• Title/Summary/Keyword: Conserved gene

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SSR Profiling and Its Variation in Soybean Germplasm (콩 유전자원의 SSR Profiling과 변이)

  • Yoon, Mun-Sup;Lee, Jeong-Ran;Baek, Hyung-Jin;Cho, Gyu-Taek;Kim, Chang-Yung;Cho, Yang-Hee;Kim, Tae-San;Cho, Eun-Gi
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.52 no.1
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    • pp.81-88
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    • 2007
  • The evaluation of soybean germplasm has mainly been carried out by morphological characters at Genetic Resources Division, Rural Development Administration (RDA). However, this information has been limited serving a diverse information for user and effectively managing the soybean germplasm. To resolve this problem, soybean collection conserved at RDA gene bank was profiled using nine soybean SSR (Simple Sequence Repeat) markers. Soybean SSR allele was confirmed using genescan and genotyper softwares of automatic sequencer for accurate genotyping of each accession and continuous accumulation of data. SSR profiling of soybean germplasm has been carried out from 2,855 (Satt458) to 4,368 (Satt197) accessions by locus. The number of allele revealed 267 with an average of 29.6 in total accession, and varied from a low of 21 (Satt532 and Satt141) to a high of 58 (Sat_074). Although the number of accessions of wild soybean is less than that of soybean landraces, Korean wild soybean is more variable than other soybean landraces populations in total number of alleles. However, Korean soybean landraces were more variable than Korean wild soybeans in 5 loci. In the allele frequency, wild soybean accessions showed an even distribution in all alleles and higher distribution in low ladder than in high ladder. Also, Korean soybean landraces revealed a high condensed frequency in Satt286 (202 bp, 232 bp), Chinese soybean landraces in Satt197 (171 bp) and Satt458 (173 bp), and Japanese soybean landraces in Sat_074 (244 bp) and Satt458 (170 bp). These SSR profile information will be provided as indications of redundancies or omissions of accessions and can aid in managing soybean collection held at RDA gene bank. The information on diversity analysis could help to enlarge the genetic diversity of materials in breeding program, and could be used to develop a core collection of soybean germplasm.

Human metapneumovirus infection in Korean children (소아에서 human metapneumovirus 감염)

  • Yeom, Hee-Hyun;Park, Joon-Soo;Jeong, Dong-Jun;Kim, Chang-Jin;Kim, Yong-Bae;Lee, Dea-Hoon;Kim, Kyung-Joong;Chun, Jong-Yoon;Kang, Chun;Chung, Yoon-Seok;Cheong, Hyang-Min
    • Clinical and Experimental Pediatrics
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    • v.49 no.4
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    • pp.401-409
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    • 2006
  • Purpose : Human metapneumovirus(hMPV) is a respiratory viral pathogen that causes a wide spectrum of illnesses, ranging from asymptomatic infection to severe bronchiolitis. The virus has been identified world widely, but so far it has not been published in Korea. Methods : We obtained clinical samples by nasopharyngeal aspiration from 218 children hospitalized due to acute lower respiratory tract infections at Soonchunhyang University Hospital in Cheonan from October, 2004 to April, 2005. We designed specific primers from conserved region of fusion glycoprotein of hMPV. Total RNA was extracted and RT-PCR was performed, and single specific 423 bp product was obtained. The PCR product was confirmed to be fusion glycoprotein RNA by sequencing. Results : We detected hMPV in 15(6.9 percent) of the 218 hospitalized children. The infected children comprised nine boys and six girls; their mean age was 2.8 years(5 mo-12 yrs) and they were diagnosed with pneumonia(60 percent), bronchiolitis(33.3 percent), croup(6.6 percent). The number of cases of detected hMPV in Korea increased dramatically during the period from March to May 2005. Conclusion : hMPV is circulating in Korean children and is associated with respiratory tract infection. Additional studies are required to define the epidemiology and the extent of diseases in the general population caused by hMPV.

