Distribution of chloropigments in suspended particulate matter and benthic microbial mat of a meromictic lake, Lake Kaiike, Japan

We investigated the distribution of chloropigments in a small meromictic lake, Lake Kaiike, south-west Japan. In the water-column, concentrations of Chl a related to cyanobacteria, BChl a related to purple sulphur bacteria, and three types of BChl e homologues (BChls e1, e2 and e3) related to brown-coloured green sulphur bacteria, were maximal at the redox boundary. Below the redox boundary, absolute concentrations of Chl a and BChl a gradually decreased with depth, whereas BChls e remained rather constant. Suspended particulate matter (SPM) at the deeper region of the anoxic water-column was enriched in highly alkylated BChl e homologues compared with SPM at the redox boundary. The shift in the relative content of highly alkylated BChl e homologues beneath the boundary was associated with community related adaptation of brown-coloured green sulphur bacteria to changes in light quality/quantity, resulting from the optical absorption and reflectance of SPMs in the overlying water-column. Benthic microbial mats were characterized by high abundances of BChls e, in which highly alkylated homologues were substantially abundant. This suggests that the BChls e in the microbial mat may be derived from the low-light adapted brown-coloured green sulphur bacteria forming the bacterial mat.     

Trimorphic DNA variation in the receptor-like protein kinase gene in the F18L15-130 region of the wild plant Arabidopsis thaliana

DNA variation in the F18L15-130 region, which contains a receptor-like protein kinase gene, was analyzed for the wild plants Arabidopsis thaliana and Arabis gemmifera. In A. thaliana, at least three divergent sequence types were observed (trimorphism), instead of two distinct sequence types (dimorphism) detected in most of other nuclear gene regions studied for this plant species. Intragenic recombinations among the divergent sequence types generated four recombinant sequence types, although pattern of intragenic recombinations was complex. The estimated nucleotide variation in A. thaliana was the highest (pi = 0.0226 and theta = 0.0228) among genes investigated in this plant so far. The high level of nucleotide variation is due to divergence among the three distinct sequence types, each of which has a low level of nucleotide variation. Tests of Tajima, and Fu and Li did not detected deviation from neutrality, except for replacement sites, for which significantly negative Fu and Li's test value was detected. These results suggest that the receptor-like protein kinase gene in this region is functional. Possible causes for the trimorphic pattern of DNA polymorphism was discussed.     

Biogeochemical processes in the saline meromictic Lake Kaiike, Japan: implications from molecular isotopic evidences of photosynthetic pigments

Stable carbon and nitrogen isotopic compositions were determined for individual photosynthetic pigments isolated and purified from the saline meromictic Lake Kaiike, Japan, to investigate species-independent biogeochemical processes of photoautotrophs in the natural environment. In the anoxic monimolimnion and benthic microbial mats, the carbon isotopic compositions of BChls e and isorenieratene related to brown-coloured strains of green sulfur bacteria are substantially ( approximately 10 per thousand) depleted in (13)C relative to those found in the chemocline. In conjunction with 16S rDNA evidence reported previously, it strongly suggests that Pelodyctyon luteolum inhabited and photosynthesized in the anoxic monimolimnion and benthic microbial mats by using (13)C-depleted regenerated CO(2). By contrast, both Chl a and BChl a in the monimolimnion and microbial mats have similar isotopic compositions as they do in the chemocline, implying that the source organisms live only in the chemocline. In the chemocline, the nitrogen isotopic compositions of BChl e homologues ranges from -7.7 to-6.5 per thousand, whereas that of BChl a is -2.1 per thousand. These isotopic compositions suggest that green sulfur bacteria Chlorobium phaeovibrioides would conduct nitrogen fixation in the chemocline, whereas purple sulfur bacteria Halochromatium sp. and cyanobacteria Synechococcus sp. may assimilate nitrite.     

Dominant expression of ATP-binding cassette transporter-1 on basolateral surface of Caco-2 cells stimulated by LXR/RXR ligands

ATP-binding cassette transporter-1 (ABCA1) is a cause of Tangier disease, which is a familial deficiency of plasma high density lipoproteins (HDL). This molecule is known to be expressed in the multiple tissues and organs including small intestines, liver, and macrophages in the blood vessels. Recent in vivo studies suggested that ABCA1 plays some roles in the flux of cholesterol in the intestines. One of the major questions to understand the roles of ABCA1 in the intestines is the expression pattern in the intestinal epithelial cells. To address this issue, we have investigated the expression and regulation of ABCA1 in Caco-2 cells cultured on Transwell as a model, especially focusing on possible polarized expression of ABCA1. The expression of ABCA1 was up-regulated during the differentiation and under the stimulation of LXR/RXR by the addition of 9-cis-retinoic acid (9-cis-RA) and 22-R-hydroxycholesterol (22-OH). Apolipoprotein-AI-mediated cholesterol efflux was dominant toward the basolateral side of polarized cells when stimulated by 9-cis-RA and 22-OH. The cell surface biotinylation experiment followed by Western blot analyses demonstrated a markedly dominant expression of ABCA1 on the basolateral surface, which was clearly confirmed by the confocal laser scanning microscopy. In conclusion, the present study demonstrates that ABCA1 is dominantly expressed on the basolateral surface of Caco-2 cells tested, suggesting that this molecule may play a role in the basolateral movement of cholesterol at least when stimulated by LXR/RXR ligands.     

