Large sulfur isotope fractionation does not require disproportionation

The composition of sulfur isotopes in sedimentary sulfides and sulfates traces the sulfur cycle throughout Earth's history. In particular, depletions of sulfur-34 ((34)S) in sulfide relative to sulfate exceeding 47 per mil (‰) often serve as a proxy for the disproportionation of intermediate sulfur species in addition to sulfate reduction. Here, we demonstrate that a pure, actively growing culture of a marine sulfate-reducing bacterium can deplete (34)S by up to 66‰ during sulfate reduction alone and in the absence of an extracellular oxidative sulfur cycle. Therefore, similar magnitudes of sulfur isotope fractionation in sedimentary rocks do not unambiguously record the presence of other sulfur-based metabolisms or the stepwise oxygenation of Earth's surface environment during the Proterozoic.     

ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage

Cellular responses to DNA damage are mediated by a number of protein kinases, including ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related). The outlines of the signal transduction portion of this pathway are known, but little is known about the physiological scope of the DNA damage response (DDR). We performed a large-scale proteomic analysis of proteins phosphorylated in response to DNA damage on consensus sites recognized by ATM and ATR and identified more than 900 regulated phosphorylation sites encompassing over 700 proteins. Functional analysis of a subset of this data set indicated that this list is highly enriched for proteins involved in the DDR. This set of proteins is highly interconnected, and we identified a large number of protein modules and networks not previously linked to the DDR. This database paints a much broader landscape for the DDR than was previously appreciated and opens new avenues of investigation into the responses to DNA damage in mammals.     

Investigation into the durability of washed rice straw for equine bedding and the repetitive use of washing water

The present experiment investigated durability during the repetitive use of washed rice straw, as bedding material, and washing water as a model study. Residual nitrogen levels, elasticity, and water suction rates for washed rice straw‐adhered urea were measured. In addition, outflow levels of nitrogen and mineral ions (Na⁺, NO₂^‐ + NO₃^‐, SO₄^2?, PO₄^3?, Cl^‐) for washing water were measured to determine durability. Nitrogen levels of rice straw significantly (P < 0.05) decreased after two washings. There was no significant change in elasticity of repetitively used rice straw. Suction rates of rice straw after the second and third washings increased significantly (P < 0.05) compared to the first time. With regard to the number of washings, the mineral ion outflow level in the washing water for nitrogen, Na⁺, NO₂^‐ + NO₃^‐ and PO₄^3? after each washing was not significant. However, nitrogen outflow level tended to decrease after the third washing. SO₄^‐ and Cl^‐ did significantly decrease (P < 0.05) with the number of washings. In this study, it was considered that rice straw and washing water could be used repetitively three times. Furthermore, in order to maintain effluent standards, washing water from the first washing needs to be processed in a septic tank.     

Is there a relationship between the intrinsic rate of propagation and <Emphasis Type="Italic">in-vitro</Emphasis> migration and virulence of the pinewood nematode, <Emphasis Type="Italic">Bursaphelenchus xylophilus</Emphasis>?

We investigated if rates of propagation and migration were related with the level of virulence in the pinewood nematode Bursaphelenchus xylophilus using 17 offspring lines from the F₂ crosses between virulent and avirulent isolates. Virulence was tested by inoculating seedlings of Pinus thunbergii with the nematodes. The proportion of dead seedlings ranged from 13.3% to 77.8%, 20 weeks after inoculation. Migration rate of the nematodes was estimated by measuring their migration distance per unit time in an artificial substrate that imitated pathways in pine trees. Migration rate varied from 0.85 to 3.53 mm min⁻¹. Propagation rate was determined based on population growth on the fungus Botrytis cinerea, and it ranged between 10^3.88 and 10^4.99 per 12 days. Statistical analyses revealed that virulence was not correlated with migration rate, but was negatively correlated with propagation rate on Botrytis cinerea, suggesting that the nematodes paid some cost for virulence. Also, there was no relationship between rates of migration and propagation. Cluster analysis showed that the biological parameters varied between crossbred lines, with no kinship bias, suggesting the absence of sex-linked inheritance in virulence and rates of propagation and migration.     

Seasonal change in N<Subscript>2</Subscript>O flux from forest soils in a forest catchment in Japan

Temperate forest soils are one source of nitrous oxide (N₂O), which is an important greenhouse gas and the most important ozone-depleting substance. To clarify N₂O flux mechanisms in relation to soil temperature, moisture, and nitrification activity, we measured N₂O fluxes and net nitrification rates over 3 years at the lower (Japanese cedar) and upper (deciduous broad-leaved trees) parts of a hill slope in a small forest catchment in the northern Kanto region of Japan. The N₂O flux was measured by the closed-chamber technique every month, along with soil temperature and water-filled pore space (WFPS). At the lower slope, the N₂O flux increased with increasing soil temperature (r ² = 0.383, P < 0.01) owing to an increase in the nitrification rate. At the upper slope, no positive linear correlation of N₂O flux with soil temperature, WFPS, or nitrification rate was observed. The low N₂O flux at the upper slope during summer was caused by the low summertime WFPS there. We attributed the higher mean N₂O fluxes observed at the lower slope (median 2.36 μg N m⁻² h⁻¹) than at the upper slope (median 1.10 μg N m⁻² h⁻¹) to a high soil moisture during summer season in the surface soil of the lower slope.     

