A mammalian circadian clock model incorporating daytime expression elements

Models of the mammalian clock have traditionally been based around two feedback loops-the self-repression of Per/Cry by interfering with activation by BMAL/CLOCK, and the repression of Bmal/Clock by the REV-ERB proteins. Recent experimental evidence suggests that the D-box, a transcription factor binding site associated with daytime expression, plays a larger role in clock function than has previously been understood. We present a simplified clock model that highlights the role of the D-box and illustrate an approach for finding maximum-entropy ensembles of model parameters, given experimentally imposed constraints. Parameter variability can be mitigated using prior probability distributions derived from genome-wide studies of cellular kinetics. Our model reproduces predictions concerning the dual regulation of Cry1 by the D-box and Rev-ErbA/ROR response element (RRE) promoter elements and allows for ensemble-based predictions of phase response curves (PRCs). Nonphotic signals such as Neuropeptide Y (NPY) may act by promoting Cry1 expression, whereas photic signals likely act by stimulating expression from the E/E' box. Ensemble generation with parameter probability restraints reveals more about a model's behavior than a single optimal parameter set

Influence of phosphate and iron ions in selective uptake of arsenic species by water fern (Salvinia natans L.)

In the present study, the effect of phosphate ion and iron hydroxides (Fe-plaques) on the selective uptake of arsenic species by water fern (Salvinia natans L.) was investigated. The plants were grown for 5 days in aqueous Murashige and Skoog (MS) culture media modified in arsenic and phosphate concentrations. Arsenic accumulations in S. natans L. increased with the increase of arsenate and DMAA concentrations in the culture solutions. Compared to the control treatment, S. natans L. accumulated significantly higher amount of arsenic from phosphate-deficient solutions, when the source was arsenate. However, arsenic uptake was not affected significantly by phosphate, when the source was dimethylarsinic acid (DMAA). From solutions containing 100 μM of phosphate and 4.0 μM of either arsenate or DMAA, the S. natans L. accumulated 0.14 ± 0.02 and 0.02 ± 0.00 μmol (g dry weight)-1 of arsenic, respectively. In contrast, plants accumulated 0.24 ± 0.06 and 0.03 ± 0.00 μmol (g dry weight)-1 of arsenic from solutions containing 4.0 μM of either arsenate and DMAA in phosphate deficient conditions, respectively. Thus, it is reasonable to state that increasing phosphate concentration in culture solutions decreased the arsenic uptake into the water fern significantly, when the source was arsenate. Moreover, arsenic and phosphate content in plant tissue correlated significantly (r = -0.66; p 0.05). Similarly, significant correlation was observed between arsenic and iron content in plant tissues (r = 0.66; p < 0.05), when initial source was arsenate while the correlation was not significant (r = 0.23; p < 0.05), when initial source was DMAA. The results indicate the adsorption of arsenate on Fe-plaques of aquatic plant surfaces. Furthermore, the study demonstrates that the DMAA uptake mechanisms into the water fern are deferent from those of arsenate. © 2008 Elsevier B.V. All rights reserved

Hydroxyiminodisuccinic acid (HIDS): A novel biodegradable chelating ligand for the increase of iron bioavailability and arsenic phytoextraction

The influence of biodegradable chelating ligands on arsenic and iron uptake by hydroponically grown rice seedlings (Oryza sativa L.) was investigated. Even though the growth solution contained sufficient Fe, the growth of rice seedlings gradually decreased up to 76% with the increase of pH of the solution from 7 to 11. Iron forms insoluble ferric hydroxide complexes at neutral or alkaline pH in oxic condition. Chelating ligands produce soluble 'Fe-ligand complex' which assist Fe uptake in plants. The biodegradable chelating ligand hydroxyiminodisuccinic acid (HIDS) was more efficient then those of ethylenediaminetetraacetic acid (EDTA), ethylenediaminedisuccinic acid (EDDS), and iminodisuccinic acid (IDS) in the increase of Fe uptake and growth of rice seedling. A total of 79 ± 20, 87 ± 6, 116 ± 15, and 63 ± 18 mg dry biomass of rice seedlings were produced with the addition of 0.5 mM of EDDS, EDTA, HIDS, and IDS in the nutrient solution, respectively. The Fe concentrations in rice tissues were 117 ± 15, 82 ± 8, 167 ± 25, and 118 ± 22 μmol g-1 dry weights when 0.25 mM of EDDS, EDTA, HIDS, and IDS were added to the nutrient solution, respectively. Most of the Fe accumulated in rice tissues was stored in roots after the addition of chelating ligands in the solution. The results indicate that the HIDS would be a potential alternative to environmentally persistent EDTA for the increase of Fe uptake and plant growth. The HIDS also increased As uptake in rice root though its translocation from root to shoot was not augmented. This study reports HIDS for the first time as a promising chelating ligand for the enhancement of Fe bioavailability and As phytoextraction. © 2009 Elsevier Ltd. All rights reserved