Expansion of a CD28-intermediate subset among CD8 T cells in patients with infectious mononucleosis

Infectious mononucleosis (IM) is an acute sporadic infection that usually affects young adults, and during infection a massive expansion of CD8 T cells is generally considered to occur. However, CD28 expression of the expanded cells has not been characterized. When peripheral blood mononuclear cells of acute IM (AIM) patients were analyzed by flow cytometry, a continuous spectrum of CD28 intensity ranging from negative to high, which could be separated into CD28 negative, intermediate (int), and positive, was seen for CD8 T cells. We studied 26 IM patients who were diagnosed on the basis of standard methods and found that all patients had the continuous CD28 spectrum. CD28 is a costimulatory molecule on T cells, and its expression is associated with the subdivision of CD8 cells into cytotoxic (CD28-positive) and suppressor (CD28-negative) T cells. After 24 h of ex vivo culturing, however, the continuous spectrum was found to consist of only CD28-positive and CD28-negative CD8 T cells, because the CD28-int cells had disappeared due to apoptosis. The CD28-int T cells have several cytotoxic functions, suggesting that CD28-int T cells are effectors. Examination of other costimulatory markers in AIM patients showed that CD80 and CD152 were not affected. In patients with other viral infections, such as measles or rubella, however, the continuous spectrum was not detected. These results suggest that there is an unusual CD28 expression pattern in patients with AIM, namely, the presence of a functional CD28-int subset among CD8 T cells. These findings are of special importance for clarifying the defense mechanism against Epstein-Barr virus infection, and the role of CD28 molecules in humans and should also be helpful for the diagnosis of AIM.     

Relationship between leaf characteristics, tree sizes and species distribution along a slope in a warm temperate forest

The relationships between some leaf characteristics, tree size and species distribution were investigated for evergreen tree species along a slope in a warm temperate forest in Japan. Tree species were classified into three groups based on their dominance on the slope: ridge species that were aggregated in an uppersite, valley species that were aggregated in a lowersite, and uniform species that were distributed almost uniformly. The ridge species had a more positive leaf carbon isotope ratio than the valley species, which suggests that the ridge species have larger water use efficiency than the valley species. This may give some advantage to the ridge species over the valley species in the uppersite where water availability would be limited. However, the ridge species had smaller leaf nitrogen content on a mass basis and larger leaf mass per area than the valley species, which suggests that the ridge species had a smaller mass-based leaf photosynthetic capacity than the valley species. This may be disadvantageous to ridge species in the lowersite, because smaller leaf photosynthetic capacities cause lower leaf carbon gain and thus lower growth than the valley species. These differences in leaf characteristics between the ridge and the valley species were affected by microenvironments, and were also partly affected by the difference in species specific responses to microenvironments on the slope.     

Nucleotide polymorphism in the Adh2 region of the wild rice Oryza rufipogon

DNA variation in the alcohol dehydrogenase (Adh2) region of the wild rice Oryza rufipogon and its related species was analyzed to clarify maintenance mechanisms of the DNA variation in these species. A dimorphic pattern was detected in the Adh2 region of O. rufipogon. The silent nucleotide diversity (π) in the Adh2 region in O. rufipogon was 0.011, which was higher than that of the Adh1 region in O. rufipogon. Especially, a high nucleotide diversity was detected at synonymous sites of the catalytic domain 1. Average nucleotide diversity at silent sites within each of the dimorphic sequence types of the Adh2 region was similar to that in the Adh1 region, indicating that the high level of silent polymorphism in the Adh2 region was caused by the difference between the dimorphic sequence types. On the other hand, the level of replacement polymorphism in the Adh2 region was as low as that in the Adh1 region. The neutrality test of Fu and Li indicated significantly negative deviation from the neutral mutation model for the replacement sites of the Adh2 region. This result suggests purifying selection on the replacement sites of the Adh2 region, as detected for the Adh1 region. Significant linkage disequilibria (16.4% of the tests) were detected between the Adh1 and Adh2 regions. Even when nonrandom association was tested for the strains belonging to one of the divergent sequence types of the Adh2 region, significant interlocus linkage disequilibria were detected. The close physical distance and/or epistasis between the two Adh regions could be invoked to explain these nonrandom associations.     

Development of dense microsatellite markers in the entire SLA region and evaluation of their polymorphisms in porcine breeds

We developed 40 microsatellite markers in the entire swine leukocyte antigen (SLA) region, spanning over 2.35 Mb. The average span between markers was 59 kb, and the largest interval between markers was 127 kb. We also evaluated polymorphisms of length for the markers using 97 pigs derived from 12 breeds, including representative commercial breeds. All of the markers were successfully amplified in genomic DNA and shown to be polymorphic. These markers will provide an alternative method for determining the SLA haplotypes instead of direct typing of SLA genes per se. They will be valuable for transplantation studies and for association studies between immunological traits such as disease susceptibility and tumor rejection. Electronic supplementary material Supplementary material is available for this article at and accessible for authorised users.     

The minimum endpoint variance trajectory depends on the profile of the signal-dependent noise

It has been proposed that the central nervous system determines reaching movement trajectories so as to minimize the positional variance of the endpoint in the presence of signal-dependent noise. The hypothesis well reproduces the empirical movement trajectories for noise to the control signal whose variance is proportional to the second power of the amplitude of the control signal. However, empirical studies do not necessarily exhibit such a simple signal-noise relationship. The studies exhibit a wide distribution of estimates of the value of the exponent. This discrepancy raises the question of how the minimum endpoint variance trajectory depends on the value of the exponent. To address this question, we calculated minimum endpoint variance trajectories in simulations in which the value of the exponent was varied from 0 to 3. We found that the optimal trajectories differed according to the value of the exponent, and the profiles of optimal trajectories gradually diverged from the empirical ones as the value approached 0, though this change was not remarkable for larger values. Moreover, the optimal trajectories failed to replicate Fitts' law when the value was not equal to 2. These results suggest that the acceptability of the minimum endpoint variance theory depends on the value of the exponent in our motor system.