• Molecules and Cells
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• v.43 no.3
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• pp.298-303
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• 2020

Cryo-electron microscopy (cryo-EM) is now the first choice to determine the high-resolution structures of huge protein complexes. Grids with two-dimensional arrays of holes covered with a carbon film are typically used in cryo-EM. Although semi-automatic plungers are available, notable trial-and-error is still required to obtain a suitable grid specimen. Herein, we introduce a new method to obtain thin ice specimens using real-time measurement of the liquid amounts in cryo-EM grids. The grids for cryo-EM strongly diffracted laser light, and the diffraction intensity of each spot was measurable in real-time. The measured diffraction patterns represented the states of the liquid in the holes due to the curvature of the liquid around them. Using the diffraction patterns, the optimal time point for freezing the grids for cryo-EM was obtained in real-time. This development will help researchers rapidly determine high-resolution protein structures using the limited resource of cryo-EM instrument access.

• Animal Bioscience
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• v.36 no.7
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• pp.1067-1074
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• 2023

Objective: Better feed efficiency can be achieved by selecting rabbit genotypes with lower residual feed intake (RFI) under high ambient temperatures. Methods: Two genotypes of rabbits (Jabali, Saudi local breed and imported, Spanish V-line) were used to derive RFI and to investigate the relationship between RFI and productive traits. In total, 250 animals (125 each) were housed in individual wire mesh cages in a semi-closed rabbitry. Growth performance, feed criteria, carcass evaluation, biochemical blood analysis, and immune responses were determined. Results: Superiority in growth performance, feed efficiency, carcass characteristics, and cellular immunity was recorded in the Jabali breed compared to the V-line genotype. According to regression analysis, a significant effect of daily body weight gain was found, upon computing the expected feed intake in both genotypes. Moreover, mid-body weight^0.75 had a significant effect only in the Jabali breed. Positive correlation coefficients between RFI and dry matter feed intake or feed conversion ratio were found. The same trend in this relationship between RFI and productive traits was observed in some cases for both genotypes. An opposite trend in correlations was observed in the studied genotypes for some traits. Conclusion: The results suggest that the relationship between RFI and productive traits must be taken into consideration in rabbit breeding programs under the prevailing environment. However, further studies are required to investigate the effect of rabbit genotype and environmental factors on computing RFI.

• Applied Biological Chemistry
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• v.41 no.4
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• pp.228-234
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• 1998

An adaptive measure of photosynthetic cells to a condition identified with a reduction of cellular energy charge, caused by water deficit-induced impairment of photosynthetic ATP production, was investigated using hydroponically cultured rice seedlings. Water stress treatment of the seedlings resulted in a marked decrease in cellular ATP level, a significant increase in the content of NAD(H) and concurrent decrease in that of NADP(H) in shoots, which accompanied a decrease in the activity of NAD kinase (EC 2.7.1.23) that specifically converts NAD(H) to NADP(H). The decline in the enzyme activity was particularly evident in the $Ca^{2+}/calmodulin-dependent$ kinase, the major form of NAD kinase in plants, whereas the level of active calmodulin remained unchanged during water deficit. The ratio of $NADP^+$ to NADPH was maintained nearly constant and no increases were seen in the level of $H_2O_2$ and the activities of $superoxide/H_2O_2-detoxifying$ enzymes in shoots stress-treated for two days. Based on these results, it may be suggested that rice plants take a strategy to cope with an adverse situation of limited photophosphorylation created by water deficit in that cells facilitate ATP production through glycolysis and oxidative phosphorylation; in doing so, rice cells suppress NAD kinase activity, consequently up-sizing the NAD(H) pool at the expense of the NADP(H) pool. Several parameters associated with the stress symptoms are also of implicative that there is no overproduction of superoxide radical or the related active oxygen at least in rice seedlings.