Arsenic uptake by aquatic macrophyte Spirodela polyrhiza L.: Interactions with phosphate and iron

The uptake of arsenate (As(V)) and dimethylarsinic acid (DMAA) by aquatic macrophyte Spirodela polyrhiza L. was investigated to determine the influence of arsenic interaction with PO43- and Fe ions. Plants were grown hydroponically on standard Murashige and Skoog (MS) culture solutions. Arsenic concentrations in Fe-oxide (Fe-plaque) on plant surfaces were determined by citrate-bicarbonate-ethylenediaminetetraacetic acid (CBE) technique. S. polyrhiza L. accumulated 51-fold arsenic from arsenate solution compared to that from DMAA solution with initial concentrations of 4.0 and 0.02 μM of arsenic and phosphate, respectively. The arsenate uptake was negatively (p 0.05) with iron accumulation. The results suggest that adsorption of arsenate on Fe-plaque of the surface of S. polyrhiza L. contributes to the arsenic uptake significantly. Thus, arsenate uptake in S. polyrhiza L. occurred through the phosphate uptake pathway and by physico-chemical adsorption on Fe-plaques of plant surfaces as well. The S. polyrhiza L. uses different mechanisms for DMAA uptake. © 2008 Elsevier B.V. All rights reserved

Influence of EDTA and chemical species on arsenic accumulation in Spirodela polyrhiza L. (duckweed)

The influence of ethylenediaminetetraacetic acid (EDTA) and chemical species on arsenic accumulation in aquatic floating macrophyte Spirodela polyrhiza L. (duckweed) was investigated. The uptake of inorganic arsenic species (arsenate; As(V) and arsenite; As(III)) into the plant tissue and their adsorption on iron plaque of plant surfaces were significantly (p0.05) by EDTA addition to the culture media while its concentration in CBE-extract decreased significantly (p<0.05). The As(inorganic)/Fe ratios in plant were higher than those of CBE-extract which indicate the increased uptake of these arsenic species into the plant relative to the iron. The lower As(organic)/Fe ratios in plant and on CBE-extract suggest the reduction of accumulation of these arsenic species relative to the iron. © 2007 Elsevier Inc. All rights reserved

Arsenic accumulation in duckweed (Spirodela polyrhiza L.): A good option for phytoremediation

Some unavoidable drawbacks of traditional technologies have made phytoremediation a promising alternative for removal of arsenic from contaminated soil and water. In the present study, the potential of an aquatic macrophyte Spirodela polyrhiza L. for phytofiltration of arsenic, and the mechanism of the arsenic uptake were investigated. The S. polyrhiza L. were grown in three test concentrations of arsenate and dimethylarsinic acid (DMAA) (i.e. 1.0, 2.0 and 4.0 μM) with 0 (control), 100 or 500 μM of phosphate. One control treatment was also set for each test concentrations of arsenic. The PO43 - concentration in control treatment was 0.02 μM. When S. polyrhiza L. was cultivated hydroponically for 6 d in culture solution containing 0.02 μM phosphate and 4.0 μM arsenate or DMAA, the arsenic uptake was 0.353 ± 0.003 μmol g-1 and 7.65 ± 0.27 nmol g-1, respectively. Arsenic uptake into S. polyrhiza L. was negatively (p 0.05) with iron accumulation in plant tissues, which indicates that S. polyrhiza L. uses different mechanisms for DMAA uptake. © 2007 Elsevier Ltd. All rights reserved

Single hole doped strongly correlated ladder with a static impurity

We consider a strongly correlated ladder with diagonal hopping and exchange interactions described by $t-J$ type hamiltonian. We study the dynamics of a single hole in this model in the presence of a static non-magnetic (or magnetic) impurity. In the case of a non-magnetic (NM) impurity we solve the problem analytically both in the triplet (S=1) and singlet (S=0) sectors. In the triplet sector the hole doesn't form any bound state with the impurity. However, in the singlet sector the hole forms bound states of different symmetries with increasing $J/t$ values. Binding energies of those impurity-hole bound states are compared with the binding energy of a pair of holes in absence of any impurity. In the case of magnetic impurity the analytical eigenvalue equations are solved for a large (50 X 2) lattice. In this case also, with increasing $J/t$ values, impurity-hole bound states of different symmetries are obtained. Binding of the hole with the impurity is favoured for the case of a ferromagnetic (FM) impurity than in the case of antiferromagnetic (AFM) impurity. However binding energy is found to be maximum for the NM impurity. Comparison of binding energies and various impurity-hole correlation functions indicates a pair breaking mechanism by NM impurity.Comment: 15 Pages, 6 figure

