A new sigillid ostracod from submarine caves of the Ryukyu Islands, Japan

A new troglobitic sigillid genus, Kasella , is found in the submarine caves of the Ryukyu Islands. Sigillids are primitive podocopid ostracods having ancient characters such as unequal valves and many small adductor muscle scars. Kasella is possibly derived from the sigillid Cardobairdia , a deep-sea muddy bottom inhabitant, or its relatives. Submarine caves are characterized as both 'safe places', where biological factors such as competition and predation are reduced, and as 'crypts', representing dark and oligotrophic environments. It is likely that Kasella has successfully colonized hard substrates in caves, particularly exploiting the crevices on cave walls and ceilings. Kasella may have adapted to this cryptic habitat in response to strong cytheroidean competition and predation by, for example, gastropods that do not survive well in dark and oligotrophic submarine caves. In adapting to an oligotrophic cave environment, Kasella has undergone significant divergence in carapace morphology, possibly accompanying functional and behavioural changes.     

Dielectric analysis of mitochondria isolated from rat liver. I. Swollen mitoplasts as simulated by a single-shell model

A re-evaluation of the dielectric studies on isolated mitochondria (Pauly, H., Packer, L. and Schwan, H.P. (1960) J. Biophys. Biochem. Cytol. 7, 589-601, and ibid. 7, 603-612) is presented. The suspensions of 'mitoplasts' prepared from rat liver mitochondria by a hyposmotic (10 mM KCl) treatment showed a dielectric dispersion with its characteristic frequency lying in the 1-100 MHz range. In the analysis of data special emphasis was put on the choice of the theoretical models to employ after scrutiny of their applicability to the suspensions tested. As such we adopted the theory of Hanai et al. (Hanai, T., Asami, K., and Koizumi, N. (1979) Bull. Inst. Chem. Res., Kyoto Univ. 57, 297-305) that was advanced to include concentrated suspensions of shelled spheres. Curve fittings based on that theory resulted in a better agreement with experiment than the fittings based on a conventional theory for dilute suspensions. Major findings from our analyses on the swollen mitoplasts are that: (i) the limiting membrane of the mitoplasts has a specific electrical capacity of 1 microF/cm2, (ii) the ratio of permittivity (or dielectric constant) for the mitoplast interior and permittivity for the external medium is 0.6-0.7, and (iii) the conductivity ratio between the interior phase and the medium is approx. 0.6. Reasons for discrepancy between the results of Pauly et al. and ours are discussed.     

Redox-dependent structural ambivalence of the cytoplasmic domain in the inner ear-specific cadherin 23 isoform

Cadherin 23 (Cdh23), an essential factor in inner ear mechano-electric transduction, exists in two alternatively spliced forms, Cdh23(+68) and Cdh23(−68), depending on the presence and absence of exon 68. Cdh23(+68) is inner ear-specific. The exon 68-corresponding region confers an α-helical configuration upon the cytoplasmic domain (Cy) and includes a cysteine residue, Cys³²⁴⁰. We demonstrate here that Cy(+68) as well as the transmembrane (TM) plus Cy(+68) region is present in two different forms in transfected cells, reduced and non-reduced, the latter existing in more compact configuration than the former. The observed characteristic of Cy(+68) was completely abolished by Cys³²⁴⁰Ala substitution. Treatment of TMCy(+68)-transfected cells with diethyl maleate, a glutathione depleting reagent, resulted in conversion of the non-reduced to the reduced form of TMCy(+68), suggesting glutathione to be a Cys³²⁴⁰-binding partner. Multiple alignment of mammalian Cdh23Cy sequences indicated the occurrence of conformation-inducible Cys in Cdh23Cy of mammals, but not lower vertebrates. The implications of Cys-dependent structural ambivalence of Cdh23 in inner ear mechanosensation are discussed.     

Phylogeography of ten native herbaceous species in the temperate region of Japan: implication for the establishment of seed transfer zones for revegetation materials

Revegetation using native species requires the development of seed transfer zones that capture genetic distinctiveness and adaptive potentials while avoiding potential maladaptation and genetic contamination by exotic genotypes. Delineation based on phylogeographic information has recently been used to establish seed transfer zones; however, only a few herbaceous species that are suitable for revegetation have been investigated in the temperate regions of Japan. We investigated the phylogeography of non-coding regions of chloroplast DNA of ten native species in the temperate regions of Japan. Although no species showed clear-cut geographical distributions of the 2–14 haplotypes identified, spatially constrained Bayesian clustering showed two clusters in five species (Calamagrostis epigejos, Eragrostis ferruginea, Imperata cylindrica, Microstegium japonicum, and Microstegium vimineum) but not for others. Posterior modes of clusters for I. cylindrica and M. vimineum showed delineations at Chubu (the middle of Honshu Island), which divide the study region into northeastern and southwestern regions, indicating that these species had recovered from glacial refugia. Posterior mode of cluster for E. ferruginea showed that one consists of a coastal zone along the Pacific Ocean side of western Japan, while the other consists of the remaining area, indicating range expansion from south coast to north. Delineation of C. epigejos and M. japonicum were unclear. The mixed results indicated that establishing seed transfer zones for herbaceous species in Japan will require phylogeographical studies on a wide range of species that may be suitable for revegetation.     