MicroRNA-23b is a Potential Tumor Suppressor in Diffuse Large B-cell Lymphoma (미만성 거대 B 세포 림프종(DLBCL)에서 microRNA-23b의 잠재적 종양 억제자로서의 효과)

  • Nam, Jehyun;Kim, Eunkyung;Kim, Jinyoung;Jeong, Dawoom;Kim, Donguk;Kwak, Bomi;Kim, Sang-Woo
    • Journal of Life Science
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    • v.27 no.2
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    • pp.149-154
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    • 2017
  • Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-hodgkin lymphoma. Advances in the chemotherapeutic treatment of this disease have improved the outcomes of DLBCL; nonetheless, many patients still die of DLBCL, and therefore, a better understanding of this disease and identification of novel therapeutic targets are urgently required. In a recent gene expression profiling study, PDE (phosphodiesterase) 4B was found to be overexpressed in chemotherapy-resistant tumors. The major function of PDE4B is to inactivate the second messenger cyclic 3',5' monophosphate (cAMP) by catalyzing the hydrolysis of cAMP to 5'AMP. It is known that cAMP induces cell cycle arrest and/or apoptosis in B cells, and PDE4B abolishes cAMP's effect on B cells. However, the mechanism by which PDE4B is overexpressed remains unclear. Here, we show that the aberrant expression of miRNA may be associated with the overexpression of this gene. The PDE4B 3' untranslated region (UTR) has three functional binding sites of miR-23b, as confirmed by luciferase reporter assays. Interestingly, miR-23b-binding sites were evolutionarily conserved from humans to lizards, implying the critical role of PDE4B-miR-23b interaction in cellular physiology. The ectopic expression of miR-2 3b repressed PDE4B mRNA levels and enhanced intracellular cAMP concentrations. Additionally, miR-23b expression inhibited cell proliferation and survival of DLBCL cells only in the presence of forskolin, an activator of adenylyl cyclase, suggesting that miR-23b's effect is via the downregulation of PDE4B. These results together suggest that miR-23b could be a therapeutic target for overcoming drug resistance by repressing PDE4B in DLBCL.

A Novel Human BTB-kelch Protein KLHL31, Strongly Expressed in Muscle and Heart, Inhibits Transcriptional Activities of TRE and SRE

  • Yu, Weishi;Li, Yongqing;Zhou, Xijin;Deng, Yun;Wang, Zequn;Yuan, Wuzhou;Li, Dali;Zhu, Chuanbing;Zhao, Xueying;Mo, Xiaoyang;Huang, Wen;Luo, Na;Yan, Yan;Ocorr, Karen;Bodmer, Rolf;Wang, Yuequn;Wu, Xiushan
    • Molecules and Cells
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    • v.26 no.5
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    • pp.443-453
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    • 2008
  • The Bric-a-brac, Tramtrack, Broad-complex (BTB) domain is a protein-protein interaction domain that is found in many zinc finger transcription factors. BTB containing proteins play important roles in a variety of cellular functions including regulation of transcription, regulation of the cytoskeleton, protein ubiquitination, angiogenesis, and apoptosis. Here, we report the cloning and characterization of a novel human gene, KLHL31, from a human embryonic heart cDNA library. The cDNA of KLHL31 is 5743 bp long, encoding a protein product of 634 amino acids containing a BTB domain. The protein is highly conserved across different species. Western blot analysis indicates that the KLHL31 protein is abundantly expressed in both embryonic skeletal and heart tissue. In COS-7 cells, KLHL31 proteins are localized to both the nucleus and the cytoplasm. In primary cultures of nascent mouse cardiomyocytes, the majority of endogenous KLHL31 proteins are localized to the cytoplasm. KLHL31 acts as a transcription repressor when fused to GAL4 DNA-binding domain and deletion analysis indicates that the BTB domain is the main region responsible for this repression. Overexpression of KLHL31 in COS-7 cells inhibits the transcriptional activities of both the TPA-response element (TRE) and serum response element (SRE). KLHL31 also significantly reduces JNK activation leading to decreased phosphorylation and protein levels of the JNK target c-Jun in both COS-7 and Hela cells. These results suggest that KLHL31 protein may act as a new transcriptional repressor in MAPK/JNK signaling pathway to regulate cellular functions.

Current status, mechanism and control of herbicide resistant weeds in rice fields of Korea (한국 논에서 제초제 저항성잡초의 발생 현황, 메카니즘 및 방제)

