Crystal structure of hyperthermophilic archaeal initiation factor 5A: a homologue of eukaryotic initiation factor 5A (eIF-5A)

Eukaryotic initiation factor 5A (eIF-5A) is ubiquitous in eukaryotes and archaebacteria and is essential for cell proliferation and survival. The crystal structure of the eIF-5A homologue (PhoIF-5A) from a hyperthermophilic archaebacterium Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by the molecular replacement method. PhoIF-5A is predominantly composed of beta-strands comprising two distinct folding domains, an N-domain (residues 1-69) and a C-domain (residues 72-138), connected by a short linker peptide (residues 70-71). The N-domain has an SH3-like barrel, while the C-domain folds in an (oligonucleotide/oligosaccharide binding) OB fold. Comparison of the structure of PhoIF-5A with those of archaeal homologues from Methanococcus jannaschii and Pyrobaculum aerophilum showed that the N-domains could be superimposed with root mean square deviation (rmsd) values of 0.679 and 0.624 A, while the C-domains gave higher values of 1.824 and 1.329 A, respectively. Several lines of evidence suggest that eIF-5A functions as a biomodular protein capable of interacting with protein and nucleic acid. The surface representation of electrostatic potential shows that PhoIF-5A has a concave surface with positively charged residues between the N- and C-domains. In addition, a flexible long hairpin loop, L1 (residues 33-41), with a hypusine modification site is positively charged, protruding from the N-domain. In contrast, the opposite side of the concave surface at the C-domain is mostly negatively charged. These findings led to the speculation that the concave surface and loop L1 at the N-domain may be involved in RNA binding, while the opposite side of the concave surface in the C-domain may be involved in protein interaction.     

Measuring the number of co-dominants in ecological communities

We suggest a concept that allows the objective determination of the number of co-dominants in a community. We define co-dominants as a subset of species that are more abundant and more uniformly distributed than other species in a given sample. We compare the sample with a model community and use Simpsons diversity index to estimate the apparent number of co-dominants. Dominant species determined in this way are responsible for 70–90% of the total measure of abundance in the sample. The statistical significance of the apparent number of co-dominants may be assessed by a randomization test.     

Mapping QTLs influencing rice floral morphology using recombinant inbred lines derived from a cross between <Emphasis Type="Italic">Oryza sativa</Emphasis> L. and <Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff

To understand the genetic basis of floral traits associated with the mating system in rice, we analyzed pistil, stamen and glume traits using a recombinant inbred line population, derived from a cross between an Asian cultivated rice ( Oryza sativa L.), Pei-kuh, and a wild rice ( Oryza rufipogon Griff.), W1944. Quantitative trait loci (QTLs) affecting floral morphology were detected by composite interval mapping using a linkage map constructed using 147 markers, mostly RFLPs. A total of 7, 4, 14 and 6 QTLs were detected for traits related to pistil, stamen, and size and shape of the glume, respectively. Comparison of 31 QTLs affecting these organs revealed ten QTLs affecting the different organs in four adjacent regions on chromosomes 2, 4, 5 and 10, but most QTLs (68%) were located separately on the whole chromosomes. Although four QTLs for stigma breadth, anther length and thickness of lemma and palea explained more than 25% of the total phenotypic variance, most QTLs (87%) had smaller effects. These results suggest that quantitative variation observed for pistil, stamen and glume traits is controlled by several distinct genes with small effects.     

Continuous culture of novel mitochondrial cells lacking nuclei

We isolated stable cell lines, designated as mitochondrial cells, from cybrids obtained by fusing mitochondria-less HeLa cells with platelets from patients with Leigh syndrome, a subtype of mitochondrial encephalomyopathy. The cells contain a pathogenic point mutation, T9176C, in the mitochondrial DNA. Hematoxylin-eosin staining, confocal fluorescent microscopy and flow cytometry in fixed or living cells showed that the majority of these mitochondrial cells lack nuclear DNA and nuclei, but contain active mitochondria. Despite the absence of nuclear DNA, these cells can be continuously generated in culture. Therefore, it is likely that they arise from the minority of cells which possess a nucleus.     

Radical scavenging by N-aminoazaaromatics

N-Aminoazaaromatics were found to react with nitric oxide in the presence of oxygen to afford deaminated products in high yields. The reaction proceeded almost instantaneously in various solvents including water, and one to two equivalent of NO was consumed depending upon the amount of oxygen coexisted, and 1 equivalent of N2O was released in the reaction. In addition, N-aminoazoles were deaminated by potassium superoxide to give parent azoles in good yields. Two equivalents of superoxide was consumed, and about half equivalents of both nitrite and nitrate ion were released. The results demonstrated that N-aminoazoles have ability to protect the biological system against the oxidation promoted by radicals such as nitrogen oxides and superoxide.     

Effect of 1,25(OH)2D3 on expression of estrogen receptor-alpha mRNA on rat osteosarcoma cell line (ROS 17/2.8)

In order to investigate the regulatory mechanisms of estrogen receptors (ER) in bone cells, changes in ER-alpha mRNA levels of rat osteosarcoma cell line (ROS 17/2.8) before and after exposure to 1,25(OH)2D3 and 17-beta estradiol respectively were measured by quantitative polymerase chain reaction using an internal standard. ER mRNA levels in the ROS 17/2.8 cultured with the medium alone had 5.029 +/- 1.623 mol/g total RNA x 10(-13) and were not statistically different from those cultured in the presence of 1,25(OH)2D3 at concentrations of 10(-12) M and less. ER mRNA levels in the ROS 17/2.8 cell line showed a small but a significant increase as a result of stimulation by 1,25(OH)2D3 at concentrations of 10(-10) and 10(-11) M. However, ER mRNA levels in ROS 17/2.8 cultured in the presence of 1,25(OH)2D3 at concentrations of 10(-9) M were not statistically different from those of the control. On the other hand, the expression of ER in ROS 17/2.8 cells cultured for 3 hours with various doses of 1,25(OH)2D3 showed, by immunoblotting methods, a significant increase at the dose of 10(-10) M in the expression of ER. Although a physiological significance is obscure, these observations suggest that 1,25(OH)2D3 plays a part in the expression of ER in ROS 17/2.8. No significant changes were seen in the expression of ER mRNA and the synthesis of ER as a result of stimulation by the estradiol.     

