Isolation of clustered genes that are notably homologous to the eicosapentaenoic acid biosynthesis gene cluster from the docosahexaenoic acid-producing bacterium Vibrio marinus strain MP-1

A 40-kbp DNA fragment was isolated from the cosmid library of Vibrio marinus strain MP-1. Among the 22 putative open reading frames (ORFs) in this fragment, ORFs 8, 9, 10 and 11 had high homology with ORFs 5, 6, 7 and 8 of the eicosapentaenoic acid biosynthesis gene cluster, respectively. Then, we speculate that these ORFs are responsible for docosahexaenoic acid biosynthesis in this bacterium.     

Cloning and sequencing of clustered genes involved in fatty acid biosynthesis from the docosahexaenoic acid-producing bacterium, Vibrio marinus strain MP-1

A cluster of genes involved in fatty acid biosynthesis (fab) was isolated from docosahexaenoic acid (DHA)-producing Vibrio marinus strain MP-1. This fab gene cluster included five genes highly homologous to the Escherichia coli counterparts, and their order in the cluster was the same with that of the E. coli fab gene cluster except that the latter included the additional fabH gene. These fab genes should be involved in early steps of DHA biosynthesis in V. marinus strain MP-1.     

Spatial distribution patterns of trees at different life stages in a warm temperate forest

We have investigated tree distributions in relation to topography between different tree life history stages, from the seed-dispersal stage to the adult stage in a warm temperate evergreen broadleaved forest on Yakushima Island, Japan, to clarify the critical stages in determining adult tree distributions. We conducted a census of all living trees > or =30 cm tall and collected seed falls over three years using 25 seed traps in a 50 m x 50 m quadrat. Four life stages were defined: stage 1, dispersed seed; stage 2, individuals taller than 30 cm and diameter at breast height (DBH) < 1 cm; stage 3, trunks 1 cm < or = DBH < 10 cm; stage 4, trunks with DBH > or = 10 cm. We classified 17 common tree species into three groups; group A was distributed mainly on the upper slope, group B on the lower slope, and group C on both. Most of group A and B trees at stages 2-4 showed an aggregated distribution along the topographical gradient. The densities at stage 1 showed weaker aggregations according to slope. Topography-specific tree distribution was probably determined at the regeneration stage, and later survival was less effective as a mechanism of vegetation differentiation.     

The concentrations of major and trace elements in rat kidney: Aging effects and mutual relationships

The concentrations of 26 major to trace elements in rat kidneys aging from 5 to 113 weeks old were determined. The rats investigated were the same rats used previously reported to have 29 elements in bones (femurs). The samples were decomposed by high purity nitric acid and hydrogen peroxide. Eight elements (Na, Mg, Si, P, K, Ca, Fe and Zn) were determined using inductively coupled plasma atomic emission spectrometry (ICP-AES) and 18 elements (Mn, Co, Ni, Cu, As, Se, Rb, Sr, Mo, Cd, Sn, Sb, Cs, Ba, Tl, Pb, Bi and U) were determined using inductively coupled plasma mass spectrometry (ICP-MS). The aging effects on the concentrations of these elements and mutual elemental relationships were investigated. Analysis of variance (ANOVA) for age variations indicated that the concentrations of P, K, Mn and Mo were almost constant across the age of rats (p > 0.3). The concentration of many elements such as Na, Mg, Ca, Fe, Co, Cu, Zn, As, Se, Cd, Sn, Sb, Tl, Pb and Bi, showed significant increasing trends (p < 0.01) with different patterns. Rubidium, Cs, Pb and Bi showed significant age variations but not monotonic trends. Silicon, Ni, Sr, Ba and U showed large concentration scatterings without any significant trends (p > 0.01). The metabolism of these elements may not be well established in the kidney. Many toxic elements such as As, Cd, Sn, Pb and Bi showed a narrow concentration range among age-matched rats. The kidney may have established metabolic mechanisms to confine or accumulate these toxic elements even though their concentrations are very low (e.g., 10 ng g^?1 of Cd). These elements also closely coupled with Fe. A cluster analysis was performed using an elemental correlation matrix and indicated that these elements, including Fe, formed a cluster. However, another cluster analysis using “an aging effect eliminated” elemental correlation showed different clustering in which the Fe, Cd cluster disappeared.     

Theoretical modeling of the O-intermediate structure of bacteriorhodopsin

Bacteriorhodopsin is a prototype of efficient molecular machinery functioning as a light-activated proton pump. Among the five distinct intermediates (K, L, M, N, and O) of the photocycle, there is less structural information on the later stages compared with the early intermediates. Here, we report the structural modeling of the O-intermediate for which the determination of experimental structure remains difficult. Hypothetical conformational change of the molecule from the light-adapted state to the O-intermediate state was simulated by gradually changing the protonation state of two residues. To achieve accurate molecular modeling, we carefully constructed a realistic system of the native purple membrane. The modeled structure of the O-intermediate has some implications about proton transfer in the later stages of the photocycle and the structural response of bacteriorhodopsin to the inner charge distribution.     