• Korean Journal of Agricultural Science
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• v.16 no.2
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• pp.163-168
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• 1989

Fourty-four isolates showed acetylene-reducing(nitrogenase)activity under the atmosphere of 89% Ar, 10% $C_2H_2$ and 1 % $O_{2{\cdot}}$, these nitrogen-fixing isolates characterized chemotaxonomically and their taxonomic status was disscussed; twenty-three isolates corresponded to Azospirillum. They were curved/spiral rods, gram negative, motile by a polar flagellum, and also utilized glucose in nitrogen free medild by a polar flagellum, and also utilized glucose in nitrogen free medium. but the cellular fatty acid composition and quinone system of these isolates showed quite different characteristics with reference strains. Therefore, the taxonomic status of this nitrogen-fixing bacteria is disscussed and a new species Azospirillum. Sixty forur isolates utilized C-l compounds such as methanol and formic acid. phenotypic and chemotaxonomic characteristics of methanol utilizing isolates were investigated and their taxonomic status was discussed; Twenty-one isolates corresponded to Hyphomicrobium and for the other regular rods and irregular rods utilizing isolates showed different cellular fatty acid composition. These isolates were grouped into 8 cluster analysis and similarity values based on correlation coefficients. Among these 8 clusters, two corresponded Pseudomonas and for the other were not decided.

• The Plant Pathology Journal
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• v.22 no.2
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• pp.139-146
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• 2006

The 3' region of Potato virus X (PVX) has the 74 nt 3'-nontranslated region (NTR) that is conserved among all potexviruses and contains several cis-acting elements for minus-strand and plus-strand RNA accumulation. Three stem-loop structures (SL1-SL3), especially formation of SL3 and U-rich sequence of SL2, and near upstream elements in the 3' NTR were previously demonstrated as important cis-acting elements. To Investigate the binding of these cis-acting elements within 3' end with host protein, we used the electrophoretic mobility shift assays (EMSA) and UV-cross linking analysis. The EMSA with cellular extracts from tobacco and RNA transcripts corresponding to the 150 nt of the 3' end of PVX RNA showed that the 3' end of PVX formed complexes with cellular proteins. The specificity of protein binding was confirmed through competition assay by using with 50-fold excess of specific and non-specific probes. We also conducted EMSA with RNAs containing various mutants on those cis-acting elements (${\Delta}10$10, SL3B, SL2A and ${\Delta}21$; J Mol Biol 326, 701-720) required for efficient PVX RNA accumulation. These analyses supported that these cis-acting elements are required for interaction with host protein(s). UV-cross linking analysis revealed that at least three major host proteins of about 28, 32, and 42 kDa in mass bound to these cis-elements. These results indicate that cis-acting elements from 3' end which are important for minus and plus-strand RNA accumulation are also required for host protein binding.

• Molecules and Cells
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• v.24 no.1
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• pp.83-94
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• 2007

During monocarpic senescence in higher plants, functional stay-green delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green retains leaf greenness without sustaining photosynthetic activity. Thus, functional stay-green is considered a beneficial trait that can increase grain yield in cereal crops. A stay-green japonica rice 'SNU-SG1' had a good seed-setting rate and grain yield, indicating the presence of a functional stay-green genotype. SNU-SG1 was crossed with two regular cultivars to determine the inheritance mode and identify major QTLs conferring stay-green in SNU-SG1. For QTL analysis, linkage maps with 100 and 116 DNA marker loci were constructed using selective genotyping with $F_2$ and RIL (recombinant inbred line) populations, respectively. Molecular marker-based QTL analyses with both populations revealed that the functional stay-green phenotype of SNU-SG1 is regulated by several major QTLs accounting for a large portion of the genetic variation. Three main-effect QTLs located on chromosomes 7 and 9 were detected in both populations and a number of epistatic-effect QTLs were also found. The amount of variation explained by several digenic interactions was larger than that explained by main-effect QTLs. Two main-effect QTLs on chromosome 9 can be considered the target loci that most influence the functional stay-green in SNU-SG1. The functional stay-green QTLs may help develop low-input high-yielding rice cultivars by QTL-marker-assisted breeding with SNU-SG1.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.6
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• pp.928-935
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• 2012

