Stand structure and regeneration in a Kamchatka mixed boreal forest

Abstract. A 1‐ha plot was established in a Betula platyphylla‐Picea ajanensis mixed boreal forest in the central Kamchatka peninsula in Russia to investigate stand structure and regeneration. This forest was relatively sparse; total density and stand basal area were 1071/ha and 25.8 m²/ha, respectively, for trees > 2.0 cm in trunk diameter at breast height (DBH). 25% of Betula regenerated by sprouting, and its frequency distribution of DBH had a reverse J‐shaped pattern. In contrast, Picea had a bimodal distribution. The growth rates of both species were high, reaching 20 m in ca. 120 yr. The two species had clumped distributions, especially for saplings. Betula saplings were not distributed in canopy gaps. Small Picea saplings were distributed irrespective of the presence/absence of gaps, while larger saplings aggregated in gaps. At the examined spatial scales (6.25–400 m²) the spatial distribution of Betula saplings was positively correlated with living Betula canopy trees and negatively with dead Picea canopy trees. This suggests that Betula saplings regenerated under the crowns of Betula canopy trees and did not invade the gaps created by Picea canopy trees. The spatial distribution of Picea saplings was negatively correlated with living and dead Betula canopy trees and positively with dead Picea canopy trees. Most small Picea seedlings were distributed under the crowns of Picea trees but not under the crowns of Betula trees or in gaps. This suggests that Picea seedlings establish under the crowns of Picea canopy trees and can grow to large sizes after the death of overhead Picea canopy trees. Evidence of competitive exclusion between the two species was not found. At a 20 m × 20 m scale both skewness and the coefficient of variation of DBH frequency distribution of Picea decreased with an increase in total basal area of Picea while those of Betula were unchanged irrespective of the increase in total basal area of Betula. This indicates that the size structure of Picea is more variable with stand development than that of Betula on a small scale. This study suggests that Betula regenerates continuously by sprouting and Picea regenerates discontinuously after gap formation and that the species do not exclude each other.     

Diazirine-containing tag-free RNA probes for efficient RISC-loading and photoaffinity labeling of microRNA targets

We designed and synthesized a photo-reactive and tag-free RNA probe for the identification of microRNA (miRNA) targets. To synthesize the RNA probe, we designed a novel nucleoside analog 1-O-[3-ethynyl-5-(3-trifluoromethyl-3H-diazirine-3-yl)]benzyl-β-d-ribofuranose containing aryl trifluoromethyl diazirine and ethynyl moieties. The RNA probe containing this analog was observed to form crosslinks with complementary RNA by UV irradiation and was rapidly tagged by Cu-catalyzed azide alkyne cycloaddition (CuAAC). In addition, the tag-free and photo-reactive miRNA-145 probe showed comparable gene silencing activity to that of unmodified miRNA-145. Therefore, miRNA probes containing the nucleoside analog are promising candidates for the identification of target mRNAs of miRNAs.     

Identification of the protocatechuate transporter gene in Sphingobium sp. strain SYK-6 and effects of overexpression on production of a value-added metabolite

Applied Microbiology and Biotechnology - Sphingobium sp. strain SYK-6 expresses the best characterized catabolic systems for lignin-derived aromatic compounds. However, the uptake systems for these...     

Imaging mass spectroscopy delineates the thinned and thickened walls of intracranial aneurysms

Object

The wall thickness of intracranial aneurysms (IAs) is heterogeneous. Although thinning of the IA wall is thought to contribute to IA rupture, the underlying mechanism remains poorly understood. Recently, imaging mass spectroscopy (IMS) has been used to reveal the distribution of phospholipids in vascular diseases. To investigate the feature of phospholipid composition of IA walls, we conducted IMS in a rat model of experimentally induced IA.

Activation of prothrombin by two subtilisin-like serine proteases from Acremonium sp

Two novel subtilisin-like serine proteases (AS-E1 and -E2) that activate prothrombin have been identified in a culture of the fungus Acremonium sp. The enzymes were purified through repeated hydrophobic interaction chromatography. The N-terminal sequences of AS-E1 (34.4 kDa) and AS-E2 (32 kDa) showed high similarity to the internal sequences of two distinct subtilisin-like hypothetical proteins from Chaetomium globosum. Both enzymes proteolytically activated prothrombin to meizothrombin(desF1)-like molecules, while the activation cleavage seemed to occur at a site (Tyr(316)-Ile(317)) that is four residues proximal to the canonical Xa cleavage site (Arg(320)-Ile(321)). Both enzymes inhibited plasma clotting, possibly due to extensive degradation of fibrinogen and production of meizothrombin(desF1)-like molecule.     

