Molecular cloning, tissue expression, and subcellular localization of porcine peptidoglycan recognition proteins 3 and 4

Peptidoglycan recognition proteins (PGRPs) are innate immune molecules that are present in most invertebrates and vertebrates. Mammals have four PGRPs, PGLYRP1-4. In the present study, we cloned the cDNAs encoding porcine PGLYRP3 and 4 from the esophagus of adult swine. The length of the complete open reading frames of porcine PGLYRP3 and 4 are identical and contain 1125bp encoding 374 amino acid residues. The amino acid sequences of these two proteins were more similar to their human orthologs (78.9% [PGLYRP3] and 73.9% [PGLYRP4]) than to their mouse orthologs (71.3% [PGLYRP3] and 67.9% [PGLYRP4]). Expression analysis revealed that both PGLYRP3 and 4 were more strongly expressed in digestive tract, especially the esophagus, than in immune organs such as spleen or mesenteric lymph nodes in both newborn and adult swine. To analyze the subcellular distribution of porcine PGLYRP1-4, we constructed transfectant cell lines. Western blot and flow cytometric analyses revealed that porcine PGLYRP3 and 4 are not only secreted, but also expressed on the cell surface, unlike PGLYRP1 and 2. These results should help contribute to the understanding of PGLYRP3- and 4-mediated immune responses via their recognition of intestinal microorganisms in newborn and adult swine.     

Chloritization in lowland paddy soils

This paper is concerned with the alteration of clay minerals which takes place when well-aerated lowland soils (Brown lowland soils) are cultivated for growing rice. For this purpose the clay mineral compositions of paddy soils were compared with those of adjacent arable soils at four locations.

In the case of arable soils a larger part of the 14Å spacings collapsed to 10Å on treatment with NH₄NO₃ solution, or on drying at about 100°C, whereas in paddy soils the spacings were more stable to thelie treatments. Cation exchange capacities of clays were always smaller In paddy soils than in arable soils. Alternate treatments of reduction and oxidation somewhat increased the stability of the 14Å spacings to heat treatment.

These results indicate that chloritization is a very common process occurring in lowland paddy sons. Chloritization In paddy soils appears to be closely associated with the seasonal cycle of reduction and oxidation.     

Proton consumption with phosphate adsorption on amorphous fe(iii) hydroxide

Proton consumption with phosphate adsorption on amorphous Fe (III) hydroxide (am-Fe(OH)₃) was compared between two different pH-controlled conditions in a 0.1 mol dm^-3 NaClO₄ solution at initial pH values of 5.50 and 4.50, at 298±0.005 K.

The number of protons caused by phosphate dissociation was subtracted from the total number of protons consumed, then the amount of surface OH groups released by the ligand exchange reaction were determined. When a sequential acid titration by a pH-stat maintained pH values of the systems at initial pH values, the percentage of OH groups released during the ligand exchange reaction was almost constant, 29–37%. When the pH values of the systems increased with phosphate adsorption, the percentage of OH groups released by the ligand exchange reaction varied from -4.3 to 33%. The difference in the proton migration between the two pH-controlled conditions not only depended on the phosphate dissociation, but on the difference in the adsorption mechanism, i.e. the ratio of ligand exchange with OH groups to total phosphate adsorption.     

Changes in aluminum pools of andisols due to soil acidification

Abstract

Aluminum concentrations in soil solutions are not only controlled by inorganic clay minerals but also by organically bound aluminum. The objective of this study was to determine which pools contribute to Al dissolution. Soil samples were taken at various distances from tree trunks and at various depths at the Rolling Land Laboratory (RLL), Hachioji, Tokyo. Selective dissolution techniques were used to analyze the changes in pools of solid-phase aluminum. Soil pH values around Hinoki cypresses were in the aluminum buffer range. Exchangeable aluminum contents in soils under Hinoki cypresses were 104 mmol_c kg-^?1 on the average. This value was similar to that of the cation exchange capacity (CEC) of Andisols at RLL at a soil pH of 4. The relationship between the soil pH and exchangeable, organically bound, and amorphous aluminum pools showed that dissolved aluminum ions in the soil solution were primarily derived from the amorphous Al pool. Dissolved aluminum ions were substituted with base cations of soils, resulting in the increase of the content of exchangeable Al and/or the formation of complexes with organic matter which increased the proportion of organically bound Al pools. Increase in the proportion of organically bound Al pools indicated the importance of complexation with soil organic matter for controlling the aluminum concentration in the soil solution.     