53BP1, a mediator of the DNA damage checkpoint

53BP1 binds to the tumor suppressor protein p53 and has a potential role in DNA damage responses. We used small interfering RNA (siRNA) directed against 53BP1 in mammalian cells to demonstrate that 53BP1 is a key transducer of the DNA damage checkpoint signal. 53BP1 was required for p53 accumulation, G2-M checkpoint arrest, and the intra-S-phase checkpoint in response to ionizing radiation. 53BP1 played a partially redundant role in phosphorylation of the downstream checkpoint effector proteins Brca1 and Chk2 but was required for the formation of Brca1 foci in a hierarchical branched pathway for the recruitment of repair and signaling proteins to sites of DNA damage.     

Effects of slag silicate fertilizer on silicon content of rice plants grown in paddy fields on the Shounai Plain,Yamagata, Japan

Abstract

Slag silicate fertilizer (SSF) is applied to paddy fields with different soil chemical properties to increase silicon (Si) concentration in rice (Oryza sativa L.) plants. However, the effects of soil chemical properties on Si availability of SSF to rice Si uptake is poorly understood. To investigate the relationships between chemical properties of soils and the effects of SSF application on the Si concentration in rice plants, a field experiment was conducted in 2007 and 2008 at 18 paddy fields on the Shounai Plain, Yamagata, Japan. Two treatments were implemented: SSF applied at 1.5 t ha^?1 and a no-SSF control. The Si concentrations of rice tissues were measured at the tillering and ripening stages. The difference in the Si concentrations of rice tissues between treatments (ΔSi concentration) was used to evaluate the effect of SSF. The Si concentrations in the shoots and aboveground parts of the rice plants were significantly increased by the SSF application in six or more of the fields at the two growth stages, whereas the Si concentrations in the panicles of the rice plants at the ripening stage were not increased significantly in most fields. Results of two-way analysis of variance evidenced a significant effect of field on the ΔSi concentrations in the shoots and aboveground parts at both growth stages. Furthermore, the ΔSi concentrations in the same rice plant tissues and at the same growth stages in the first year and in the second year were found to be positively correlated. These results indicate that the effect of SSF on the Si concentration in shoots and aboveground parts of rice plants varies from field to field. The ΔSi concentrations in shoots and aboveground plant parts at both growth stages were also found to be negatively correlated with soil chemical properties, i.e., available Si, Si adsorption capacity, contents of Si adsorbents (acid oxalate-extractable iron and manganese) and the pH under flooded soil conditions. These findings imply that those soil chemical properties of paddy fields should be taken into account for better prediction of ΔSi concentration of rice plants.     

Extension of von Bertalanffy growth model incorporating growth patterns of soft and hard tissues in bivalve molluscs

ABSTRACT:   A new practical growth model through the partial reconstruction for the von Bertalanffy function (VBF) has been proposed. In numerous studies on various species, VBF has been recognized as an appropriate function to describe growth. Here the difference in growth dynamics between soft and hard tissues is considered using VBF. A differential equation in which the growth rates of these two tissue types are described, gives a four parameter model. This advanced model showed characteristics such as: (i) S-shape curve similar to the Gompertz model; (ii) unfixed point of inflection; and (iii) definition as an implicit function. The characteristic indicated in (iii) makes it impossible to apply the method of least squares to data analysis. Therefore, a solution was introduced combining Lagrange's method of indeterminate coefficients and the Newton method. Data analysis for verifying the performance of the advanced model was conducted on published data on growth of the bivalve Spisula sachalinensis . As a result of the comparison among the existing growth models, the advanced model produced the minimum value of Akaike information criterion (AIC).     

Identification of Renieramycin A as an Antileishmanial Substance in a Marine Sponge Neopetrosia sp.

The newly developed assay system using recombinant Leishmania amazonensis expressing enhanced green fluorescent protein (La/egfp) has been applied to the screening of Japanese marine sponges for antileishmanial activity. Bioassay-guided fractionation of an active sponge Neopetrosia sp. afforded an active compound which was identified as renieramycin A by spectroscopic analysis. It inhibited La/egfp with an IC₅₀ value of 0.2 μg/mL.     

Time course of changes in antioxidant activity of milk from dairy cows fed a trehalose‐supplemented diet

This study was to investigate the time course of changes to the antioxidant activity of milk from cows fed a trehalose‐supplemented diet, and to determine possible underlying mechanisms for observed changes. Six Holstein cows were used, and subjected to two experimental feeding periods consisting of a 1% trehalose‐supplemented diet for 10 days, followed by a basal diet only (no trehalose) for 10 days. 1,1‐Diphenyl‐2‐picrylhydrazyl (DPPH) radical scavenging activities in milk were gradually increased during the trehalose supplementation period and were highest at the end of the second period. However, trehalose was not detected in the milk and plasma of dairy cows fed a diet supplemented with trehalose for 10 days, indicating that the increased antioxidant activity in the milk of trehalose‐fed cows is not due to the direct transfer of trehalose to the milk. Plasma DPPH activities exhibited a similar time course to that seen for milk. Relative superoxide dismutase (SOD) activities in the rumen were higher 3 days after the end of trehalose supplementation than at any other time during the experimental periods. These results suggested that the improved antioxidant activity in milk and plasma of cows fed a trehalose‐supplemented diet was due to improved ruminal relative SOD activity.