Genome‐wide identification of pathogenicity genes in Xanthomonas oryzae pv. oryzae by transposon mutagenesis

A transposon mutant library was constructed from the bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) KACC10331 by Tn5 transposon mutagenesis. The susceptible rice cultivar Milyang 23 was inoculated with a total of 24 540 mutants resistant to kanamycin and 67 avirulent or reduced‐pathogenicity mutant strains were selected for study. Southern hybridization verified that 84 mutant strains had single‐copy insertions and their single‐transposon insertion sites were identified by sequencing analysis combined with thermal asymmetric interlaced (TAIL)‐PCR. The single‐transposon‐tagged sequences of 21 mutant strains belonged to pathogenicity‐related genes previously reported in Xanthomonas species, while the other 46 single‐transposon‐tagged sequences included diverse functional genes encoding, five cell‐wall‐degrading enzymes, three fimbrial and flagella assembly regulators, five regulatory proteins, 15 metabolic regulators and 18 hypothetical proteins, which were identified as novel pathogenicity genes of Xoo.     

Relationship between albacore (Thunnus alalunga) fishing grounds in the Indian Ocean and the thermal environment revealed by cloud-free microwave sea surface temperature

Using cloud-free Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) sea surface temperature (SST) and daily set longline fishery data, we studied the relationship between albacore (ALB) fishing grounds and thermal conditions in the southern Indian Ocean. SST and Jensen-Shannon divergence (JSD) maps with a daily spatiotemporal resolution were related to sites with high catches per unit effort (CPUE) (>11 fish/10³ hooks). A high JSD is considered to be an index of a SST front. In winter, high CPUE occurred in the vicinity of the North Subtropical Front (Belkin and Gordon, 1996), where SST was 15-19 °C and JSD was 0.3-0.9. Histograms of the high CPUE plotted against SST and JSD indicated that 95% of the high CPUEs were in the 16-18.5 °C SST range and 97% were in the 0.4-0.9 JSD range. These ranges of SST and JSD are optimum ranges. These cloud-free SST/JSD analyses clearly demonstrate the seasonal north-south movement of the optimum SST and JSD band, which corresponds to the North Subtropical Front in the southern Indian Ocean. Monthly maps of joint probability density (JPD) with the optimum ranges of SST and JSD revealed that high CPUEs are located in the narrow bands with high JPD (>50%).     

Estimation of productivity growth,technical progress,and efficiency changes in the Korean offshore fisheries

In this study, changes in total factor productivity of 12 Korean offshore fisheries between 1997 and 2009 were estimated through the Malmquist productivity index, which is a nonparametric method. Also, the cause of such changes in productivity of each fishery was analyzed more specifically by segmenting into factors for technological progress and technical efficiency. As a result of this analysis, the total factor productivity change of the entire offshore fisheries was −6.0 %. Changes in the technical efficiency and technological level factors, respectively, contributed 0.2 and −6.2 % to this rate of decrease in total factor productivity; that is, inactivity of technological progress led to the decrease in productivity of the offshore fisheries. In addition, technological progress and technical efficiency were found to differently influence the change in total factor productivity of each fishery. In order for each fishery to improve productivity, better rational fisheries management policies by the government and efforts by the fishing industry and individual fishing business units must accompany factors that promote productivity increase.     

Effects of low environmental salinity on the cellular profiles and expression of Na+, K+-ATPase and Na+, K+, 2Cl? cotransporter 1 of branchial mitochondrion-rich cells in the juvenile marine fish Monodactylus argenteus

The goal of this study was to determine the osmoregulatory ability of a juvenile marine fish, silver moony (Monodactylus argenteus), for the purpose of developing a new experimental species for ecophysiological research. In this study, M. argenteus was acclimated to freshwater (FW), brackish water (BW), or seawater (SW). The salinity tolerance of this euryhaline species was effective, and the fish survived well upon osmotic challenges. The largest apical surface of mitochondrion-rich cells was found in the FW individuals. Immunohistochemical staining revealed that Na(+), K(+)-ATPase immunoreactive (NKA-IR) cells were distributed in the interlamellar region of the gill filaments of the silver moony in all experimental groups. In addition to the filaments, NKA-IR cells were also found in the lamellae of the FW individuals. The number of NKA-IR cells in the gills of the FW individuals exceeded that of the BW and SW individuals. The NKA-IR cells of FW and SW individuals exhibited bigger size than that of BW fish. The NKA activities and protein expression of the NKA α-subunit in the gills of the FW individuals were significantly higher than in the BW and SW groups. Additionally, the relative amounts of Na(+), K(+), 2Cl(-) cotransporter 1 (NKCC1) were salinity-dependent in the gills. Immunofluorescent signals of NKCC1 were localized to the basolateral membrane of NKA-IR cells in all groups. In the gills of the FW individuals, however, some NKA-IR cells did not exhibit a basolateral NKCC1 signal. In conclusion, the present study illustrated the osmoregulatory mechanisms of this easy- and economic-to-rear marine teleost with euryhaline capacity and proved the silver moony to be a good experimental animal.     