Tin concentrations in river / bay sediments of Tokyo in 1984 and 2000

Abstract

To analyze in greater detail the fate and behavior of toxic organotin compounds in the environment, total tin (Sn) concentrations were determined for sediments of the Arakawa River, the Sumida River, and Tokyo Bay by using a graphite furnace atomic absorption spectrophotometer (GFAAS). Sn concentrations in 2000 were compared with those of 1984 (8 years before the regulation on tributyltin-based antifouling paint) as well as with other heavy metals (Cu, Ni, Pb, and Zn). The Sn concentrations ranged from 1.04 to 4.43 mg kg^?1 for sediments sampled in 2000. Although the average concentration of Sn in the sediments was low compared with that of 1984, the concentration tended to increase at several sites in 2000. Moreover, the Sn concentration showed significant correlations with the Cu, Ni, Pb, and Zn concentrations. These results suggest that a significant proportion of the overall Sn content in these sediments was probably introduced from the sources other than antifouling paint. The metals extracted from air-dried sediments with 0.1 m HCl showed that the mobility and bioavailability of Sn was low compared with those of other heavy metals.     

Effect of volcanic fumes from Mt. Oyama,Miyakejima Island,on atmospheric deposition,soil solution,and soil properties in Kumagaya,central Japan

Abstract

The chemical nature of Mn in the leaves of Acanthopanax seiadophylloides, Ilex crenata var. paludosa and Kalopanax pictus was investigated.

Successive extraction of freeze-dried and fresh leaf sam pies with various solvents showed that the major portion of Mn (>90%) was extractable with water and 0.2 M HCl.

Electron probe X-ray microanalysis was performed with the fresh leaf tissues of Mn hyper accumulator A. seiadophylloides, before and after shaking with distilled water, 80% methanol and 1 M HCl. Water removed large parts of Mn in the tissue as a whole except in the region of the epidermis. A negligible amount of Mn was removed by 80% methanol; on the other hand, 1 M HCl removed almost all of the Mn in the tissues.

Paper electrophoretic experiments conducted with water and 0.2 M HCl extracts using pyridine-acetic acid buffer (pH 6.5) indicated that Mn in the extracts behaved similarly to Mn²⁺, presumably due to the labile nature of Mn components in the tissues.     

Effect of winter-flooding on methanogenic archaeal community structure in paddy field under organic farming

Paddy field is a major emission source of methane. Methane is the terminal product of anaerobic decomposition of organic matter and generated by methanogenic archaea under flooded conditions in paddy fields. This study aimed to reveal the effect of winter flooding on methanogenic archaeal community structure in paddy fields of Andosols under organic farming. Soil samples were collected from experimental paddy fields in the Field Science Center, Tohoku University, for two years. They were under flooding conditions during winter with organic farming, under non-flooding conditions during winter with organic farming and under non-flooding conditions during winter with conventional farming (non-organic farming). Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of methanogenic archaeal 16S rRNA gene revealed that the DGGE patterns were nearly the same irrespective of the treatment and sampling times. Twenty-three bands were observed from each treatment and 4, 13 and 6 sequences were closely related to Methanomicrobiales, Methanosarcinales and Methanocellales, respectively. Real-time quantitative PCR analysis indicated that the abundance of methanogenic archaeal 16S rRNA gene and mcrA gene, encoding α subunit of methyl-coenzyme M reductase, was not significantly different among the paddy fields. This study first revealed a methanogenic archaeal community in an Andosol paddy field and showed that the community was not affected by winter flooding under organic farming.     

Effects of successive soil freeze-thaw cycles on nitrification potential of soils

