River confluences enhance riparian plant species diversity

In riparian zones along the banks of streams and rivers, flooding often causes large changes in environmental conditions immediately downstream of confluences. In turn, spatial heterogeneity in flooding along rivers and streams likely affects local species diversity. Furthermore, flooding during the plant growing season can strongly affect plant survival. In this study, we hypothesized that confluences have impacts on plant species diversity, and that these impacts are larger during the plant growing season. To test this hypothesis, we measured plant species diversity and the extent of natural bare ground at 11 river confluences during two different seasons (summer and spring) within the Mukogawa River basin system, Japan. Species diversity was highest at down-confluence areas in the summer. We linked the pattern of species diversity to that of bare ground creation by floods around the confluences and to the seasonality of annual plant recruitment. The extent of bare ground was significantly greater at down-confluence areas than at up-confluence areas. The recruitment of annual species was higher in the summer than in the spring and included rapid occupancy of bare ground in the summer. We suggest that within river systems, spatial and seasonal differences in patterns of flooding function together to regulate plant species diversity.     

Restoration of floating mat bog vegetation after eutrophication damages by improving water quality in a small pond

We studied vegetation changes in a small floating mat bog in Mizorogaike Pond (Kyoto, Japan), which had experienced a severe decrease in the number and area of hummocks caused by nutrient loading in the 1960s and 1970s, to examine whether reducing the extent of nutrient loading can restore degraded wetland vegetation. However, nutrient loading in the region has been minimized since the 1980s. We examined the distributions of hummocks and Sphagnum cuspidatum mats in 1980, 1988, and 2006, as well as nine major vascular plants that dominated the hollows on the floating mat in 1980 and 2006. The total area of normal hummocks formed by Sphagnum palustre increased from 5865.3 m² in 1980 to 5913.6 m² in 1988 and 8485.2 m² in 2006. The total area of the S. cuspidatum mats also changed, from 416.4 m² in 1980 to 322.3 m² in 1988 and 1012.5 m² in 2006. Examination of the spatial distribution patterns of major plants revealed that emergent plants decreased in the northern part of the mat, but increased in the southern part. Thus, the improved pond water quality was effective at restoring hummocks, although nutrient loading may have caused some irreversible changes in the wetland vegetation.     

Molecular organization of 5S rDNA in bitterlings (Cyprinidae)

Molecular organization and nucleotide sequences of the 5S rRNA gene and NTS were investigated in freshwater fish, bitterlings (Acheilognathinae), including 10 species/subspecies of four genera, Acheilognathus, Pseudoperilampus, Rhodeus, and Tanakia, to understand the evolutionary trait of 5S rDNA arrays. Southern hybridization analysis revealed a general trend with tandem repeats of 5S rDNA in all the examined bitterlings. Sequence analysis demonstrated a conserved 120 bp sequence of the 5S rRNA gene and a short NTS of 56–67 bp with two distinct portions, a conserved (5′-flanking portion; at positions −1 to −38) and a variable part (3′-flanking portion), in 6 of 10 species/subspecies examined. The conserved NTS region was most likely an external promoter so far observed in various vertebrates, whereas the variable NTS region could be divided into two types due to its nucleotide polymorphisms. Molecular phylogeny using the 5S rRNA gene and NTS sequences suggested the occurrence of 5S rDNA duplication before speciation and a concerted evolution for the gene and conserved NTS regions, but a birth-and-death process to maintain the variable NTS region. Thus, the 5S rDNA in the examined bitterlings might have evolved under a mixed process of evolution.     

Nature-oriented park use of satoyama ecosystems can enhance biodiversity conservation in urbanized landscapes

Satoyama is one of the semi-natural ecosystems in Japan. Traditional agricultural practices in satoyama provide preferable habitats for many species, thus, enhancing biodiversity. However, many satoyama ecosystems have been altered by agricultural intensification and rapid urbanization. Meanwhile, ageing and shrinking population has led to the abandonment of remaining satoyama ecosystems, resulting in their potential degradation. We argue that counteracting the abandonment of satoyama is particularly essential in urbanized landscapes because conserving its biodiversity would have a payoff for urban communities. We focused on nature-oriented park use of satoyama ecosystems, utilizing their original scenery, topography, water features, and vegetation. To evaluate the potential of nature-oriented park use for biodiversity conservation, we examined the differences in diversity and species composition of vascular plants and butterflies among three land-use types (agricultural-use, park-use, and abandoned sites) of satoyama ecosystems. Diversity of native plants and butterflies did not significantly differ between agricultural-use and park-use sites and that of native plants was significantly lower at abandoned sites than at agricultural-use sites. Although species composition of native plants at agricultural-use sites and park-use sites significantly differ, that of native butterflies did not. The efficacy of park use for biodiversity conservation, thus, depended on the taxa. Nonetheless, for striking a balance between the difficulty in maintaining agricultural use and accelerating satoyama abandonment, our study highlights the utility of park use as an alternative usage, contributing to biodiversity conservation. Balancing the wise use of satoyama in urbanized landscapes is a fundamental step toward the conservation of its biodiversity and human–nature interactions.

