Determination of iron species, including biomineralized jarosite, in the iron-hyperaccumulator moss Scopelophila ligulata by Mössbauer, X-ray diffraction, and elemental analyses.

Scopelophila ligulata is an Fe-hyperaccumulator moss growing in acidic environments, but the mechanism of Fe accumulation remains unknown. To understand the mechanism, we determined Fe species in S. ligulata samples. The moss samples were collected from four sites in Japan. The concentrations of Fe, P, S, Cl, and K in them were measured by induced coupled plasma mass spectrometry. Fe species in some of them were determined by Mössbauer spectroscopy and were confirmed by X-ray diffraction analysis. Fe species in S. ligulata samples were determined to be jarosite, ferritin, high-spin Fe(II) species, and akaganeite. To our knowledge, this is the first report on the biomineralization of jarosite in mosses. This result, combined with the fact that bacteria, a fungus, and a grass mineralize jarosite, suggests that its biomineralization is a common characteristic in a wide variety of living organisms. These findings indicate that the biomineralization of jarosite occurs not only in the region-specific species but in species adapted to a low-pH and metal-contaminated environment in different regions, provide a better understanding of the mechanism of Fe accumulation in the Fe-hyperaccumulator moss S. ligulata, and offer new insights into the biomineralization of jarosite.

Relationship between metal and pigment concentrations in the Fe-hyperaccumulator moss Scopelophila ligulata.

Scopelophila ligulata is known to be a Fe-hyperaccumulator moss; however, its mechanism of accumulation and the effects of Fe on pigments remain unclear. To clarify the effects, we measured its metal and pigment concentrations. The Fe concentration in S. ligulata was 10-61 times higher than that in normal mosses, confirming that the moss is a Fe-hyperaccumulator. The black samples of S. ligulata had the highest Fe concentration (2.9 wt%) and the second in the order of decreasing Fe concentration (2.2 wt%), which explains their color and indicates that the excess amount of Fe is distributed through the plant body. Moreover, we observed that the concentration of Ca is negatively correlated with the concentrations of pigments and, conversely, that the concentration of K is positively correlated with the concentrations of pigments. This inverse relationship between Ca and K can be explained by the reduced uptake of K in S. ligulata in response to Ca stress, which is supported by the fact that the concentration of Ca is negatively correlated with that of K. These findings provide a better understanding of the relationships between metals and pigments in the Fe-hyperaccumulator moss S. ligulata.

Primordial oscillations in life: Direct observation of glycolytic oscillations in individual HeLa cervical cancer cells.

We report the first direct observation of glycolytic oscillations in HeLa cervical cancer cells, which we regard as primordial oscillations preserved in living cells. HeLa cells starved of glucose or both glucose and serum exhibited glycolytic oscillations in nicotinamide adenine dinucleotide (NADH), exhibiting asynchronous intercellular behaviors. Also found were spatially homogeneous and inhomogeneous intracellular NADH oscillations in the individual cells. Our results demonstrate that starved HeLa cells may be induced to exhibit glycolytic oscillations by either high-uptake of glucose or the enhancement of a glycolytic pathway (Crabtree effect or the Warburg effect), or both. Their asynchronous collective behaviors in the oscillations were probably due to a weak intercellular coupling. Elucidation of the relationship between the mechanism of glycolytic dynamics in cancer cells and their pathophysiological characteristics remains a challenge in future.

Effects of Cu on the content of chlorophylls and secondary metabolites in the Cu-hyperaccumulator lichen Stereocaulon japonicum.