  • Park, Tae Seon;Seong, Ki Yeong;Cho, Hyun Suk;Seo, Myung Chul;Kang, Hang Won;Park, Kee Woong
    • Korean Journal of Agricultural Science
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    • v.41 no.2
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    • pp.85-99
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    • 2014
  • Sulfonylurea (SU)-resistant weeds of eight annual weeds, Monochoria vaginalis, Scirpus juncoides and Cyperus difformis, etc., and four perennial weeds, Scirpus planiculmis, Sagittaria pigmaea, Eleocharis acicularis and Sagittaria trifolia as of 2013 since identification Monochoria korsakowii in the reclaimed rice field in 1998. And the resistant Echinochloa oryzoides to ACCase and ALS inhibitors has been confirmed in rice fields of the southern province, Korea in 2009. In the beginning, the M. vaginalis, S. juncoides and C. difformis of these SU-resistant weeds were rapidly and individually spreaded in different fields, however, these resistant weeds have been occurring simultaneously in the same filed recently. The resistant biotype by weed species demonstrated about 10-to 1,000-fold resistance, based on $GR_{50}$ values of the SU herbicides tested. And the resistant biotype of E. oryzoides to cyhalofop-butyl, pyriminobac-methyl, and penoxsulam was about 14, 8, and 11 times more resistant than the susceptible biotype base on $GR_{50}$ values. The products and applied area of SU-included herbicides have been increased rapidly, and have accounted for about 69% and 96% in Korea, respectively. In Korea, the main cause of SU-resistant weed is extensive use of these herbicides. The top ten herbicides by applied area were composed of all SU-included herbicides by 2003. The concentrated and successive treatment of ACCase and ALS inhibitors for control of barnyardgrass in rice led up to the resistance of E. oryzoides. Also, SU-herbicides like pyrazosulfuron-ethyl and imazosulfuron which effective to barnyardgrass can be bound up with the resistance of E. oryzoides. The ALS activity isolated from the resistant biotype of M. korsakowii to SU-herbicides tested was less sensitive than that of susceptible biotype. The concentration of herbicide required for 50% inhibition of ALS activity ($I_{50}$) of the SU-resistant M. korsakowii was 14-to 76-fold higher as compared to the susceptible biotype. No differences were observed in the rates of [$^{14}C$]bensulfuron uptake and translocation. Acetolactate synthase (ALS) genes from M. vaginalis resistant and susceptible biotypes against SU-herbicides revealed a single amino acid substitution of proline (CCT), at 197th position based on the M. korsakowii ALS sequence numbering, to serin (TCT) in conserved domain A of the gene. Carfentrazone-ethyl and pyrazolate were used mainly to control SU-resistant M. vaginalis by 2006 in Korea. However, the alternative herbicides such as benzobicyclone, to be possible to control simultaneously the several resistant weeds, have been developing and using broadly, because the several resistant weeds have been occurring simultaneously in the same fieled. The top ten herbicides by applied area in Korea have been occupied by products of 3-way mixture type including herbicides with alternative mode of action for the herbicide resistant weeds. Mefenacet, fentrazamide and cafenstrole had excellent controlling effects on the ACCase and ALS inhibitors resistant when they were applied within 2nd leaf stage.

Isolation and functional analysis of three microsomal delta-12 fatty acid desaturase genes from Camelina sativa (L.) cv. CAME (카멜리나 (Camelina sativa L. cv. CAME)로부터 3 microsomal delta-12 fatty acid desaturase 유전자들의 분리 및 기능 분석)

  • Kim, Hyojin;Go, Young Sam;Kim, Augustine Yonghwi;Lee, Sanghyeob;Kim, Kyung-Nam;Lee, Geung-Joo;Kim, Gi-Jun;Suh, Mi Chung
    • Journal of Plant Biotechnology
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    • v.41 no.3
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    • pp.146-158
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    • 2014
  • Camelina sativa that belongs to Brassicaceae family is an emerging oilseed crop. Camelina seeds contain approximately 40% storage oils per seed dry weight, which are useful for human and animal diets and industrial applications. Microsomal delta-12 fatty acid desaturase2 (FAD2) catalyzes the conversion of oleic acid to linoleic acid. The polymorphisms of FAD2 genes are correlated with the levels of oleic acids in seed oils. Microsomal delta-12 fatty acid desaturase2 (FAD2) catalyzes the conversion of oleic acid to linoleic acid. The polymorphisms of FAD2 genes are correlated with the levels of oleic acids in seed oils. In this study, three CsFAD2 genes (CsFAD2-1, CsFAD2-2 and CsFAD2-3.1) were isolated from developing seeds of Camelina sativa (L.) cv. CAME. The nucleotide and deduced amino acid sequences of three CsFAD2 genes were compared with those from dicotyledon and monocotyledon plants including Camelina cultivars Sunesone and SRS933. Three histidine motifs (HECGH, HRRHH, and HVAHH) required for FAD activity and a hydrophobic valine or isoleucine residue, which is a SNP (single nucleotide polymorphism) marker related with enzyme activity are well conserved in three CsFAD2s. The expressions of CsFAD2-1 and CsFAD2-3.1 were ubiquitously detected in various Camelina organs, whereas the CsFAD2-2 transcripts were predominantly detected in flowers and developing seeds. The contents of oleic acids decreased, whereas the amounts of linoleic acid increased in dry seeds of transgenic fad2-2 lines expressing each CsFAD2 gene compared with fad2-2 mutant, indicating that three CsFAD2 genes are functionally active. The isolated CsFAD2 genes might be applicable in metabolic engineering of storage oils with high oleic acids in oilseed crops.

