• Title/Summary/Keyword: DNA-DNA hybridization

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Characterization of Genes Related to the Cell Size Growth and CCN Family According to the Early Folliculogenesis in the Mouse (쥐의 초기 난포 발달에 관여하는 Cell Size Growth 및 CCN Family 유전자에 관한 연구)

  • Kim, Kyeoung-Hwa;Park, Chang-Eun;Yoon, Se-Jin;Lee, Kyung-Ah
    • Clinical and Experimental Reproductive Medicine
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    • v.32 no.3
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    • pp.269-277
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    • 2005
  • Objectives: Previously, we sought to compile a list of genes expressed during early folliculogenesis by using cDNA microarray to investigate follicular gene expression and changes during primordialprimary follicle transition and development of secondary follicles (Yoon et al., 2005). Among those genes, a group of genes related to the cell size growth was characterized during the ovarian development in the present study. Methods: We determined ovarian expression pattern of six genes related to the cell size growth (cyr61, emp1, fhl1, socs2, wig1 and wisp1) and extended into CCN family (${\underline{c}}onnective$ tissue growth factor/${\underline{c}}ysteine$-rich 61/${\underline{n}}ephroblastoma$-overexpressed), ctgf, nov, wisp2, wisp3, including cyr61 and wisp1 genes. Expression of mRNA and protein according to the ovarian developmental stage was evaluated by in situ hybridization, and/or semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR), and immunohistochemistry, respectively. Results: Among 6 genes related to the cell size growth, cyr61 and wisp1 mRNA was detected only in oocytes in the postnatal day5 mouse ovaries. cyr61 mRNA expression was limited to the nucleolus of oocytes, while wisp1 was expressed in the cytoplasm and nucleolus of oocytes, except nucleus. cyr61 mRNA expression, however, was found in granulosa cells from secondary follicles. The rest 4 genes in the cell size growth group were detected in oocytes, granulosa and theca cells. Cyr61 and Wisp1 proteins were expressed in the oocyte cytoplasm from primordial follicle stage. Especially, Cyr61 protein was detected in pre-granulosa cells, Wisp1 protein was not. By using RT-PCR, we evaluated and decided that Cyr61 protein is produced by their own mRNA in pre-granulosa cells that was not detected by in situ hybridization. cyr61 and wisp1 genes are happen to be the CCN family members. The other members of CCN family were also studied, but their expression was detected in oocytes, granulose and theca cells. Conclusions: We firstly characterized the ovarian expression of genes related to the cell size growth and CCN family according to the early folliculogenesis. Cyr61 protein expression in the pre-granulosa cells is profound in meaning. Further functional analysis for cyr61 in early folliculogenesis is under investigation.

Analysis of Differentially Expressed Genes in Kiwifruit Actinidia chinensis var. 'Hongyang' (참다래 '홍양' 품종의 차등발현유전자 분석)

  • Bae, Kyung-Mi;Kwack, Yong-Bum;Shin, II-Sheob;Kim, Se-Hee;Kim, Jeong-Hee;Cho, Kang-Hee
    • Korean Journal of Breeding Science
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    • v.43 no.5
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    • pp.448-456
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    • 2011
  • We used suppression subtractive hybridization (SSH) combined with mirror orientation selection (MOS) method to screen differentially expressed genes from red-fleshed kiwifruit 'Hongyang'. As a result, the 288 clones were obtained by subcloning PCR product and 192 clones that showed positive clones on colony PCR analysis were selected. All the positive clones were sequenced. After comparisons with the NCBI/Genbank database using the BLAST search revealed that 30 clones showed sequence similarity to genes from other organisms; 10 clones showed significant sequence similarity to known genes. Among these clones, 3 clones (AcF21, AcF42 and AcF106) had sequence homology to 1-aminicyclopropane-carboxylic acid (ACC)-oxidase (ACO) that known to be related to fruit ripening. The expression patterns of differentially expressed genes were further investigated to validate the SSH data by reverse transcription PCR (RT-PCR) and quantitative real-time PCR (qReal-time PCR) analysis. All the data from qReal-time PCR analysis coincide with the results obtained from RT-PCR analysis. Three clones were expressed at higher levels in 'Hongyang' than 'Hayward'. AcF21 was highly expressed in the other genes at 120 days after full bloom (DAFB) and 160 DAFB of 'Hongyang'.