Understanding the relationship between Cu and Cu-hyperaccumulator lichens is important for their application in monitoring and assessing heavy metal pollution. We investigated the Cu-hyperaccumulator lichen Stereocaulon japonicum at several Cu-polluted and control sites in Japan, and found the lichen to be widely distributed. Its concentrations of Cu, chlorophylls, and secondary metabolites, chlorophyll-related indices, and absorption spectra were measured, and we observed negative effects of Cu on these concentrations and indices. For highly Cu-polluted samples (>100ppm dry weight), however, we found significant linear correlations between Cu and chlorophyll concentrations. This can be considered as the response of the photobiont in S. japonicum to Cu stress. In highly Cu-polluted samples the chlorophyll-related indices and concentration of total secondary metabolites were almost constant regardless of Cu concentration. This suggests that the increase in chlorophyll concentration with the increase in Cu concentration enhances photosynthetic productivity per unit biomass, which will allow the production of extra structure and energy for maintaining the chlorophyll-related indices under Cu stress. The relationship between the increase in chlorophyll concentration of S. japonicum and the decrease in secondary metabolite concentration of the lichen can be explained by considering the balance of carbohydrates in the lichen. We found that a spectral index A372-A394 can be a useful index of the concentrations of Cu and total secondary metabolites in S. japonicum. These findings show the adjustment of the content of chlorophylls and secondary metabolites in S. japonicum to Cu stress, and provide a better understanding of the relationship between Cu and the Cu-hyperaccumulator lichen.

Collective and individual glycolytic oscillations in yeast cells encapsulated in alginate microparticles.

Yeast cells were encapsulated into alginate microparticles of a few hundred micrometers diameter using a centrifuge-based droplet shooting device. We demonstrate the first experimental results of glycolytic oscillations in individual yeast cells immobilized in this way. We investigated both the individual and collective oscillatory behaviors at different cell densities. As the cell density increased, the amplitude of the individual oscillations increased while their period decreased, and the collective oscillations became more synchronized, with an order parameter close to 1 (indicating high synchrony). We also synthesized biphasic-Janus microparticles encapsulating yeast cells of different densities in each hemisphere. The cellular oscillations between the two hemispheres were entrained at both the individual and population levels. Such systems of cells encapsulated into microparticles are useful for investigating how cell-to-cell communication depends on the density and spatial distribution of cells.

Effect of metal stress on photosynthetic pigments in the Cu-hyperaccumulating lichens Cladonia humilis and Stereocaulon japonicum growing in Cu-polluted sites in Japan.

To understand the ecology and physiology of metal-accumulating lichens growing in Cu-polluted sites, we investigated lichens near temple and shrine buildings with Cu roofs in Japan and found that Stereocaulon japonicum Th. Fr. and Cladonia humilis (With.) J. R. Laundon grow in Cu-polluted sites. Metal concentrations in the lichen samples collected at some of these sites were determined by inductively coupled plasma mass spectroscopy (ICP-MS). UV-vis absorption spectra of pigments extracted from the lichen samples were measured, and the pigment concentrations were estimated from the spectral data using equations from the literature. Secondary metabolites extracted from the lichen samples were analyzed by high-performance liquid chromatography (HPLC) with a photodiode array detector. We found that S. japonicum and C. humilis are Cu-hyperaccumulating lichens. Differences in pigment concentrations and their absorption spectra were observed between the Cu-polluted and control samples of the 2 lichens. However, no correlation was found between Cu and pigment concentrations. We observed a positive correlation between Al and Fe concentrations and unexpectedly found high negative correlations between Al and pigment concentrations. This suggests that Al stress reduces pigment concentrations. The concentrations of secondary metabolites in C. humilis growing in the Cu-polluted sites agreed with those in C. humilis growing in the control sites. This indicates that the metabolite concentrations are independent of Cu stress.

The ecological roles of bacterial populations in the surface sediments of coastal lagoon environments in Japan as revealed by quantification and qualification of 16S rDNA.