The simple and rapid quantification method for L-3,4-dihydroxyphenylalanine (L-DOPA) from plant sprout using liquid chromatography-mass spectrometry

L-3,4-dihydroxyphenylalanine (L-DOPA) is one of the important secondary metabolites of plants and has been used for various purposes, such as in clinical treatment for Parkinson’s disease and dopamine-responsive dystonia. In plants, L-DOPA is a precursor of many alkaloids, catecholamines, and melanin; the L-DOPA synthesis pathway is similar to that in mammals. L-DOPA acts as an allelochemical, has an important role in several biological processes, such as stress response and metabolism, in plants. L-DOPA is widely used in the clinical treatment as well as a dietary supplement or psychotropic drug, understanding of biosynthesis of L-DOPA in plant could lead to a stable supply of L-DOPA. This paper describes an improved method for simple and rapid quantification of L-DOPA content using liquid chromatography-tandem mass spectrometry. The standard quantitative methods for L-DOPA require multiple purification steps or relatively large amounts of plant material. In our improved method, quantification of L-DOPA was possible with extract of one–two pieces of cotyledon without any partitioning or column for purification. The endogenous L-DOPA (approximately 4,000 µg g⁻¹ FW (fresh weight)) could be detected from the one pieces of cotyledon of the faba bean sprout using this method. This method was also effective for samples with low endogenous amounts of L-DOPA such as broccoli, Japanese white radish, pea, and red cabbage sprouts. Therefore, this improved method will allow to measurement of L-DOPA content easily and accurately from a small amount of plant tissue and contribute to understanding biosynthesis, catabolism, and transport of L-DOPA.     

Variation in tree growth,mortality and recruitment among topographic positions in a warm temperate forest

Questions: Do the population dynamics of trees differ among topographic positions and, if so, how does topographic position affect the population dynamics of species that are distributed in a topography‐specific manner? Which is the most important life stage in determining vegetation patterns? Location: Primary and secondary warm temperate evergreen broad‐leaved forest (40 ‐ 280 m a.s.l.) on the western part of Yakushima Island, Japan. Methods: Mortality, recruitment, DBH growth and distribution of stems (= 5 cm DBH) in a 2.62‐ha plot were surveyed in 1992 and 2002 to determine the relationships between population parameters and (1) topography and (2) distribution patterns of 17 common tree species. Results: Common species (n = 17) were classified into three distribution pattern groups: group A, distributed mainly on convex slopes; group B, on concave slopes, and group C, not aggregated with respect to topographic position. Stem mortality, recruitment and DBH growth were greater in group A than in group B within each topographic class. The hierarchy of stem mortality among topographic classes for groups A and B was convex > planar > concave. Stem recruitment density was relatively high on the convex and concave slopes, respectively, for groups A and B. Conclusions The topographical positions of adult trees were not always most suited for adult survival and growth. For group A, the distribution pattern of adults was determined in the juvenile stage, while this was not the case for group B. Studies of juvenile stages are important for understanding the demographic basis of vegetation distribution patterns.     

Acetylation-induced alteration of catalytic and regulatory properties of aspartase

Acetylation of Escherichia coli aspartase (L-aspartate ammonia-lyase, EC 4.3.1.1) with acetic anhydride or N-hydroxysuccinimide acetate resulted in the alteration of catalytic and regulatory properties as follows. At pH 7.0, 2-fold activation was observed in 30 min, whereas at pH 8.5 the activity of the acetylated enzyme was lower than that of the native enzyme throughout the range of substrate concentrations tested, while maintaining the Vmax unchanged. The Hill coefficient values of the substrate saturation curves were also altered under both pH conditions to an appreciable extent toward higher values. The enzyme activity's requirement for divalent metal ions increased at both pH 7.0 and 8.5. In particular the ratio of the activities in the presence vs. absence of Mg2+ reached as high as 84.5 at the latter pH. Inspection of the acetylation-induced conformational change by difference absorption spectroscopy revealed that a red shift occurred in the ultraviolet region. Chemical analyses, including high-performance liquid chromatography, of the acetylated residues revealed that approximately three amino groups per subunit were acetylated concomitant with a 2.1-fold activation and that the acetylation site was restricted to a relatively specific region of the enzyme molecule. Acylation of the enzyme with other acid anhydrides such as n-butyric and propionic anhydrides also increased the activity at pH 7.0, although to a lesser extent.