UnaL2 function and that the bulged cytidine and the U–U mismatch are required for efficient retrotransposition.     

A monoclonal antibody to the carbohydrate chain on human hepatocellular carcinoma-associated antigen which suppressed tumor growth in nude mice

Summary There have been few reports stating that monoclonal antibody alone inhibits human solid tumor growth in vivo. The present study demonstrated that monoclonal antibody S1 (IgG2a), which recognized the antigenic determinant of the carbohydrate moiety, showed antibody-dependent cell (or macrophage)-mediated cytotoxicity (ADCC or ADMC) in conjunction with murine splenocytes of both BALB/c and athymic mice. In vivo experiments demonstrated that the antibody S1 clearly prolonged the survival of athymic mice which had been inoculated with a human liver carcinoma cell line. In addition, the antibody S1 significantly suppressed the human hepatoma line transplanted s.c. into nude mice. ¹²⁵I-Labeled monoclonal antibody S1 revealed that the antibody accumulated significantly in the tumor mass. Many mononuclear cells were observed surrounding tumor cells when the antibody was given. This model system might be useful for analyzing the ADCC (or ADMC) mechanism in vivo.     

Phosphorylation of a Protein (pp56) is Related to the Regeneration of Rice Cultured Suspension Cells

Short-term cultured suspension cells of rice (Oryza sativa L.)are capable of regeneration, but not in long-term culture. Forclarification of the mechanism of regeneration, protein phosphorylationin short-term and long-term cultured suspension cells was comparedby two dimensional- polyacrylamide gel electrophoresis. A 56kDa protein having an isoelectric point of 4.5 was phosphorylatedin vitro in short-term cultured suspension cells, but was notphosphorylated after regeneration. This protein in longtermcultured suspension cells remained phosphorylated after transferto the regeneration medium. However, using an antibody raisedagainst this protein from short-term cultured suspension cells,it was always detected in long-term and short-term culturedsuspension cells after transfer to the regeneration medium.The partial amino acid sequence of the HPLC-purified proteinshowed homology to a calcium-binding protein from maize. Thephosphorylation of the 56 kDa protein (pp56) appears to be associatedwith the regeneration of cultured rice cells. (Received December 11, 1995; Accepted June 3, 1996)     

BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes

Microarray technology has become employed widely for biological researchers to identify genes associated with conditions such as diseases and drugs. To date, many methods have been developed to analyze data covering a large number of genes, but they focus only on statistical significance and cannot decipher the data with biological concepts. Gene Ontology (GO) is utilized to understand the data with biological interpretation; however, it is restricted to specific ontology such as biological process, molecular function, and cellular component. Here, we attempted to apply MeSH (Medical Subject Headings) to interpret groups of genes from biological viewpoint. To assign MeSH terms to genes, in this study, contexts associated with genes are retrieved from full set of MEDLINE data using machine learning, and then extracted MeSH terms from retrieved articles. Utilizing the developed method, we implemented a software called BioCompass. It generates high-scoring lists and hierarchical lists for diseases MeSH terms associated with groups of genes to utilize MeSH and GO tree, and illustrated a wiring diagram by linking genes with extracted association from articles. Researchers can easily retrieve genes and keywords of interest, such as diseases and drugs, associated with groups of genes. Using retrieved MeSH terms and OMIM in conjunction with, we could obtain more disease information associated with target gene. BioCompass helps researchers to interpret groups of genes such as microarray data from a biological viewpoint.     