Based on quantification and qualification of bacterial 16S rDNA, we verified the bacterial ecological characteristics of surface sediments of Lakes Shinji and Nakaumi, which are representative of coastal lagoons in Japan. Quantification and qualification of the 16S rDNA sequences was carried out using real time polymerase chain reaction and polymerase chain reaction denaturing gradient gel electrophoresis and non-metric multidimensional scaling, respectively. The results revealed that the copy number per gram of sediment ranged from 8.33 × 10(8) (Lake Nakaumi) to 1.69 × 10(11) (Honjo area), suggesting that bacterial carbon contributed only 0.05-9.64 % of the total carbon content in the samples. Compared with other aquatic environments, these results indicate that sedimentary bacteria are not likely to be important transporters of nutrients to higher trophic levels, or to act as carbon sinks in the lagoons. The bacterial compositions of Lake Shinji and Lake Nakaumi and the Honjo area were primarily influenced by sediment grain sizes and salinity, respectively. Statistical comparisons of the environmental properties suggested that the areas that were oxygen-abundant (Lake Shinji) and at a higher temperature (Honjo area) presented efficient organic matter degradation. The 16S rDNA copy number per gram of carbon and nitrogen showed the same tendency. Consequently, the primary roles of bacteria were degradation and preservation of organic materials, and this was affected by oxygen and temperature. These roles were supported by the bacterial diversity rather than the differences in the community compositions of the sedimentary bacteria in these coastal lagoons.

Toluene dioxygenase expression correlates with trichloroethylene degradation capacity in Pseudomonas putida F1 cultures.

Trichloroethylene (TCE) is extensively used in commercial applications, despite its risk to human health via soil and groundwater contamination. The stability of TCE, which is a useful characteristic for commercial application, makes it difficult to remove it from the environment. Numerous studies have demonstrated that TCE can be effectively removed from the environment using bioremediation. Pseudomonas putida F1 is capable of degrading TCE into less hazardous byproducts via the toluene dioxygenase pathway (TOD). Unfortunately, these bioremediation systems are not self-sustaining, as the degradation capacity declines over time. Fortunately, the replacement of metabolic co-factors is sufficient in many cases to maintain effective TCE degradation. Thus, monitoring systems must be developed to predict when TCE degradation rates are likely to decline. Herein, we show evidence that tod expression levels correlate with the ability of P. putida F1 to metabolize TCE in the presence of toluene. Furthermore, the presence of toluene improves the replication of P. putida F1, even when TCE is present at high concentration. These findings may be applied to real world applications to decide when the bioremediation system requires supplementation with aromatic substrates, in order to maintain maximum TCE removal capacity.

Effect of copper stress on cup lichens Cladonia humilis and C. subconistea growing on copper-hyperaccumulating moss Scopelophila cataractae at copper-polluted sites in Japan.

We investigated lichen species in the habitats of the copper (Cu)-hyperaccumulating moss Scopelophila cataractae and found that the cup lichens Cladonia subconistea and C. humilis grow on this moss. We performed X-ray fluorescence and inductively coupled plasma mass (ICP-MS) analysis of lichen samples and measured the visible absorption spectra of the pigments extracted from the samples to assess the effect of Cu stress on the cup lichens. The chlorophyll a/b ratio and degradation of chlorophyll a to pheophytin a were calculated from the spectral data. X-ray fluorescence analysis indicated that Cu concentrations in cup lichens growing on S. cataractae were much higher than those in control samples growing on non-polluted soil. Moreover, Cu microanalysis showed that Cu concentrations in parts of podetia of C. subconistea growing on S. cataractae increased as the substrate (S. cataractae) was approached, whereas those of C. humilis growing on S. cataractae decreased as the substrate was approached. This reflects the difference in the route of Cu ions from the source to the podetia. Furthermore, ICP-MS analysis confirmed that C. subconistea growing on S. cataractae was heavily contaminated with Cu, indicating that this lichen is Cu tolerant. We found a significant difference between the visible absorption spectra of pigments extracted from the Cu-contaminated and control samples. Hence, the spectra could be used to determine whether a cup lichen is contaminated with Cu. Chlorophyll analysis showed that cup lichens growing on S. cataractae were affected by Cu stress. However, it also suggested that the areas of dead moss under cup lichens were a suitable substrate for the growth of the lichen. Moreover, it suggested that cup lichens had allolepathic effects on S. cataractae; it is likely that secondary metabolites produced by cup lichens inhibited moss growth.