Development and Validation of Real-time PCR to Determine Branchiostegus japonicus and B. albus Species Based on Mitochondrial DNA (Real-time PCR 분석법을 이용한 옥돔과 옥두어의 종 판별법 개발)

  • Chung, In Young;Seo, Yong Bae;Yang, Ji-Young;Kim, Gun-Do
    • Journal of Life Science
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    • v.27 no.11
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    • pp.1331-1339
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    • 2017
  • DNA barcoding is the identification of a species based on the DNA sequence of a fragment of the cytochrome C oxidase subunit I (COI) gene in the mitochondrial genome. It is widely applied to assist with the sustainable development of fishery-product resources and the protection of fish biodiversity. This study attempted to verify horse-head fish (Branchiostegus japonicus) and fake horse-head fish (Branchiostegus albus) species, which are commonly consumed in Korea. For the validation of the two species, a real-time PCR method was developed based on the species' mitochondrial DNA genome. Inter-species variations in mitochondrial DNA were observed in a bioinformatics analysis of the mitochondrial genomic DNA sequences of the two species. Some highly conserved regions and a few other regions were identified in the mitochondrial COI of the species. In order to test whether variations in the sequences were definitive, primers that targeted the varied regions of COI were designed and applied to amplify the DNA using the real-time PCR system. Threshold-cycle (Ct) range results confirmed that the Ct ranges of the real-time PCR were identical to the expected species of origin. Efficiency, specificity and cross-reactivity assays showed statistically significant differences between the average Ct of B. japonicus DNA ($21.85{\pm}3.599$) and the average Ct of B. albus DNA ($33.49{\pm}1.183$) for confirming B. japonicus. The assays also showed statistically significant differences between the average Ct of B. albus DNA ($22.49{\pm}0.908$) and the average Ct of B. japonicus DNA ($33.93{\pm}0.479$) for confirming B. albus. The methodology was validated by using ten commercial samples. The genomic DNA-based molecular technique that used the real-time PCR was a reliable method for the taxonomic classification of animal tissues.

Biochemical Characterization of a Novel Thermostable Esterase from the Metagenome of Dokdo Islets Marine Sediment (독도 심해토 메타게놈 유래 신규 내열성 에스테라아제의 생화학적 특성규명)

  • Lee, Chang-Muk;Seo, Sohyeon;Kim, Su-Yeon;Song, Jaeeun;Sim, Joon-Soo;Hahn, Bum-Soo;Kim, Dong-Hern;Yoon, Sang-Hong
    • Microbiology and Biotechnology Letters
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    • v.45 no.1
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    • pp.63-70
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    • 2017
  • A functional screen of 60,672 fosmid metagenomic clones amplified from marine sediment obtained from the Dokdo islets in Korea identified the gene EstES1, whose product, EstES1, displayed lipolytic properties on tributyrin-supplemented media. EstES1 is a 576 amino acid protein with a predicted molecular weight of 59.4 kDa including 37 N-terminal leader amino acids. EstES1 exhibited the highest sequence similarity (44%) to a carboxylesterase found in Haliangium ochraceum DSM14365. Phylogenetic analysis indicated that EstES1 belongs to a currently uncharacterized family of lipases. Within the conserved domain, EstES1 retains the catalytic triad that consists of the consensus penta-peptide motif, GESAG. EstES1 demonstrated a broad substrate specificity toward the long acyl group of ethyl esters (C2-C12), and its optimal activity was recorded toward p-Nitrophenyl butyrate (C4) at pH 9.0 and $40^{\circ}C$ (specific activity of 255.4 U/mg). The enzyme remained stable in the ranges of $60-65^{\circ}C$ and pH 9.0-10.5 and in the presence of methanol, ethanol, isopropanol, and dimethyl sulfoxide. Therefore, EstES1 has potential for use in industrial applications involving high temperature, organic solvents, and/or alkaline conditions.

