Expression of <Emphasis Type="Italic">Ruminococcus albus</Emphasis> Xylanase Gene (<Emphasis Type="Italic">xyn</Emphasis>A) in <Emphasis Type="Italic">Streptococcus bovis</Emphasis> 12-U-1

The objective of this study was to ligate the xylanase gene A (xynA) isolated from Ruminococcus albus 7 into the promoter and signal-peptide region of the lichenase [β-(1,3-1,4)-glucanase] gene of Streptococcus bovis JB1. This fusion gene was inserted into the pSBE11 vector, and the resulting recombinant, plasmid pXA, was used to transform S. bovis 12-U-1 cells. The transformant, S. bovis 12UXA, secreted the xylanase, which was stable against freeze-thaw treatment and long-time incubation at 37°C. The introduction of pXA and production of xylanase did not affect cell growth, and the xylanase produced degraded xylan from oat-spelt and birchwood. Received: 24 June 2002 / Accepted: 7 October 2002     

Splash seed dispersal by raindrops

Splash seed dispersal by raindrops was investigated for plants in southern Japan. Nine families, 10 genera and 19 species were confirmed as raindrop-dispersed plants. The 10 genera were Gentiana, Gratiola, Chrysosplenium, Mazus, Mitella, Ophiorrhiza, Sagina, Sedum, Trigonotis and Veronica. The method of splash rain dispersal in these species was clarified. Raindrop-dispersed species were all small herbaceous plants with a vertical pedicel and an apically opening fresh capsule when the seeds mature. Open capsules were cup-shaped or boat-shaped and can accommodate raindrops easily. The raindrops splashed the seeds from the capsule. In general, the seeds weighed very little, but they were heavier than powder or dust seeds dispersed by wind. A strong negative correlation was found between seed weight and the number of seeds per capsule. In the case of Trigonotis brevipes (Maxim.) Maxim., raindrops were received into the cup-shaped calyx-tube and dispersed the fruitlets. Some species, such as Gentiana thunbergii (G. Don) Griseb., Gentiana zollingeri Fawcett and Ophiorrhiza japonica Blume, had hydroscopic movement capsules that opened widely only when wet. Raindrop-dispersed plants were found in various habitats. For example, some plants grew together on rocks along the mountain torrents where splash water could easily be caught. The results of the laboratory and field experiments indicated that the dispersal distance of seeds by raindrops was 1m or less. For small herbaceous plants, splash dispersal by rain might be an effective and advantageous method of seed dispersal because dispersal is not affected by plant height.     

Life history of the endangered Japanese striped loach,Cobitis kaibarai (Cypriniformes: Cobitidae), with special reference to its reproductive ecology and the influence of creek reshapings on its population density

In recent years, the biodiversity of freshwater fishes has been markedly decreasing worldwide because of anthropogenic activities. The Japanese striped loach, Cobitis kaibarai (Cypriniformes: Cobitidae), is a primary freshwater fish endemic to northern Kyushu, Japan. This species is designated as endangered IB class in the Red List by the Japan Ministry of the Environment. Its population is decreasing, possibly because of habitat loss and degradation. To conserve C. kaibarai populations, information on its basic ecology is necessary; nonetheless, its detailed life history and reproductive ecology have yet to be clarified. In this study, the authors conducted monthly capture–mark–recapture surveys and periodical observations to investigate the life history, spawning sites and season of C. kaibarai. They also evaluated the influence of creek reshaping (concrete revetment) on the C. kaibarai population in Saga Plain, northern Kyushu. Between 2015 and 2018, more individuals were captured during winter than summer. The average body width of females peaked in early June and small immatures were confirmed from July. Some individuals were captured across 15 or more months after their initial marking. In the survey of reproductive sites, eggs and larvae of C. kaibarai were found in shallow areas in mid-June; these were temporarily submerged following the increase in water level from early June. Therefore, C. kaibarai spawns in shallow areas during this season. Based on the capture–mark–recapture surveys, the estimated population density of C. kaibarai significantly decreased in a census site that had undergone creek reshaping, which contrasted with the results in a control site, where no significant difference was detected. The standard length of C. kaibarai increased following creek reshaping, suggesting that the proportion of C. kaibarai postponing spawning had increased, possibly because of degradation of spawning environments. The results of this study provide important ecological knowledge for the conservation of C. kaibarai and emphasize the importance of shallow waters for floodplain spawners.     

