The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation

EF-P is a bacterial tRNA-mimic protein, which accelerates the ribosome-catalyzed polymerization of poly-prolines. In Escherichia coli, EF-P is post-translationally modified on a conserved lysine residue. The post-translational modification is performed in a two-step reaction involving the addition of a β-lysine moiety and the subsequent hydroxylation, catalyzed by PoxA and YfcM, respectively. The β-lysine moiety was previously shown to enhance the rate of poly-proline synthesis, but the role of the hydroxylation is poorly understood. We solved the crystal structure of YfcM and performed functional analyses to determine the hydroxylation mechanism. In addition, YfcM appears to be structurally distinct from any other hydroxylase structures reported so far. The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology. Furthermore, YfcM has a metal ion-coordinating motif, similar to YbeY. The metal ion-coordinating motif of YfcM resembles a 2-His-1-carboxylate motif, which coordinates an Fe(II) ion and forms the catalytic site of non-heme iron enzymes. Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the β-lysylated lysine residue of EF-P. Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM.     

Embryonic development of the jumping bristletail Pedetonutus unimaculatus Machida,with special reference to embryonic membranes (Hexapoda: Microcoryphia,Machilidae)

In the machilid Pedetonutus unimaculatus, a germ disc is formed by the aggregation and proliferation of cells within a broadly defined embryonic area. Cells adjacent to the embryonic area form the serosal fold that grows beneath the embryo. Then the embryonic margin is extended to form a cell layer or amnion that lies between the embryo and serosal fold. Thus, an amnioserosal fold is formed by the addition of the amnion to the serosal fold. Serosal cells cover the entire surface of the egg and begin to secrete a serosal cuticle. Soon the amnioserosal fold is withdrawn, and the embryo is exposed to the egg surface. The spreading amnion replaces the serosal cells that finally degenerate through the formation of a secondary dorsal organ. In the areas of amnion anterior and lateral to the embryo, yolk folds form and encompass the embryo. The amnion is a provisional dorsal closure and never participates in the formation of the definitive one. The amnioserosal fold of the Microcoryphia appears to have the functional role of secreting a serosal cuticle beneath the embryo. This fold of the Microcoryphia may be regarded as an ancestral form of the amnioserosal folds of the Thysanura-Pterygota. the yolk folds may appear to be passive transformation of the yolk mass linked to positioning of the growing embryo within the egg. There is no evidence that the yolk folds and the cavity appearing between them in the Microcoryphia are homologous to the amnioserosal fold and amniotic cavity in the Thysanura-Pterygota. The yolk folds appear to be one of the embryological autapomorphies in the Microcoryphia. © 1994 Wiley-Liss, Inc.     

Synthesis of vinyl arabinose ester catalyzed by protease from Streptomyces sp.

The transesterification of 0.5 M divinyladipate with 0.25 M arabinose in dimethylformamide for 7 days was catalyzed by Streptomyces sp. alkaline protease to give 5-O-vinyladipoyl-d-arabinofuranose at ca. 50% yield. Only enzymatic transesterification of primary hydroxyl group of arabinofuranose proceeded without esterification of arabinopyranose.     

A low-temperature method for maintaining plant regeneration activity in embryogenic callus of rice (Oryza sativa L.)

 A method was developed to maintain plant regeneration activity of rice cells (Oryza sativa L.) using embryogenic callus. Calluses were cultured in suspension, then on solid medium, to form compact globular callus resistant to low-temperature stress and with high plant regeneration activity. Callus preserved at 5  °C for 5 months regenerated plants from protoplasts at a frequency higher than from non-preserved callus from cv. Nipponbare, and cv. Koshihikari, but at lower rates from cv. Akitakomachi. Similar results were obtained from protoplasts of the three cultivars. Callus preserved at 5  °C for 8 months incurred cell damage, yet some surviving cells divided in suspension culture and eventually regenerated whole plants. Preserved and non-preserved regenerated plants showed similar levels of somaclonal variation. Received: 7 January 1999 / Revision received: 28 April 1999 / Accepted: 26 May 1999     

Over expression of PQQ glucose dehydrogenase in Escherichia coli under holo enzyme forming condition

Summary The over expression of PQQ glucose dehydrogenase PQQGDH was investigated. The level of PQQGDH expressed in E.coli PP2418/pGEc1 was more than 10 fold when the cultivation was carried out under holo enzyme forming condition in the presence of 600 nM of PQQ and 10 mM of MgCl₂, compared with those of apo condition. It may be due to the difference in thermal stability of apo and holo PQQGDH.     

In vitro studies of skin fibroblasts from a patient with a new type of primary cortisol resistance: glucocorticoid receptor status and glucocorticoid effect on DNA synthesis

Studies made on cultured skin fibroblasts obtained from a patient with primary cortisol resistance are described. Whole cell in vitro assays, using the patient's fibroblasts revealed a reduction in the dexamethasone binding capacity (7.86 +/- 0.73 fmol/micrograms DNA, mean +/- SD, n = 3; normal: 15.2 +/- 1.90 fmol/micrograms DNA, n = 8) and an apparently normal dissociation constant (3.69 +/- 0.15 nM; normal: 3.74 +/- 0.40 nM). In addition, the effects of glucocorticoids on DNA synthesis in these cells were examined. DNA synthesis was inhibited by dexamethasone both in normal fibroblasts and in the patient's cells, but the patient's cells were less sensitive to this inhibition, indicating resistance of the cells to glucocorticoid in vitro. These results suggest that the resistance of target tissues to glucocorticoids is due to the reduction in receptor number and that this is the primary defect in this new type of primary cortisol resistance in man.     

Notes onOrdus chiayiensis in Tsukuba

Ordus chiayiensis isolated from discolored red pine needles is redescribed and illustrated.     

Generalizable brain network markers of major depressive disorder across multiple imaging sites

Many studies have highlighted the difficulty inherent to the clinical application of fundamental neuroscience knowledge based on machine learning techniques. It is difficult to generalize machine learning brain markers to the data acquired from independent imaging sites, mainly due to large site differences in functional magnetic resonance imaging. We address the difficulty of finding a generalizable marker of major depressive disorder (MDD) that would distinguish patients from healthy controls based on resting-state functional connectivity patterns. For the discovery dataset with 713 participants from 4 imaging sites, we removed site differences using our recently developed harmonization method and developed a machine learning MDD classifier. The classifier achieved an approximately 70% generalization accuracy for an independent validation dataset with 521 participants from 5 different imaging sites. The successful generalization to a perfectly independent dataset acquired from multiple imaging sites is novel and ensures scientific reproducibility and clinical applicability.

Biomarkers for psychiatric disorders based on neuroimaging data have yet to be put to practical use. This study overcomes the problems of inter-site differences in fMRI data by using a novel harmonization method, thereby successfully constructing a generalizable brain network marker of major depressive disorder across multiple imaging sites.     

Syntheses and preventive effects of analogues related to 1α,25-dihydroxy-2β-(3-hydroxypropoxy)vitamin D3 (ED-71) on bone mineral loss in ovariectomized rats

Analogues related to 1α,25-dihydroxy-2β-(3-hydroxypropoxy)vitamin D₃ (ED-71) (2), 26,27-dimethyl ED-71 (3) and 26,27-diethyl ED-71 (4), were synthesized from lithocholic acid (5). In the study of the preventive effects of these analogues and ED-71 (2) on bone mineral loss in ovariectomized rats, 26,27-dimethyl ED-71 (3) showed the most potent activity.