World Agriculture faces daunting challenges in feeding the growing population today. Reduction in arable land extent due to numerous reasons threatens achievement of food and nutritional security. Under this back ground, agricultural use of acidic soils, which account for approximately 40 % of the world arable lands is of utmost important. However, due to aluminum (Al) toxicity and low available phosphorous (P) content, crop production in acidic soils is restricted. Citrus, in this context, gains worldwide recognition as a crop adapted to harsh environments. The present paper reviewed Al toxicity and possible toxicity alleviation tactics in citrus. As reported for many other crops, inhibition of root elongation, photosynthesis and growth is experienced in citrus also due to Al toxicity. Focusing at toxicity alleviation, interaction between boron (B) and Al as well as phosphorus and Al has been discussed intensively. Al toxicity in citrus could be alleviated by P through increasing immobilization of Al in roots and P level in shoots rather than through increasing organic acid secretion, which has been widely reported in other crops. Boron-induced changes in Al speciation and/or sub-cellular compartmentation has also been suggested in amelioration of root inhibition in citrus. Despite the species-dependent manner of response to Al toxicity, many commercially important citrus species can be grown successfully in acidic soils, provided toxicity alleviation Agro-biological tactics such as addition of phosphorous fertilizers are used properly.

• Journal of Microbiology and Biotechnology
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• v.9 no.2
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• pp.201-205
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• 1999

The effects of growth temperature and a carbon source on the expression of $\beta$-galactosidase gene of Lactococcus lactis ssp. lactis ATCC 7962 (L. lactis 7962) were investigated. At $25^{\circ}C$, L. lactis 7962 had a higher $\beta$-galactosidase activity than cells grown at $30^{\circ}C$ or $37^{\circ}C$, although cells grew most quickly at $37^{\circ}C$ The highest $\beta$-galactosidase activity was observed in cells grown in M17 with lactose (l %) followed by cells grown in a galactose (1 %) medium. L. lactis 7962 exhibited the minimum $\beta$-galactosidase activity in glucose media, indicating catabolite repression. When the cellular levels of $\beta$-galactosidase mRNA were examined using slot blot hybridization, no significant differences were observed between cells grown at $25^{\circ}C$ and cells at $30^{\circ}C$ or $37^{\circ}C$ in the same media. This suggests that the quantity of $\beta$-galactosidase mRNA may not be the reason for the higher $\beta$-galactosidase activities of L. lactis 7962 at $25^{\circ}C$ The level of ccpA (Catabolite Control Protein) transcript remained almost constant during the exponential growth phase irrespective of a carbon sourse.

• Molecules and Cells
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• v.37 no.2
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• pp.149-160
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• 2014

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 $F_7$ recombinant inbred lines (RILs) from a cross of japonica rice line 'SNU-SG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

• The Plant Pathology Journal
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• v.31 no.2
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• pp.108-114
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• 2015

Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China, and several key pathogenic factors have been isolated. An yeast two-hybrid (Y2H) library is a very useful platform to further unravel novel pathogenic factors in C. lunata. To construct a high-quality full length-expression cDNA library from the C. lunata for application to pathogenesis-related protein-protein interaction screening, total RNA was extracted. The SMART (Switching Mechanism At 5' end of the RNA Transcript) technique was used for cDNA synthesis. Double-stranded cDNA was ligated into the pGADT7-Rec vector with Herring Testes Carrier DNA using homologous recombination method. The ligation mixture was transformed into competent yeast AH109 cells to construct the primary cDNA library. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about $6.39{\times}10^5$ transformants/$3{\mu}g$ pGADT7-Rec. The titer of the primary cDNA library was $2.5{\times}10^8cfu/mL$. The numbers for the cDNA library was $2.46{\times}10^5$. Randomly picked clones show that the recombination rate was 88.24%. Gel electrophoresis results indicated that the fragments ranged from 0.4 kb to 3.0 kb. Melanin synthesis protein Brn1 (1,3,8-hydroxynaphthalene reductase) was used as a "bait" to test the sufficiency of the Y2H library. As a result, a cDNA clone encoding VelB protein that was known to be involved in the regulation of diverse cellular processes, including control of secondary metabolism containing melanin and toxin production in many filamentous fungi was identified. Further study on the exact role of the VelB gene is underway.