Real-time reverse transcription PCR analysis of trichloroethylene-regulated toluene dioxygenase expression in Pseudomonas putida F1.

Toluene dioxygenase (tod) is a multicomponent enzyme system in Pseudomonas putida F1. Tod can mediate the degradation of Trichloroethylene (TCE), a widespread pollutant. In this study, we try to explore the TCE-regulated tod expression by using real-time qRT-PCR. The minimal culture media were supplemented with glucose, toluene, or a mixture of glucose/toluene respectively as carbon and energy sources. The TCE was injected into each medium after a 12-hour incubation period. The TCE injection severely affected bacterial growth when cultured with toluene or toluene/glucose mixtures. The cell density dropped 61 % for bacteria growing in toluene and 36 % for bacteria in the glucose/toluene mixture after TCE injection, but the TCE treatment had little effect on bacteria supplied with glucose alone. The decrease in cell number was caused by the cytotoxicity of the TCE metabolized by tod. The results from the real-time qRT-PCR revealed that TCE was capable of inducing tod expression in a toluene-dependent manner and that the tod expression level increased 50 times in toluene and 3 times in the toluene/glucose mixture after 6 hours of TCE treatment. Furthermore, validation of the rpoD gene as a reference gene for P. putida F1 was performed in this study, providing a valuable foundation for future studies to use real-time qRT-PCR in the analysis of the P. putida F1 strain.

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure.

Response of secondary metabolites to Cu in the Cu-hyperaccumulator lichen Stereocaulon japonicum.

Lichen secondary metabolites are known to be associated with heavy metal uptake and tolerance in lichens. Understanding the relationship between their secondary metabolites and heavy metals in them is important for clarifying the mechanisms of their heavy metal accumulation and tolerance. To determine the relationships between the concentrations of secondary metabolites and Cu in the Cu-hyperaccumulator lichen Stereocaulon japonicum and to clarify its response to Cu, we collected Cu-contaminated and uncontaminated samples of the lichen and determined relative concentrations of secondary metabolites and concentrations of Cu, K, glucose, and sugar alcohols in them. We found significant negative correlations between the relative concentrations of secondary metabolites-atranorin and stictic acid-and the concentration of Cu. These negative correlations can be interpreted in one of two ways: (a) S. japonicum itself reduced the relative concentrations of secondary metabolites in response to the increase of Cu concentration or (b) its carbon and energy metabolism was damaged by Cu stress, resulting in the reduction of the relative concentrations of secondary metabolites. The analysis of K, glucose, and sugar alcohols showed no effect of Cu on these concentrations, which means that the carbon and energy metabolism was not damaged by Cu stress. Therefore, the negative correlations can be interpreted that S. japonicum itself reduced the relative concentrations of secondary metabolites with the increase of Cu concentration. These findings provide a deeper understanding of the response of secondary metabolites to Cu in the lichen.

Effect of Cu on the fluorescence of the Cu-hyperaccumulator lichen Stereocaulon sorediiferum.

Stereocaulon sorediiferum is expected to be a Cu-hyperaccumulator lichen and has fluorescent substances. To clarify the relationship between the fluorescence (FL) of the lichen and its Cu concentration, we collected S. sorediiferum samples at Cu-contaminated and uncontaminated sites in Japan, determined the concentration of Cu, K, Mg, Al, Ca, Mn, Fe, Zn, chlorophyll a,b, and total carotenoids in them, analyzed lichen secondary metabolites and fluorescent substances extracted from them, and measured the FL of them and their extracts. We found that the FL intensity of S. sorediiferum samples is significantly negatively correlated with their Cu concentration. The application of its FL for Cu monitoring may allow a new nondestructive quantitative method for assessing Cu contamination. The spectroscopic and chromatographic analysis shows that the fluorescent substances negatively correlated with Cu concentration are not major lichen secondary metabolites (lobaric acid and atranorin) and remain after immersion in acetone. The correlation analysis and the comparison with the causal relationship between Cu concentration and the chlorophyll a/b ratio suggest that the reason for the decrease in FL intensity with increasing Cu concentration is a structural change of the fluorescent substances by accumulated Cu. These findings lead to a better understanding of the relationship between the FL of S. sorediiferum and its Cu concentration and provide new insights into fluorescent lichen substances.