THE ECOLOGY, PHYTOGEOGRAPHY AND ETHNOBOTANY OF GINSENG

  • Hu Shiu Ying
    • Proceedings of the Ginseng society Conference
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    • 1978.09a
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    • pp.149-157
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    • 1978
  • Ginseng is the English common name for the species in the genus Panax. This article gives a broad botanical review including the morphological characteristics, ecological amplitude, and the ethnobotanical aspect of the genus Panax. The species of Panax are adapted for life in rich loose soil of partially shaded forest floor with the deciduous trees such as linden, oak, maple, ash, alder, birch, beech, hickory, etc. forming the canopy. Like their associated trees, all ginsengs are deciduous. They require annual climatic changes, plenty of water in summer, and a period of dormancy in winter. The plant body of ginseng consists of an underground rhizome and an aerial shoot. The rhizome has a terminal bud, prominent leafscars and a fleshy root in some species. It is perennial. The aerial shoot is herbaceous and annual. It consists of a single slender stem with a whorl of digitately compound leaves and a terminal umbel bearing fleshy red fruits after flowering. The yearly cycle of death and renascence of the aerial shoot is a natural phenomenon in ginseng. The species of Panax occur in eastern North America and eastern Asia, including the eastern portion of the Himalayan region. Such a bicentric generic distributional pattern indicates a close floristic relationship of the eastern sides of two great continental masses in the northern hemisphere. It is well documented that genera with this type of disjunct distribution are of great antiquity. Many of them have fossil remains in Tertiary deposits. In this respect, the species of Panax may be regarded as living fossils. The distribution of the species, and the center of morphological diversification are explained with maps and other illustrations. Chemical constituents confirm the conclusion derived from morphological characters that eastern Asia is the center of species concentration of Panax. In eastern North America two species occur between longitude $70^{\circ}-97^{\circ}$ Wand latitude $34^{\circ}-47^{\circ}$ N. In eastern Asia the range of the genus extends from longitude $85^{\circ}$ E in Nepal to $140^{\circ}$ E in Japan, and from latitude $22^{\circ}$ N in the hills of Tonkin of North Vietnam to $48^{\circ}$ N in eastern Siberia. The species in eastern North America all have fleshy roots, and many of the species in eastern Asia have creeping stolons with enlarged nodes or stout horizontal rhizomes as storage organs in place of fleshy roots. People living in close harmony with nature in the homeland of various species of Panax have used the stout rhizomes or the fleshy roots of different wild forms of ginseng for medicine since time immemorial. Those who live in the center morphological diversity are specific both in the application of names for the identification of species in their communication and in the use of different roots as remedies to relieve pain, to cure diseases, or to correct physiological disorders. Now, natural resources of wild plants with medicinal virtue are extremely limited. In order to meet the market demand, three species have been intensively cultivated in limited areas. These species are American ginseng (P. quinquefolius) in northeastern United States, ginseng (P. ginseng) in northeastern Asia, particularly in Korea, and Sanchi (P. wangianus) in southwestern China, especially in Yunnan. At present hybridization and selection for better quality, higher yield, and more effective chemical contents have not received due attention in ginseng culture. Proper steps in this direction should be taken immediately, so that our generation may create a richer legacy to hand down to the future. Meanwhile, all wild plants of all species in all lands should be declared as endangered taxa, and they should be protected from further uprooting so that a. fuller gene pool may be conserved for the. genus Panax.

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Identification of Compound Heterozygous Alleles in a Patient with Autosomal Recessive Limb-Girdle Muscular Dystrophy (상염색체 열성 지대형 근이영양증 환자로부터 TTN 유전자의 복합 이형접합성 대립유전자의 분리)

  • Choi, Hee Ji;Lee, Soo Bin;Kwon, Hye Mi;Choi, Byung-Ok;Chung, Ki Wha
    • Journal of Life Science
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    • v.31 no.10
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    • pp.913-921
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    • 2021
  • Limb-girdle muscular dystrophy (LGMD) which is characterized by progressive muscle weakening of the hip and shoulder shows both dominant and recessive inheritances with many pathogenic genes including TTN. This study performed to identify genetic causes of a male patient with late onset (45 years old) autosomal recessive LGMD and atrial flutter. By application of the whole exome sequencing, we identified bi-allelic variants of TTN gene in the patient. One allele had a single missense variant of [c.24124G>T (p.V8042F)], while the other allele consisted of three missense variants of [c.29222G>C (p.R9741P) + c.67490A>G (p.H22497R) + c.75376C>T (p.R25126C)]. The p.V8042F allele was transmitted from his mother, while the other haplotype allele was putatively transmitted from his father. His two unaffected sons had only the p.R9741P. These variants have been not reported or rarely reported in the public human genome databases (1,000 Genome, gnomAD, and KRGDB). Most variants were located in the highly conserved immunoglobulin or fibronectin domains and were predicted to be pathogenic by the in silico analyses. The TTN giant protein plays a key role in muscle assembly, force transmission at the Z-line, and maintenance of resting tension in the I-band. In conclusion, we think that these bi-allelic compound heterozygous mutations may play a role as the genetic causes of the LGMD phenotype.