Modeling wet deposition and concentration of inorganics over Northeast Asia with MRI-PM/c

We conducted a regional-scale simulation over Northeast Asia for the year 2006 using an aerosol chemical transport model, with time-varying lateral and upper boundary concentrations of gaseous species predicted by a global stratospheric and tropospheric chemistry-climate model. The present one-way nested global-through-regional-scale model is named the Meteorological Research Institute–Passive-tracers Model system for atmospheric Chemistry (MRI-PM/c). We evaluated the model's performance with respect to the major anthropogenic and natural inorganic components, SO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;2&amp;minus;&lt;/sup&gt;, NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;, NO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;&amp;minus;&lt;/sup&gt;, Na&lt;sup&gt;+&lt;/sup&gt; and Ca&lt;sup&gt;2+&lt;/sup&gt; in the air, rain and snow measured at the Acid Deposition Monitoring Network in East Asia (EANET) stations. Statistical analysis showed that approximately 40–50 % and 70–80 % of simulated concentration and wet deposition of SO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;2&amp;minus;&lt;/sup&gt;, NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;, NO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;&amp;minus;&lt;/sup&gt;and Ca&lt;sup&gt;2+&lt;/sup&gt; are within factors of 2 and 5 of the observations, respectively. The prediction of the sea-salt originated component Na&lt;sup&gt;+&lt;/sup&gt; was not successful at near-coastal stations (where the distance from the coast ranged from 150 to 700 m), because the model grid resolution (&amp;Delta;&lt;i&gt;x&lt;/i&gt;=60 km) is too coarse to resolve it. The simulated Na&lt;sup&gt;+&lt;/sup&gt; in precipitation was significantly underestimated by up to a factor of 30

Determination of Cu, Pb, Fe, and Zn in plant component polymers of a hyperaccumulating plant

金沢大学自然計測応用研究センターエコテクノロジー研究部門金沢大学工学部Phytoremediation is an innovative technology that utilizes the natural properties of plants to remediate hazardous waste sites. For more cost-effective phytoremediation, it is important to utilize a hyperaccumulating plant after phytoremediation, i.e. the recovery of valuable metals and the production of useful materials. In this work, the determination of metals in plant component polymers in a fern, Athyrium yokoscense, as a hyper-accumulating plant was established using steam explosion, Wayman\u27s extraction method, and ICP emission spectrometry. After A. yokoscense plants were treated by steam explosion, the steam-exploded A. yokoscense were separated into four plant component polymers, i.e. water-soluble material fraction, holocellulose fraction, methanol-soluble lignin fraction, and residual lignin fraction. The concentrations of Cu, Pb, Fe, and Zn in these plant component polymers and the dry weights of plant component polymers were measured. These analytical process determining metals in the plants will contribute to not only the evaluation and the efforts of phytoremediation using a hyperaccumulating plant, but also to the development of more effective phytoremediation. 2005 © The Japan Society for Analytical Chemistry

Isolation of monomethylarsonic acid-mineralizing bacteria from arsenic contaminated soils of Ohkunoshima Island

金沢大学大学院自然科学研究科物質情報解析Chemical warfare agents, composed of harmful organoarsenic compounds have contaminated the soils of Ohkunoshima Island with high levels of arsenic. As a basic research establishing useful bioremediation techniques, environmental factors such as arsenic concentrations and bacterial biomass in the soils were investigated. Among the five stations of Ohkunoshima Island, the soils of four stations were contaminated by high levels of arsenic compounds at concentrations of 125,12.7, 3.29 and 0.504 g/kg soil, while the other station with low arsenic concentrations of 0.007 g/kg soil was considered an uncontaminated area. The distribution of arsenic compounds originating from the chemical weapon agent differs among the various areas of Ohkunoshima Island. The cell densities of arsenate-resistant bacteria also varied among the five stations, ranging from 106 to 108 cells/g soil. In an attempt to isolate bacteria that strongly mineralize the organoarsenic compounds, the mineralization activities for monomethylarsonic acid [MMAA(V)] of 48 isolates of arsenate-resistant bacteria were determined. Only nine isolates reduced 140 μg/1 of MMAA(V), giving decreasing percentages ranging from 5 to 100% within 14 days. Among the nine isolates, two remarkably converted 140 μg/1 of MMAA to more than 71 μg/1 of inorganic arsenic. Presumably only specific members of the environmental bacterial population have strong mineralization activities for MMAA. Phylogenetic analysis using 16S rDNA sequences showed that the two isolates belonged to the Pseudomonas putida strains, which are known to have strong mineralization activity for various organic compounds. In the soil contaminated by arsenic at a high level, few bacteria in the arsenate-resistant bacterial group would significantly mineralize organoarsenic compounds. Copyright © 2006 John Wiley & Sons, Ltd