Integrating remote sensing and GIS for prediction of rice protein contents

In this study, protein content (PC) of brown rice before harvest was established by remote sensing (RS) and analyzed to select the key management factors that cause variation of PC using a GIS database. The possibility of finding out the key management factors using GreenNDVI was tested by combining RS and a GIS database. The study site was located at Yagi basin (Japan) and PC for seven districts (85 fields) in 2006 and nine districts (73 fields) in 2007 was investigated by a rice grain taste analyzer. There was spatial variability between districts and temporal variability within the same fields. PC was predicted by the average of GreenNDVI at sampling points (Point GreenNDVI) and in the field (Field GreenNDVI). The accuracy of the Point GreenNDVI model (r ² > 0.424, RMSE < 0.256%) was better than for the Field GreenNDVI model (r ² > 0.250, RMSE < 0.298%). A general-purpose model (r ² = 0.392, RMSE = 0.255%) was established using 2 years data. In the GIS database, PC was separated into two parts to compare the difference in PC between the upper (mean + 0.5SD) and lower (mean − 0.5SD) parts. Differences in PC were significant depending on the effective cumulative temperature (ECT) from transplanting to harvest (Factor 4) in 2007 but not in 2006. Because of the difference in ECT depending on vegetation term (from transplanting to sampling), PC was separated into two groups based on the mean value of ECT as the upper (UMECT) and lower (LMECT) groups. In 2007, there were significant differences in PC at LMECT group between upper and lower parts depending on the ECT from transplanting to last top-dressing (Factor 2), the amount of nitrogen fertilizer at top-dressing (Factor 3) and Factor 4. When the farmers would have changed their field management, it would have been possible to decrease protein contents. Using the combination of RS and GIS in 2006, it was possible to select the key management factor by the difference in the Field GreenNDVI.     

Salinity changes in the anadromous river pufferfish,Takifugu obscurus,mediate gene regulation

This study aimed to better understand the hydromineral regulatory response of the anadromous river pufferfish, Takifugu obscurus, to salinity changes through real-time RT-PCR. After abrupt transfer from 30 or 5 psu to 5 or 30 psu, respectively, we analyzed the mRNA expression of Na⁺/K⁺ ATPase, prolactin receptor, and aquaporin from osmoregulatory organs of the river pufferfish such as gills, kidney, and intestine. Na⁺/K⁺ ATPase showed notable changes in the gills and kidney when salinity was increased. In the gills, the expression level of Na⁺/K⁺ ATPase suddenly increased within a day after abrupt transfer from 5 to 30 psu and then slightly declined within 2 days after exposure. In the kidney, Na⁺/K⁺ ATPase has shown consistently high mRNA expression after the increase in salinity. Expression levels of the prolactin receptor gene increased when environmental salinity decreased. In the intestine, gene expression of the prolactin receptor remained high, even when salinity decreased. To the contrary, there was a steady increase or decrease in mRNA expression in the kidney in response to salinity decrease or increase, respectively. As for aquaporins, aquaporin 1 was mainly expressed in the intestine and kidney, and aquaporin 3 was mainly expressed in the gills and intestine. In the gills, increased expression of aquaporin 3 was found after transfer to lower salinity and in the intestine and kidney, a decrease in salinity followed by an abrupt decrease in aquaporin 1 and aquaporin 3. Contrastingly, the expression of these genes increased in the intestine after transfer to 30 psu. Osmoregulatory genes were expressed in diverse organs, apparently to overcome an influx or exhaust of water or ions. A superior adaptation ability of the river pufferfish to a wide range of salinities is most reasonably due to active osmoregulatory processes mediated by the genes monitored here.     