Secondary succession of plant communities in a subtropical mountainous region of SW China

Since 1985, originally forested mountainous areas of China have been allowed to return to their natural state after years of exploitation including agriculture, development, and logging. The reforms began earlier in less accessible locations, so that today the successional process is more advanced there. The vegetation in Luquan, Qiongzhusi, and Xishan near Kunming, central Yunnan, exhibits, in a limited area, a range of stages of plant succession that are widely encountered throughout the broader region, and thus affords a special opportunity for a comprehensive study. We analyzed the successional sequence of these various plant communities. They ranged from pioneer coniferous and/or pioneer deciduous broad-leaved stands to pre-mature semi-humid evergreen broad-leaved stands, through mixed coniferous and broad-leaved or mixed deciduous and evergreen broad-leaved stands. The succession proceeded from pioneer coniferous Pinus and Keteleeria, and deciduous Platycarya and Alnus, to late-successional evergreen broad-leaved Cyclobalanopsis and Castanopsis. Two regeneration types of woody species in either the early successional (15–50 years), the mid-successional (40–80 years), or the late-successional (80–180 years) stage were classified. Relatively high species diversity was found in the seral phase at the three study sites. The late-successional stage was commonest where human disturbance was least evident. Poor soil chemical properties under pioneer Pinus were seen as a limitation to plant growth, while the abundance of Alnus at the early stage led to an improved level of organic matter and nitrogen.     

Landscape genetic structure of <Emphasis Type="Italic">Betula maximowicziana</Emphasis> in the Chichibu mountain range,central Japan

We evaluated the genetic structure of 16 Betula maximowicziana populations in the Chichibu mountain range, central Japan, located within a 25-km radius; all but two populations were at altitudes of 1,100–1,400 m. The results indicate the effects of geographic topology on the landscape genetic structure of the populations and should facilitate the development of local-scale strategies to conserve and manage them. Analyses involving 11 nuclear simple sequence repeat loci showed that most populations had similar intrapopulation genetic diversity parameters. Population differentiation (F _ST = 0.021, G′_ST = 0.033) parameters for the populations examined were low but were relatively high compared to those obtained in a previous study covering populations in a much larger area with a radius of approximately 1,000 km (F _ST = 0.062, G′_ST = 0.102). Three populations (Iriyama, Kanayamasawa, and Nishizawa) were differentiated from the other populations by Monmonier’s and spatial analysis of molecular variance algorithms or by STRUCTURE analysis. Since a high mountain ridge (nearly 2,000 m) separates the Kanayamasawa and Nishizawa populations from the other 14 populations and the Kanayamasawa and Nishizawa populations are themselves separated by another mountain ridge, the genetic structure appears to be partly due to mountain ridges acting as genetic barriers and restricting gene flow. However, the Iriyama population is genetically different but not separated by any clear geographic barrier. These results show that the landscape genetic structure is complex in the mountain range and we need to pay attention, within landscape genetic studies and conservation programs, to geographic barriers and local population differentiation.     

Purification and characterization of renin binding protein (RnBP) from porcine kidney

Renin binding protein (RnBP) was purified from porcine kidney using pepstatin affinity column chromatography, DEAE-Sepharose column chromatography, gel filtration on Ultrogel-AcA 34, aminohexyl-Sepharose 4B column chromatography, and high performance liquid chromatography (HPLC) on TSK-gel G-3000 SW. The purified preparation was homogeneous as judged by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, polyacrylamide disc gel electrophoresis and isoelectric focusing on polyacrylamide gel. The isoelectric point was at pH 4.85, and the apparent molecular weight of RnBP was estimated to be 42,000 by SDS-polyacrylamide gel electrophoresis. The preparation did not show any renin activity and was stable for 30 min at 37 degrees C between pH 5.0 and 9.0 or on storage for 4 weeks at 4 degrees C or -80 degrees C. The activity of renin was greatly inhibited by RnBP. From the kinetic analysis of the inhibition we roughly estimated the dissociation constant between renin and RnBP to be about 0.2 nM, assuming that the stoichiometry in the complex, i.e., high molecular weight (HMW) renin, is one to one, and that the complex is inactive. The inhibitory activity of RnBP was lost by acidification at pH 3.0 and the activity of renin was restored. The purified RnBP formed a single precipitin line with the antiserum prepared with the purified HMW renin as antigen, which is RnBP-renin complex (Takahashi, S., et al. (1983) J. Biochem. 93, 265-274), and this line fused with one of the two precipitin lines formed between HMW renin and anti-HMW renin antiserum. The other of the two lines was between renin and anti-HMW renin antiserum. The purified preparation was thus identified as RnBP. The HMW renin was reconstituted with the purified RnBP and renin, and the apparent molecular weight of the reconstituted specimen was estimated to be 60,000 by gel filtration on Ultrogel AcA 44.