Nafion film/K(+)-exchanged glass optical waveguide sensor for BTX detection.

An optical waveguide (OWG) sensor for the detection of BTX gases is reported. The highly sensitive element of this sensor was made by coating the copper Nafion film over a single-mode potassium ion exchanged glass OWG. We used the OWG sensor to detect toluene gas as a typical example BTX gas. The sensor exhibits a linear response to toluene in the range of 0.25-4250 ppm with response and recovery times less than 25 s. The sensor has a short response time, high sensitivity, and good reversibility.

Patchiness in a minimal nutrient-phytoplankton model.

We present a minimal two-component model that can exhibit various types of spatial patterns including patchiness. The model, comprising nutrients and phytoplankton, includes the effect of nutrient uptake by phytoplankton as a Holling type II functional response, and also includes the effect of zooplankton grazing on phytoplankton as a Holling type II non-dynamical term. The mean-field model without the diffusion and advection terms shows both bistability and limit-cycle oscillations as a few parameters such as the input rate of nutrients and the maximum feeding rate of zooplankton are changed. If the parameter values are chosen from the limit-cycle oscillation region, the corresponding reaction-advection-diffusion equations show spatial pattern formations by the combined effects of advection and diffusion by turbulent stirring and mixing, and biological interactions. As the nutrient input is increased, the system behaviour changes from the extinction of the entire phytoplankton to the formation of filamentous patterns, patchiness patterns and homogeneous distributions. These observations suggest that the spatial pattern of phytoplankton can function as an indicator to evaluate the eutrophication level in aquatic ecosystems.

Two-dimensional DNA gel electrophoresis mapping: a novel approach to diversity analysis of bacterial communities in environmental soil.

The diversity analysis of bacteria is useful for the environmental assessment of soil. Traditional molecular-based methods such as denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis achieve a low-resolution display of bacterial DNA fragments on a gel. To improve the resolution, a novel two-dimensional DNA gel electrophoresis (2-DGE) method was designed. This method can generate a high-resolution DNA map that facilitates the detailed analysis of soil bacteria. This map can be obtained by utilizing 2-DGE to separate genomic DNA fragments produced by polymerase chain reaction (PCR) amplification on the basis of chain length and G+C content. To develop this 2-DGE method further and to apply it to the assessment of bacterial diversity, we carried out a 2-DGE mapping of bacterial DNA fragments from different environmental soils and computed Shannon index as well as plotted rank-abundance curves on the basis of the relative intensity of each spot on the maps. DGGE mapping was also performed to compare the resolution of the two methods. 2-DGE mapping was capable of generating a higher resolution display by a factor of more than 2 using a DGGE fingerprint pattern on a piece of gel. Furthermore, the higher number of detected spots from the 2-DGE map enabled the assessment of differences in bacterial diversity in complex soil systems using a logarithmic normal rank-abundance plot.

The effects of starvation and acidification on lag phase duration of surviving yeast cells.