Electron tomographic analysis of cytokinesis in the brown alga Silvetia babingtonii (Fucales,Phaeophyceae)

In brown algae, membrane resources for the new cell partition during cytokinesis are mainly flat cisternae (FCs) and Golgi-derived vesicles. We used electron tomography coupled with rapid freezing/freeze substitution of zygotes to clarify the structure of transient membrane compartments during cytokinesis in Silvetia zygotes. After mitosis, an amorphous membranous structure, considered to be an FC intermediate was observed near endoplasmic reticulum clusters, lying between two daughter nuclei. FCs were arrayed at the cytokinetic plane, and a tubular membranous network was formed around them. This network might be formed by the consecutive fusion of spherical vesicles that are linked to the edges of FCs to form a membranous network (MN). At the initial stage of the formation of a membranous sac (MS) from the MN, the MS had flat and swollen parts, with the latter showing membranous tunnels. Coated pits were detected with high frequency at the swollen parts of the MS. This observation indicated that membranous tunnels disappeared by recycling of excess membrane via endocytosis, and the swollen part became flat. The MN appeared at the edges of the growing MS. MN and the MN-MS complex were observed along the cytokinetic plane in several spaces. The MS expanded by the incorporation of MN or other MS in its neighborhood. With the maturation of the new cell partition membrane, the thickness of the MS became constant and the membrane cavity disappeared. The changes in the surface area and volume of the transient membrane compartment during cytokinesis were analyzed from the tomographic data.     

Sport-specific characteristics of trunk muscles in collegiate wrestlers and judokas

This study evaluated the sport-specific characteristics of the cross-sectional areas (CSAs) of trunk muscles and trunk muscle strength in wrestlers and judokas. We also examined whether their trunk muscles and muscle strength depended on athletic performance levels in each sport. The subjects comprised 14 male collegiate wrestlers and 14 judokas. Magnetic resonance imaging was used to assess the trunk muscle CSAs at the L3-4 level parallel to the lumbar disc space. A Biodex System3 was used to measure isokinetic trunk flexor and extensor muscle strength of peak torque, work, average torque, and average power. The absolute and relative CSAs of the trunk muscles in the wrestlers and judokas were significantly different (rectus abdominis: wrestling > judo, P < 0.05; obliques: wrestling < judo, P < 0.05; quadratus lumborum: wrestling < judo, P < 0.01). We confirmed that the absolute and relative trunk extensor and flexor strength of peak torque, work, and average torque were significantly higher in the collegiate wrestlers than in judokas. On athletic performance, the tendency of the CSAs and muscular strength of trunk muscles was not consistent with athletic performance levels in each sport. Our findings indicated that the sport-specific characteristics of the CSAs of the trunk muscles and trunk muscle strength obviously differed between the 2 similar sports. Athletes should practice the sport-specific training of trunk muscles and develop sport specificity in their sports. Particularly, wrestlers have to train in trunk flexion and extension motions, and judokas need to strengthen trunk rotation and lateral flexion motions. This information will be available for athletes as well as strength and technical training coaches in wrestling, judo, and the other sports.     

Three-/four-repeat-dependent aggregation profile of tau microtubule-binding domain clarified by dynamic light scattering analysis

The analysis of the self-assembly mechanism of the tau microtubule-binding domain (MBD) could provide the information needed to develop an effective method for the inhibition of the tau filament formation because of its core region that forms the filament. The MBD domain in the living body consists of similar three or four 31- to 32-residue repeats, namely 3RMBD (R134) and 4RMBD (R1234), respectively. The filament formation of the MBD has been mainly investigated by fluorescence spectroscopy utilizing the β-sheet structure-binding signal sensor thioflavin. This method observes the aggregation indirectly, and provides no information on the time-dependent change in aggregation size or volume. Thus, to determine the structure necessary for initiating MBD self-association, the dynamic light scattering (DLS) method was applied to the analysis of the aggregations of 3RMBD, 4RMBD and their component single repeats and shown to be a powerful tool for directly analyzing filament formation. DLS analysis clearly showed that the building unit for initiating the aggregation is the intermolecular R3-R3 disulfide-bonded dimer for 3RMBD and the intramolecular R2-R3 disulfide-bonded monomer for 4RMBD, and their aggregation processes under physiological condition differ from each other, which has not been clearly revealed by the conventional fluorescence method. The repeat-number-dependent aggregation model of MBD, together with the function of each repeat, reported in this paper should help to devise a method of preventing tau PHF formation.