Effects of biochar on Cd and Pb mobility and microbial community composition in a calcareous soil planted with tobacco

An experiment was conducted with tobacco (Nicotiana tabacum L.) grown in a Cd- and Pb-contaminated calcareous soil amended with 0.0, 1.0, 2.5, and 5.0% (w/w) tobacco stalk biochar (BC). The BC amendment significantly increased organic matter, total C, N, P, and K contents of soil, and the C/N ratio. Bioavailable metal concentrations (DTPA extraction) decreased by increasing BC application rate. The 5.0% BC amendment significantly decreased the DTPA-extractable Cd and Pb by 10.4 and 13.6%, respectively. Correspondingly, the bioaccumulation and translocation factors of Cd and Pb also decreased by increasing the BC addition rates and this indicated that BC inhibited the uptake and transfer of both Cd and Pb by tobacco plants. Moreover, high-throughput sequencing revealed that BC increased Chao1 richness, Shannon’s diversity and Simpson’s diversity of bacterial communities of soil. The relative abundance and genera composition of Adhaeribacter, Rhodoplanes, Pseudoxanthomonas, and Candidatus Xiphinematobacter increased under BC treatments, while those of Kaistobacter, Lacibacter, and Pirellula decreased. Overall, BC increased soil nutrients (C, N, P, and K contents), enhanced bacterial diversity indexes and richness, and changed the bacterial community composition, which may all have contributed to reduce the mobility and bioavailability of both Cd and Pb in a calcareous soil.     

Nutritional Properties of Various Tissues from New Kenaf Cultivars

Kenaf is an economically important crop that contains various functional compounds. The objective of this study was to evaluate the nutritional properties of leaves, stem bark, flowers, and seeds collected from three mutant kenaf cultivars (Jangdae, Baekma, and Jeokbong) and two original cultivars (Jinju and C14). For all analyzed tissues, there were no significant differences in the proximate compositions (moisture, crude protein, crude fiber, crude fat, ash, and nitrogen-free extract) among the tested genotypes, except for the leaf crude protein content, which was highest in Jinju plants. Of the tested minerals, potassium and calcium were the most abundant in all tissues. Additionally, we detected significant differences in the mineral contents (e.g., calcium, phosphorus, potassium, magnesium, zinc, and iron) of various tissues in all cultivars. Proline and phenylalanine were the major amino acids detected in leaves, and the highest total amino acid (TAA) and essential amino acid (EAA) contents were observed in Jinju plants. The TAA and EAA contents were lower in stem bark than in the other tissues, except in Baekma plants, in which the lowest levels were observed in flowers. Moreover, the TAA and EAA contents were approximately 20 times lower in white flowers (Baekma) than in ivory flowers. Furthermore, the highest TAA and EAA concentrations were observed in Jangdae seeds. These results may be useful for identifying the optimal cultivar and tissues for use in food products.     

Evaluation of Seed Vigor Tests for Predicting Seedling Establishment at Low Temperature in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

This study was carried out to develop an evaluation method to predict rice seedling establishment (SE) under low-temperature conditions. Two Korean-bred japonica cultivars, Shindongjin and Hopum were used in the experiment. Fresh seeds were treated with an accelerated aging (AA) at 40°C and 100% RH for 1-15 days. The SEs of the fresh and AA seeds were evaluated in nursery beds at 17°C, and their correlation coefficients with seed vigor values measured by 9 test methods including standard germination test (SGT), cool germination test (CLT), cold germination test (CDT), seedling growth rate test (SGRT), ascorbate peroxidase (APX), peroxidase (POX), superoxide dismutase (SOD), catalase (CAT), and α ‐amylase (AMY) activities. The percentage of SE decreased slowly from 75 to 0% with an increasing of AA period from 0 to 15 days. The result of nine vigor tests showed different correlations with the SE. SGT, CLT, SGRT, and POX were significantly correlated with the SE. In the correlation analysis with only short-term aging seeds (1-7 days), the SE was very highly correlated with SGT, CLT, CDT, SGRT, POX, and CAT. These results suggest that seed vigor values measured by several methods including SGT and POX could be used as a reference value to secure SE at low temperatures in nursery bed rice seedling culture.