Legionella hijacks the host Golgi-to-ER retrograde pathway for the association of Legionella-containing vacuole with the ER

Legionella pneumophila (L. pneumophila) is a gram-negative bacterium that replicates in a compartment that resembles the host endoplasmic reticulum (ER). To create its replicative niche, L. pneumophila manipulates host membrane traffic and fusion machineries. Bacterial proteins called Legionella effectors are translocated into the host cytosol and play a crucial role in these processes. In an early stage of infection, Legionella subverts ER-derived vesicles (ERDVs) by manipulating GTPase Rab1 to facilitate remodeling of the Legionella-containing vacuole (LCV). Subsequently, the LCV associates with the ER in a mechanism that remains elusive. In this study, we show that L. pneumophila recruits GTPases Rab33B and Rab6A, which regulate vesicle trafficking from the Golgi to the ER, to the LCV to promote the association of LCV with the ER. We found that recruitment of Rab6A to the LCV depends on Rab33B. Legionella effector SidE family proteins, which phosphoribosyl-ubiquitinate Rab33B, were found to be necessary for the recruitment of Rab33B to the LCV. Immunoprecipitation experiments revealed that L. pneumophila facilitates the interaction of Rab6 with ER-resident SNAREs comprising syntaxin 18, p31, and BNIP1, but not tethering factors including NAG, RINT-1, and ZW10, which are normally required for syntaxin 18-mediated fusion of Golgi-derived vesicles with the ER. Our results identified a Rab33B-Rab6A cascade on the LCV and the interaction of Rab6 with ER-resident SNARE proteins for the association of LCV with the ER and disclosed the unidentified physiological role of SidE family proteins.     

Biogeochemical Signals from Deep Microbial Life in Terrestrial Crust

In contrast to the deep subseafloor biosphere, a volumetrically vast and stable habitat for microbial life in the terrestrial crust remains poorly explored. For the long-term sustainability of a crustal biome, high-energy fluxes derived from hydrothermal circulation and water radiolysis in uranium-enriched rocks are seemingly essential. However, the crustal habitability depending on a low supply of energy is unknown. We present multi-isotopic evidence of microbially mediated sulfate reduction in a granitic aquifer, a representative of the terrestrial crust habitat. Deep meteoric groundwater was collected from underground boreholes drilled into Cretaceous Toki granite (central Japan). A large sulfur isotopic fractionation of 20–60‰ diagnostic to microbial sulfate reduction is associated with the investigated groundwater containing sulfate below 0.2 mM. In contrast, a small carbon isotopic fractionation (<30‰) is not indicative of methanogenesis. Except for 2011, the concentrations of H₂ ranged mostly from 1 to 5 nM, which is also consistent with an aquifer where a terminal electron accepting process is dominantly controlled by ongoing sulfate reduction. High isotopic ratios of mantle-derived ³He relative to radiogenic ⁴He in groundwater and the flux of H₂ along adjacent faults suggest that, in addition to low concentrations of organic matter (<70 µM), H₂ from deeper sources might partly fuel metabolic activities. Our results demonstrate that the deep biosphere in the terrestrial crust is metabolically active and playing a crucial role in the formation of reducing groundwater even under low-energy fluxes.     

Complete annotated genome sequence of Mycobacterium tuberculosis Erdman

We report the completely annotated genome sequence of Mycobacterium tuberculosis Erdman (TMC 107; ATCC 35801), which is a well-known laboratory strain of M. tuberculosis.     