     

Sex change in tree species: long-term monitoring of sex expression in Acer rufinerve

We monitored sex expression in Acer rufinerve from 1986 to 1999, in order to study branch-autonomous sex changes in tree species. During this observation period, 70 of 338 stems (20.7 %) changed sexual expression. Fifty of these sex-changed stems exhibited monoecism (having both female and male branches) in the course of the sex change, while the remaining stems changed directly from male to female or vice versa. A sex change resulting in monoecism was called a partial sex change and a total male/female change was referred to as a complete sex change. The mean diameter at breast height of stems that partially changed sex was significantly greater than that of stems that changed sex completely. Thus, it was primarily large stems with many branches that underwent partial sex changes. These findings suggest that sex change is a branch autonomous event in A. rufinerve and underline the importance of taking branching structure into account when studying sex change in trees.     

A quantitative analysis of geographic color variation in two Geotrupes dung beetles

We conducted a quantitative analysis of geographic color variation in two species of dung beetles: Geotrupes auratus and G. laevistriatus. The reflectance of the dorsal surfaces was measured from 300 to 700 nm using a spectrophotometer. The reflectance curves for both beetles were bimodal; there were two distinct peaks, namely, the a peak, between 400 and 700 nm, and the beta peak at around 300 nm. A stepwise discriminant analysis indicated that geographic color variation in Geotrupes beetles was primarily characterized by a shift of the a peak. Using beetles from three locations, we compared the wavelength (nm) of the a peak (lambdamax(alpha)) and its reflectance intensity (R(a)) to investigate sex and population differences. Intraspecific geographic variation in coloration was effectively detected by discriminant analysis of spectral reflectance curves. Our results showed that G. auratus and G. laevistriatus had similar coloration within each sampling location. Our study also revealed hidden sex differences in R(a); R(a) of males were significantly higher than those of females in both species. Since the dorsal surface of the beetles shows remarkable color variation, and coloration can be assessed objectively using reflectance spectra, Geotrupes beetles may be good model organisms to investigate geographic color variation.     

Clonality and Micro-Diversity of a Nationwide Spreading Genotype of Mycobacterium tuberculosis in Japan

Mycobacterium tuberculosis transmission routes can be estimated from genotypic analysis of clinical isolates from patients. In Japan, still a middle-incidence country of TB, a unique genotype strain designated as ‘M-strain’ has been isolated nationwide recently. To ascertain the history of the wide spread of the strain, 10 clinical isolates from different areas were subjected to genome-wide analysis based on deep sequencers. Results show that all isolates possessed common mutations to those of referential strains. The greatest number of accumulated single nucleotide variants (SNVs) from the oldest coalescence was 13 nucleotides, indicating high clonality of these isolates. When an SNV common to the isolates was used as a surrogate marker of the clone, authentic clonal isolates with variation in a reliable subset of variable number of tandem repeat (VNTR) genotyping method can be selected successfully from clinical isolates populations of M. tuberculosis. When the authentic clones can also be assigned to sub-clonal groups by SNVs derived from the genomic comparison, they are classifiable into three sub-clonal groups with a bias of geographical origins. Feedback from genomic analysis of clinical isolates of M. tuberculosis to genotypic markers will be an efficient strategy for the big data in various settings for public health actions against TB.     

Neuronal peptides induce oocyte maturation and gamete spawning of sea cucumber, Apostichopus japonicus

Extracts prepared from tissues containing buccal ring nerve or longitudinal radial nerve of sea cucumber induce oocyte maturation and ovulation from ovarian tissues. We purified two small peptides, a pentapeptide and a heptapeptide, from the buccal tissues of Japanese common sea cucumber, Apostichopus japonicas. Both peptides induced oocyte maturation and gamete spawning. The pentapeptide was identified as NGIWYamide. This peptide induced in vitro germinal vesicle breakdown and ovulation of fully-grown oocytes at less than 1 pM and in vivo spawning at 10 nM. A synthetic derivative of the pentapeptide, NGLWYamide, was 10-100 times more potent compared to the natural NGIWYamide. The heptapeptide was less potent, inducing ovulation at 1 μM. NGIWYamide and NGLWYamide induced a characteristic spawning behavior when injected into sexually matured individuals. Mature eggs artificially spawned were fertilized, and developed normally and metamorphosed into young sea cucumbers. The details of the production and the mechanism of action of NGIWYamide are still unclear, but the high biopotency of the peptide will aid understanding of the neuronal and hormonal control of reproduction of sea cucumber.     

Acridone-tagged DNA as a new probe for DNA detection by fluorescence resonance energy transfer and for mismatch DNA recognition

Acridone is highly fluorescent and stable against photodegradation, oxidation, and heat. It is also a small molecule with no charge, making it a promising fluorescent agent for use in a DNA probe. Thus, we have prepared 5'-terminal acridone-labeled DNAs by post-modification, and have examined their photophysical properties and their use as donors for a fluorescence resonance energy transfer (FRET) system in combination with a 3'-terminal dabcyl-tagged DNA as an acceptor, which can detect the target DNA by emission-quenching caused by FRET. The FRET with an acridone and dabcyl pair has been found to complement that with fluorescence and dabcyl and other fluorescence-quencher pairs. Significant amounts of quenching of the acridone emissions by guanine in the DNA were observed when guanine was close to acridone, which can be applied as a quencher-free probe for the detection of special sequence of DNA. The DNA bearing acridone at the C5 position of inner thymidine could discriminate the opposite T-T base mismatch, although enhancement of discrimination ability is needed for the practical use of SNP typing.