Starvation is one of the most common forms of stress experienced in the wild life. Such conditions associate the other forms of stress such as acid, heat, oxidation, and so on. Organisms acclimate to such stresses and acquire the stress tolerances, which often trade-off their growth rates. To investigate whether starvation and the associated stresses may cause the changes in the growth and the central carbon metabolism, we stock-cultured the yeast S. cerevisiae on YNB agar plates up to a month and subsequently cultured in YNB broth. The pH of the agar medium just under the yeast's colonies sharply dropped from 5.0 to 3.9 in the first day, eventually reached approximately 3.0, and the viability logarithmically decreased. The surviving cells accumulated cell damages that were measured as the prolonged LPDs (lag phase durations). We did not, however, observe the effects of long-term stock-cultivations on the measured phenotypes: growth rates, the carrying capacities, and the glycolytic oscillations that are the temporal dynamics of the central carbon metabolism. Our study revealed that the contribution of cell damages to the total delay in growth was 78%, and that LPDs are closely related to damage-recovery mechanisms.

Promotion and inhibition of synchronous glycolytic oscillations in yeast by chitosan.

Synchronous rhythmic activities play crucial roles in diverse biological systems. Glycolytic oscillations in yeast cells have been studied for 50 years with the aim of elucidating the mechanisms underlying the intracellular oscillations and their synchronization. We investigated the effects of chemical disturbances on the individual and collective glycolytic oscillations in yeast cells encapsulated in alginate microparticles, and demonstrated that the addition of chitosan, an antimicrobial agent, decreased the duration of these oscillations. In contrast, the periods and the synchronicity states showed two different responses to the chitosan treatments. The periods were shown to be prolonged following the treatment with 5-50 mg·L-1 and shortened at 75 mg·L-1 of chitosan. Collective oscillations became more synchronized at 5 mg·L-1 of chitosan, and desynchronized at 25-75 mg·L-1 of this compound. These findings can be explained by the balance between two chitosan features, increasing cell membrane permeability and acetaldehyde scavenging. At low concentrations, chitosan presumably acts as a synchronization promoter that does not mediate the synchronization itself but induces an increase in intercellular coupling. We believe that our findings may provide new insights into the synchronous rhythmic activities in biological systems.

Interference of contaminating DNA in the quantification of a toluene-induced tod gene in Pseudomonas putida.

To determine the extent of interference of co-extracted DNA contamination in the quantification of the tod gene transcript, two different concentrations of RNA (high, 500 ng/microl; low, 250 ng/microl) from a toluene-induced culture of Pseudomonas putida were treated with different amounts of DNase (2, 4, 6 and 8 U) and incubated for 30 and 60 min. The highly sensitive and reproducible TaqMan system was used to quantify the transcript of the tod gene, the tod gene in contaminating DNA and the 16S rRNA gene in DNase-treated RNA samples. For the high RNA concentration, the shorter incubation time (30 min) lowered the level of contaminating DNA as evidenced by the presence of 2.5 x 10(6) copies of the tod gene before treatment to 1.4 x 10(5) copies/microl (8 U), whereas, irrespective of the DNase units used, the longer incubation time (60 min) considerably lowered the level of DNA contamination (2.5 x 10(6) to 6.5 x 10(2) copies of the tod gene/microl). However, for the low RNA concentration, DNase treatment was found to be equally effective in lowering the level of contaminating DNA (10(6) to 10(2) copies of the tod gene/mu), irrespective of the incubation time and the amount of DNase used. Although the results of gel electrophoresis of conventional PCR amplification of the low RNA concentration revealed the absence of the target gene in contaminating DNA, the results of the TaqMan PCR indicated that a very low amount of contaminating DNA (less than 10(3) copies of the tod gene/mul) was still present in RNA samples, even after the DNase treatment. The number of copies of the tod gene transcript in RNA samples did not show any marked variation because of the DNase treatment. However, the proportion of contaminating DNA in RNA samples considerably decreased due to the treatment (0.01 to 0.000001). Furthermore, these results suggested that the extent of the removal of contaminating DNA from RNA samples depends on the concentration of RNA, the amount of DNase used and the incubation time. It is also suggested that the copies of the catabolic genes in contaminating DNA have to be quantified along with the target genes in RNA samples to have a more accurate quantification of the target genes for better understanding of their roles in many microbial processes.