Abstract

In our previous report (Yanai et al. 2004: Soil Sci. Plant Nutr., 50, 821–829), we demonstrated that soil freeze-thaw cycles caused a partial sterilization of the soil microbial communities and exerted limited effects on the potential of organic matter decomposition of soils. In the present study, the effects of soil freeze-thaw cycles on the nitrification potential of soils were examined and the impacts of the freeze-thaw cycles on the nitrifying communities were analyzed. Samples of surface soils (0 to 10 cm depth) were collected, from tropical arable land sites, temperate forest, and arable land sites~ Nitrification potential was assayed by the incubation of soils with or without the addition of 200 fig N of ammonium sulfate per g soil to reach a moisture content adjusted to 60% of maximum water-holding capacity at 27~wC following four successive soil freeze-thaw cycles (-13 and 4°C at 12 h-intervals). Nitrification potential of the soils, in which the decrease in the microbial biomass following the freeze-thaw cycles was less appreciable, was not inhibited by the soil freeze-thaw cycles. On the other hand, the nitrification potential of the soils, in which the decrease in the microbial biomass following the soil freeze-thaw cycles was relatively more appreciable, was clearly inhibited by the freeze-thaw cycles or was undetectable even in the unfrozen control. Surprisingly, nitrate production in the samples of an arable soil collected from Vietnam was inhibited by the addition of ammonium sulfate, and thus the effects of counter-anions of ammonium salts on the nitrification potential of the soils were examined. Since a much larger amount of nitrate was produced in the Vietnam soil with the addition of ammonium acetate and ammonium hydrogen carbonate than that in the soil with the addition of ammonium sulfate, it was considered that ammonium sulfate inhibited nitrification in the soil. These results indicated that ammonium sulfate may not always be a suitable substrate for estimating the nitrification potential of soils. Relationship between soil physicochemical properties and the effect of the soil freeze-thaw cycles on the nitrification potential was evaluated and it was considered that the soil pH(KCI) was likely to be responsible for the difference in the responses among soils, assuming that the pH values changed in unfrozen water under the frozen conditions of soils.     

Sediment denitrification in waterways in a rice-paddy-dominated watershed in eastern China

Purpose

Rice-paddy-dominated watersheds in eastern China are intensively cultivated, and lands with two crops receive as much as 550–600 kg?ha^–1?year^–1 of nitrogen (N), mainly through the addition of N-based fertilizers. However, stream N concentrations have been found to be relatively low. Waterways in the watersheds are assumed to be effective “sinks” for N, minimizing its downstream movement. We directly measured net sediment denitrification rates in three types of waterways (ponds, streams/rivers, and a reservoir) and determined the key factors that control net sediment denitrification. Such information is essential for evaluating the impact of the agricultural N cycle on the quality of surface water.

Materials and methods

The pond–stream–reservoir continuum was sampled every 2 months at nine sites in an agricultural watershed between November 2010 and December 2011. Net sediment N₂ fluxes/net sediment denitrification rates were determined by membrane inlet mass spectrometry and the N₂/Ar technique. A suite of parameters known to influence denitrification were also measured.

Results and discussion

Net denitrification rates ranged between 28.2?±?18.2 and 674.3?±?314.5 μmol N₂–N?m^–2?h^–1 for the streams, 23.7?±?23.9 and 121.2?±?38.7 μmol N₂–N?m^–2?h^–1 for the ponds, and 41.8?±?17.7 and 239.3?±?49.8 μmol N₂–N?m^–2?h^–1 for the reservoir. The mean net denitrification rate of the stream sites (173.2?±?248.4 μmol N₂–N?m^–2?h^–1) was significantly higher (p?<?0.001) than that of the pond sites (48.3?±?44.5 μmol N₂–N?m^–2?h^–1), and the three types of waterways all had significantly higher (p?<?0.01) mean net denitrification rates in summer than in other seasons. Linear regression and linear mixed effect model analysis showed that nitrate (NO₃ ^?–N) concentration in surface water was the primary controlling factor for net sediment denitrification, followed by water temperature. Using monitoring data on NO₃ ^?–N concentrations and temperature of the surface water of waterways and an established linear mixed effect model, total N removed through net sediment denitrification in the pond–stream–reservoir continuum was estimated at 46.8?±?24.0 t?year^–1 from July 2007 to June 2009, which was comparable with earlier estimates based on the mass balance method (34.3?±?12.7 t?year^–1), and accounted for 83.4 % of the total aquatic N. However, the total aquatic N was only 4.4 % of the total N input to the watershed, and thus most of the surplus N in the watershed was likely to be either denitrified or stored in soil.

Conclusions

High doses of N in a rice-paddy-dominated watershed did not lead to high stream N concentrations due to limited input of N into waterways and the high efficiency of waterways in removing N through denitrification.     

Geographic variations in the whistles among three Indo-Pacific bottlenose dolphin <Emphasis Type="Italic">Tursiops aduncus</Emphasis> populations in Japan

ABSTRACT:   Whistles of Indo-Pacific bottlenose dolphins from three populations in Japan were collected and analyzed quantitatively. Geographic variations in the whistles among populations were found. Significant differences in the whistles among years within each population were also found, but those differences could not explain whole differences among populations because some parameters of the whistles had more differences among populations than among years within each population. As changes with time in the whistles within each population might cause the geographic variations among populations, researchers should take the yearly change within populations into consideration when they study the geographic variation in the whistle of dolphins.