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA‐based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high‐throughput sequencing, denoising was performed using two of the most widely used denoising packages, unoise3 and dada2 . Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (unoise3 ) and 41 (dada2 ) haplotypes were detected by eDNA analysis. When dada2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. Accordingly, although it is important to note that eDNA‐based method has some limitations and some risk of false positive and false negative, this study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large‐scale capture‐based conventional methods. Our results suggest that eDNA‐based methods could become a more efficient survey method for investigating intraspecific genetic diversity in the field.     

A brief review of bone adaptation to unloading

Weight-bearing bone is constantly adapting its structure and function to mechanical environments. Loading through routine exercises stimulates bone formation and prevents bone loss, but unloading through bed rest and cast immobilization as well as exposure to weightlessness during spaceflight reduces its mass and strength. In order to elucidate the mechanism underlying unloading-driven bone adaptation, ground-based in vitro and in vivo analyses have been conducted using rotating cell culturing and hindlimb suspension. Focusing on gene expression studies in osteoblasts and hindlimb suspension studies, this minireview introduces our recent understanding on bone homeostasis under weightlessness in space. Most of the existing data indicate that unloading has the opposite effects to loading through common signaling pathways. However, a question remains as to whether any pathway unique to unloading （and not to loading） may exist.     

Identification and Characterization of a Novel aac(6′)-Iag Associated with the bla IMP-1–Integron in a Multidrug-Resistant Pseudomonas aeruginosa

In a continuing study from Dec 2006 to Apr 2008, we characterized nine multi-drug resistant Pseudomonas aeruginosa strains isolated from four patients in a ward at the Hiroshima University Hospital, Japan. Pulsed-field gel electrophoresis of SpeI-digested genomic DNAs from the isolates suggested the clonal expansion of a single strain; however, only one strain, NK0009, was found to produce metallo-β-lactamase. PCR and subsequent sequencing analysis indicated NK0009 possessed a novel class 1 integron, designated as In124, that carries an array of four gene cassettes: a novel aminoglycoside (AG) resistance gene, aac(6′)-Iag, bla _IMP-1, a truncated form of bla _IMP-1, and a truncated form of aac(6′)-Iag. The aac(6′)-Iag encoded a 167-amino-acid protein that shows 40% identity with AAC(6′)-Iz. Recombinant AAC(6′)-Iag protein showed aminoglycoside 6′-N-acetyltransferase activity using thin-layer chromatography (TLC) and MS spectrometric analysis. Escherichia coli carrying aac(6′)-Iag showed resistance to amikacin, arbekacin, dibekacin, isepamicin, kanamycin, sisomicin, and tobramycin; but not to gentamicin. A conjugation experiment and subsequent Southern hybridization with the gene probes for bla _IMP-1 and aac(6′)-Ig strongly suggested In124 is on a conjugal plasmid. Transconjugants acquired resistance to gentamicin and were resistant to virtually all AGs, suggesting that the In124 conjugal plasmid also possesses a gene conferring resistance to gentamicin.     

Effect of Inositol Deficiency on Cellular Permeability of the Inositol Exacting Yeast

Inositol deficiency caused the abnormalities of permeability of the cell envelope of the inositol exacting yeasts. In the case of Schizosaccharomyces pombe, in which the marked leakage of cellular free-pool fraction was not detected, the uptake activity of glucose or methylglucoside decreased in inositol deficiency, especially in aerobic condition. Investigations on the compositions of lipids and fatty acids showed that the change in fatty acid composition was not so remarkable as that in phosphatides in inositol deficiency. One of the main causes of low transport activity may be due to the change in phosphatides, but not due to that in fatty acids, possibly. Intracellular contents of glucose was not less in inositol deficiency than in sufficiency. These results suggest that inositol deficiency caused the low activity of uptake, which might not be, however, the primary cause of low fermentative activity.

In the case of Saccharomyces cerevisiae Ino^– mutant A–21–20, the similar results about permeability and lipid analyses were obtained in inositol deficiency.