Use of a deviant mitochondrial genetic code in yellow-green algae as a landmark for segregating members within the phylum

Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However, due to the fact that the morphological characteristics that segregate eustigmatophytes from other closely related algae can be only obtained through laborious electron microscopic techniques, the number of members in this phylum have increased rather slowly. We attempted, therefore, to segregate two closely related groups of algae, eustigmatophytes and yellow-green algae, on the basis of a molecular phylogenetic tree as a means of providing an alternative method of distinguishing these phyla. We analyzed the mitochondrial cytochrome oxidase subunit I (COXI) gene sequences of eight algae classified as xanthophyceans and found that six manifested the expected deviant genetic code where AUA codes for methionine (AUA/Met), but not for isoleucine (AUA/Ile) as in the universal genetic code. The other two, Monodus sp. (CCMP 505) and Ophiocytium majus (CCAP 855/1), which were presumed to be yellow-green algae, and all the examined eustigmatophytes utilized AUA for Ile. In addition, the phylogenetic tree of COXI gene sequences showed that the six yellow-green algae bearing the AUA/Met deviant code composed a tight clade with a bootstrap value of 100%. The phylogenetic tree of the corresponding sequences from Monodus sp. and Ophiocytium majus and the eustigmatophytes also composed a tight cluster, but with a bootstrap value of 92%. These results strongly suggest that two previously classified members of yellow-green algae belong to the phylum Eustigmatophyta. Therefore, examination of the mitochondrial genetic code in algae appears to be a potentially very useful genetic marker for classifying these organisms, especially when it is considered with the results obtained through a molecular phylogenetic tree. Received: 14 December 1996 / Accepted: 3 April 1997     

Autophagy in regulation of Toll-like receptor signaling

Toll-like receptors (TLRs) serve as the major innate immune sensors for detection of specific molecular patterns on various pathogens. TLRs activate signaling events mainly by utilizing ubiquitin-dependent mechanisms. Recent research advances have provided evidence that TLR signaling is linked to induction of autophagy. Autophagy is currently known to affect both of the immune defense and suppression of inflammatory responses. In TLR-associated immune responses, autophagic lysis of intracellular microbes (called xenophagy) contributes to the former mechanism, while the latter seems to be mediated by the control of the mitochondrial integrity or selective autophagic clearance of aggregated signaling proteins (called aggrephagy). Several autophagy-related ubiquitin-binding proteins, such as SQSTM1/p62 and NDP52, mediate xenophagy and aggrephagy. In this review, we summarize the expanded knowledge regarding TLR signaling and autophagy signaling. After that, we will focus on autophagy-associated signaling downstream of TLRs and the effect of autophagy on TLR signaling, thus highlighting the signaling crosstalk between the TLR-associated innate immune responses and the regulation of innate immunity by xenophagy and aggrephagy.     

Effects of redecoration of a hospital isolation room with natural materials on stress levels of denizens in cold season

We investigated the effects of redecoration of a hospital isolation room with natural materials on thermoregulatory, cardiovascular and hormonal parameters of healthy subjects staying in the room. Two isolation rooms with almost bilaterally-symmetrical arrangements were used. One room (RD) was redecorated with wood paneling and Japanese paper, while the other (CN) was unchanged (with concrete walls). Seven healthy male subjects stayed in each room for over 24 h in the cold season. Their rectal temperature (T_re) and heart rate, and the room temperature (T_a) and relative humidity were continuously measured. Arterial blood pressures, arterial vascular compliance, thermal sensation and thermal comfort were measured every 4 h except during sleeping. Blood was sampled after the stay in the rooms. In RD, T_a was significantly higher by about 0.4°C and relative humidity was lower by about 5% than in CN. Diurnal T_re levels of subjects in RD significantly differed from those in CN, i.e., T_res were significantly higher in RD than in CN especially in the evening. In RD, the subjects felt more thermally-comfortable than in CN. Redecoration had minimal effects on cardiovascular parameters. Plasma levels of catecholamines and antidiuretic hormone did not differ, while plasma cortisol level was significantly lower after staying in RD than in CN by nearly 20%. The results indicate that, in the cold season, redecoration with natural materials improves the thermal environment of the room and contributes to maintaining core temperature of denizens at preferable levels. It also seems that redecoration of room could attenuate stress levels of isolated subjects.     

Occurrence and types of ectomycorrhizae present in seedlings ofPicea glehnii in a natural forest in Hokkaido

Picea glehnii seedlings whose ages ranged from 2 to 5 years and which were growing in aP. glehnii-Abies sachalinensis natural forest where the surface had been scarified 6 years before, were assessed for the occurrence and types of ectomycorrhizae. Based on the macro- and microscopic characteristics, 34 types of ectomycorrhizae were classified. The basidiomycetes were clearly dominant and it was common to observe more than one type of mycorrhiza occurring in the same root tip. The diversity of mycorrhizal types and the presence of at least one type of ectomycorrhiza in a single seedling, observed in this work, indicate a very dynamic system of mycorrhizal formation inP. glehnii seedlings, which allows them to survive and grow in a forest surface subjected to soil scarification.     

CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA

Centromere protein (CENP) B boxes, recognition sequences of CENP-B, appear at regular intervals in human centromeric alpha-satellite DNA (alphoid DNA). In this study, to determine whether information carried by the primary sequence of alphoid DNA is involved in assembly of functional human centromeres, we created four kinds of synthetic repetitive sequences: modified alphoid DNA with point mutations in all CENP-B boxes, resulting in loss of all CENP-B binding activity; unmodified alphoid DNA containing functional CENP-B boxes; and nonalphoid repetitive DNA sequences with or without functional CENP-B boxes. These four synthetic repetitive DNAs were introduced into cultured human cells (HT1080), and de novo centromere assembly was assessed using the mammalian artificial chromosome (MAC) formation assay. We found that both the CENP-B box and the alphoid DNA sequence are required for de novo MAC formation and assembly of functional centromere components such as CENP-A, CENP-C, and CENP-E. Using the chromatin immunoprecipitation assay, we found that direct assembly of CENP-A and CENP-B in cells with synthetic alphoid DNA required functional CENP-B boxes. To the best of our knowledge, this is the first reported evidence of a functional molecular link between a centromere-specific DNA sequence and centromeric chromatin assembly in humans.     

The scanning probe microscope as a novel genomic analysis tool

We have developed a novel and efficient genomic analysis tool that combines scanning probe microscopy (SPM) and image processing with molecular biology techniques to accelerate genomic research. To examine the correlation between chromosome volume and DNA content, we scanned human metaphase chromosome sets with an atomic force microscope to examine the chromosome volume distribution. We found that the chromosome volume distribution agreed with DNA length distribution (obtained from a public database), and that the short arm to long arm volume ratio showed good agreement with the genomic position of the centromere. We were also able to predict the genomic position of an arbitrary gene marker with high accuracy by combining a scanning near-field optical/atomic force microscope and image processing techniques using fluorescence in situ hybridization. Thus, a novel SPM-based system developed here will be an effective tool to rapidly and accurately map DNA markers and construct physical map, which contributes to the advancement of genomic science.     

Caloric restriction stimulates revascularization in response to ischemia via adiponectin-mediated activation of endothelial nitric-oxide synthase

Caloric restriction (CR) can extend longevity and modulate the features of obesity-related metabolic and vascular diseases. However, the functional roles of CR in regulation of revascularization in response to ischemia have not been examined. Here we investigated whether CR modulates vascular response by employing a murine hindlimb ischemia model. Wild-type (WT) mice were randomly divided into two groups that were fed either ad libitum (AL) or CR (65% of the diet consumption of AL). Four weeks later, mice were subjected to unilateral hindlimb ischemic surgery. Body weight of WT mice fed CR (CR-WT) was decreased by 26% compared with WT mice fed AL (AL-WT). Revascularization of ischemic hindlimb relative to the contralateral limb was accelerated in CR-WT compared with AL-WT as evaluated by laser Doppler blood flow and capillary density analyses. CR-WT mice had significantly higher plasma levels of the fat-derived hormone adiponectin compared with AL-WT mice. In contrast to WT mice, CR did not affect the revascularization of ischemic limbs of adiponectin-deficient (APN-KO) mice. CR stimulated the phosphorylation of endothelial nitric-oxide synthase (eNOS) in the ischemic limbs of WT mice. CR increased plasma adiponectin levels in eNOS-KO mice but did not stimulate limb perfusion in this strain. CR-WT mice showed enhanced phosphorylation of AMP-activated protein kinase (AMPK) in ischemic muscle, and administration of AMPK inhibitor compound C abolished CR-induced increase in limb perfusion and eNOS phosphorylation in WT mice. Our observations indicate that CR can promote revascularization in response to tissue ischemia via an AMPK-eNOS-dependent mechanism that is mediated by adiponectin.     

Intraspecific diversity of Oenococcus oeni strains determined by sequence analysis of target genes

Using molecular techniques and sequencing, we studied the intraspecific diversity of Oenococcus oeni, a lactic acid bacterium involved in red winemaking. A relationship between the phenotypic and genotypic characterization of 16 O. oeni strains isolated from wine with different levels of enological potential was shown. The study was based on the comparative genomic analysis by subtractive hybridization between two strains of O. oeni with opposite enological potential. The genomic sequences obtained from subtractive hybridization were amplified by polymerase chain reaction and sequenced for the 16 strains. A considerable diversity among strains of O. oeni was observed.