Chemical and genetic diversity of Ligularia vellerea in Yunnan, China

Intra-specific diversity in Liularia vellerea growing in the northwestern to central Yunnan province of China was studied by chemical and genetic approaches. Samples collected in the Jianchuan, Lijiang, and Zhongdian areas contained 6,15-dioxygenated furanoeremophilanes as their major components (type A); whereas samples from the Luguhu area accumulated 1,6-dioxygenated furanoeremophilanes (type B); a sample from near Kunming, however, contained 6,15-dioxygenated eremophilanolides (type C). 11 beta H- and 11 alpha H-6 beta-angeloyloxy-15-carboxyeremophil-7-en-12,8-olides (eremofarfugins D and E) were also isolated and their structures were determined. A correlation between the composition and the DNA sequence was observed in the ITSs.     

Localization of calcineurin in the mature and developing retina.

We studied the localization of calcineurin by immunoblotting analysis and immunohistochemistry as a first step in clarifying the role of calcineurin in the retina. Rat, bovine, and human retinal tissues were examined with subtype-nonspecific and subtype-specific antibodies for the A alpha and A beta isoforms of its catalytic subunit. In mature retinas of the three species, calcineurin was localized mainly in the cell bodies of ganglion cells and the cells in the inner nuclear layer, in which amacrine cells were distinctively positive. The calcineurin A alpha and A beta isoforms were differentially localized in the nucleus and the cytoplasm of the ganglion cell, respectively. Calcineurin was also present in developing rat retinas, in which the ganglion cells were consistently positive for it. The presence of calcineurin across mammalian species and regardless of age shown in the present study may reflect its importance in visual function and retinal development, although its function in the retina has not yet been clarified. (J Histochem Cytochem 49:187-195, 2001)     

BMP-7 counteracts TGF-beta1-induced epithelial-to-mesenchymal transition and reverses chronic renal injury

Bone morphogenic protein (BMP)-7 is a 35-kDa homodimeric protein and a member of the transforming growth factor (TGF)-beta superfamily. BMP-7 expression is highest in the kidney, and its genetic deletion in mice leads to severe impairment of eye, skeletal and kidney development. Here we report that BMP-7 reverses TGF-beta1-induced epithelial-to-mesenchymal transition (EMT) by reinduction of E-cadherin, a key epithelial cell adhesion molecule. Additionally, we provide molecular evidence for Smad-dependent reversal of TGF-beta1-induced EMT by BMP-7 in renal tubular epithelial cells and mammary ductal epithelial cells. In the kidney, EMT-induced accumulation of myofibroblasts and subsequent tubular atrophy are considered key determinants of renal fibrosis during chronic renal injury. We therefore tested the potential of BMP-7 to reverse TGF-beta1-induced de novo EMT in a mouse model of chronic renal injury. Our results show that systemic administration of recombinant human BMP-7 leads to repair of severely damaged renal tubular epithelial cells, in association with reversal of chronic renal injury. Collectively, these results provide evidence of cross talk between BMP-7 and TGF-beta1 in the regulation of EMT in health and disease.     

Analysis of expression profile using fuzzy adaptive resonance theory

MOTIVATION: It is well understood that the successful clustering of expression profiles give beneficial ideas to understand the functions of uncharacterized genes. In order to realize such a successful clustering, we investigate a clustering method based on adaptive resonance theory (ART) in this report. RESULTS: We apply Fuzzy ART as a clustering method for analyzing the time series expression data during sporulation of Saccharomyces cerevisiae. The clustering result by Fuzzy ART was compared with those by other clustering methods such as hierarchical clustering, k-means algorithm and self-organizing maps (SOMs). In terms of the mathematical validations, Fuzzy ART achieved the most reasonable clustering. We also verified the robustness of Fuzzy ART using noised data. Furthermore, we defined the correctness ratio of clustering, which is based on genes whose temporal expressions are characterized biologically. Using this definition, it was proved that the clustering ability of Fuzzy ART was superior to other clustering methods such as hierarchical clustering, k-means algorithm and SOMs. Finally, we validate the clustering results by Fuzzy ART in terms of biological functions and evidence. AVAILABILITY: The software is available at http//www.nubio.nagoya-u.ac.jp/proc/index.html