Geographical variation in the early regeneration process of Siebold's Beech (Fagus crenata BLUME) in Japan

The causes and timing of seed death in early regeneration process of Siebold's beech (Fagus crenata Blume) was studied at 15 sites along a snowfall gradient in Japan, in order to clarify why the seedling density of the species has geographic difference remarkably. Seed production did not significantly differ along the snowfall gradient. Pre-dispersal seed mortality by insect damage was higher at sites with light snowfall than at sites with heavy snowfall, but this only seemed to be a minor factor influencing the population. A large proportion of the viable nuts that fall in autumn ware killed in winter before germination. Winter mortality was much higher at sites with thin snow cover than that at sites with thick snow cover, and this factor was strongly correlated with the geographic variation of seedling regeneration probability. There was little seed mortality by winter desiccation. The main factor contributing to the geographic difference seemed to be a seed predation by rodents in winter. Deep snow cover may reduce the success of rodents finding seeds in winter. Thus the observed relationship between snowpack depth and early mortality may be due to an indirect effect through the process of seed predation.p>     

Expression of the Na+-K+-2Cl- cotransporter in the rat endolymphatic sac

The endolymphatic sac (ES) is a part of the membranous labyrinth that contains the cochlea, vestibular organs, and semicircular canals, and is believed to absorb endolymphatic fluid. Na⁺–K⁺–2Cl⁻ (NKCC) is a cotransporter that occurs as two isoforms (NKCC-1 and NKCC-2). Especially, NKCC-2 is suggested to participate in ES endolymph absorption. In the present study, the expression and cellular localization of NKCC-1 and NKCC-2 in the rat ES were examined by RT-PCR and in situ hybridization, respectively. The findings indicate that both NKCC-1 and NKCC-2 are expressed in the rat ES and suggest that NKCC is involved in ES homeostasis. NKCC-2 may be particularly involved in endolymph absorption. This is the first report confirming NKCC expression in the ES.     

Design of Strain-Sensing Devices in Microscale by Using Surface Plasmon Polaritons

We have presented a strain-sensing device in microscale by using surface plasmon polaritons and multimode interference effects. The device is numerically investigated by the finite-difference time-domain method. Optimum depths and length of the structure are designed for sensing a strain. The size of the designed structure is several micrometers and is about a thousandth compared with a fiber Bragg grating strain sensor. The sensitivity of the designed structure is 11.34 pm/μ?? that is about ten times larger than that of a fiber Bragg grating strain sensor. The temperature sensitivity of the designed structure is 34.43 pm/ ^°C. This temperature sensitivity is three times larger than that of a fiber Bragg grating strain sensor. Therefore, temperature compensation techniques are needed for the structure. The presented structure has a simple design such as a plasmonic waveguide with a trench structure. The simple structural design device has a capability of being used in micro- and nano-electromechanical systems.     

Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans

Glycosyltransferases comprise highly divergent groups of enzymes, which play a central role in the synthesis of complex glycans. Because the repertoire of glycosyltransferases in the genome determines the range of synthesizable glycans, and because the increasing amount of genome sequence data is now available, it is essential to examine these enzymes across organisms to explore possible structures and functions of the glycoconjugates. In this study, we systematically investigated 36 eukaryotic genomes and obtained 3426 glycosyltransferase homologs for biosynthesis of major glycans, classified into 53 families based on sequence similarity. The families were further grouped into six functional categories based on the biosynthetic pathways, which revealed characteristic patterns among organism groups in the degree of conservation and in the number of paralogs. The results also revealed a strong correlation between the number of glycosyltransferases and the number of coding genes in each genome. We then predicted the ability to synthesize major glycan structures including N-glycan precursors and GPI-anchors in each organism from the combination of the glycosyltransferase families. This indicates that not only parasitic protists but also some algae are likely to synthesize smaller structures than the structures known to be conserved among a wide range of eukaryotes. Finally we discuss the functions of two large families, sialyltransferases and β4-glycosyltransferases, by performing finer classifications into subfamilies. Our findings suggest that universality and diversity of glycans originate from two types of evolution of glycosyltransferase families, namely conserved families with few paralogs and diverged families with many paralogs.