Development of PCR-based markers for selecting plastid genotypes of Solanum hjertingii (Solanum hjertingii 색소체 유전자형 선발을 위한 PCR 기반 분자마커 개발)

  • Tae-Ho Park
    • Journal of Plant Biotechnology
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    • v.50
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    • pp.34-44
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    • 2023
  • The tetraploid Solanum hjertingii, a wild tuber-bearing species from Mexico is a relative of potato, S. tuberosum. The species has been identified as a potential source of resistance to blackening for potato breeding. It does not exhibit enzymatic browning nor blackspot which are physiological disorders. However, due to their sexual incompatibility, somatic hybridization between S. hjertingii and S. tuberosum must be used to introduce various traits from this wild species into potato. After somatic hybridization, molecular markers are essential for selecting fusion products. In this study, the chloroplast genome of S. hjertingii was sequenced by next-generation sequencing technology and compared with those of other Solanum species to develop specific markers for S. hjertingii. The chloroplast genome has a total sequence length of 155,545 bp, and its size, gene content, order and orientation are similar to those of the other Solanum species. Phylogenic analysis including 15 other Solanaceae species grouped S. hjertingii with S. demissum, S. hougasii, and S. stoloniferum. After detailed comparisons of the chloroplast genome sequence with eight other Solanum species, we identified one InDel and seven SNPs specific to S. hjertingii. Based on these, five PCR-based markers were developed for discriminating S. hjertingii from other Solanum species. The results obtained in this study will aid in exploring the evolutionary aspects of Solanum species and accelerating breeding using S. hjertingii.

Changes of Nitrifying Bacteria Depending on the Presence and Absence of Organic Pollutant in Nak-Dong River (낙동강에서의 유기성 오염 유무에 따른 질화세균의 변화)

  • Jin, Seon-Yeong;Lee, Young-Ok
    • Korean Journal of Microbiology
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    • v.49 no.2
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    • pp.137-145
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    • 2013
  • This study was performed at 2 sites of Nak-Dong River to investigate the changes of nitrifiers depending on the presence and absence of organic pollutants (due to the effluents of domestic wastewater treatment plant, WWTP). Conventional chemical parameters such as T-N, $NH_4$-N, $NO_2$-N, $NO_3$-N were measured and the quantitative nitrifiers at the 2 sites were analyzed comparatively by fluorescent in situ hybridization (FISH) with NSO190 and NIT3, after checking the presence of gene amoA of ammonia oxidizing bacteria (AOB) and 16S rDNA signature sequence for Nitrobacter sp. that belongs to nitrite oxidizing bacteria (NOB). Also ${\alpha}{\cdot}{\beta}{\cdot}{\gamma}$-Proteobacteria were detected using FISH to get a glimpse of the general bacterial community structure of the sites. Based on the distribution structure of the ${\alpha}{\cdot}{\beta}{\cdot}{\gamma}$-Proteobacteria and the measurement of nitrogen in different phases, it could be said that the site 2 was more polluted with organics than site 1. Corresponding to the above conclusion, the average numbers of AOB and NOB detected by NSO160 and NIT3, respectively, at site 2 [AOB, $9.3{\times}10^5$; NOB, $1.6{\times}10^6$ (cells/ml)] was more than those at site 1 [AOB, $7.8{\times}10^5$; NOB, $0.8{\times}10^6$ (cells/ml)] and also their ratios to total counts were higher at site 2 (AOB, 27%; NOB, 34%) than those at site 1 (AOB, 18%; NOB, 23%). Thus, it could be concluded that the nitrification at site 2 was more active due to continuous loading of organics from the effluents of domestic WWTP, compared to site 1 located closed to raw drinking water supply and subsequently less polluted with organics.

유전공학기법으로 변형시킨 내성유전자네 대한 수질환경에서의 전이동태

  • 이성기;김치경
    • Korean Journal of Microbiology
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    • v.30 no.4
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    • pp.322-331
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    • 1992
  • In order to understand the transfer and behavior of R gene in water environments. the Kmr gene in the genetically modified microorganisms(GMMs) w,is studied by conjugation. The plasmid variously rearranged in the conjugants were comparatively analyzied by agarosc gel electrophoresis and the specific Km' genes in the gel were tletected with DNA probe. The Kmr genes of the GMM strains(DKC600 and DKC601) were transferred at higher rate than those of natural isola~e(DKI)b, ut the ratc was a little diflurent depending upon the recipient strains. Rearrangement of the plasmids appeared morc drastic in GMM strains than in IIKI as donor. The transfer frequencies of the Km' genes in LR broth were remarkably higher than in the water of AW and FW without regards to the strains. In LA breth. the frequencies of Kmr genes were higher at 25'C-30$^{\circ}$C than at 10$^{\circ}$C and at pH - 7 than pH 9, but temperature and pH of the FW did n,,t affect to the frequency. And the conjugants from GMM strains in FW did not showed any plasmids. except tor 43 kb plasmiil. As results of Southern analysis of the plasmid, variously rearranged in eonjugant cells obtained in LB broth, the Kmr genes were detected at the same position of Km' plasrnids of the donor cell(DK1 and GMM strains). But Km' plasmid disappeared in the conjugants obtained in F'W and their chronlosomes showed strong signal of hybridization. The Kmr plasmid of DKl in the conjugants obtained in FW water was transferred and maintained its size, but the Kmr plasinids of the GMM strains were all integrated into chromosome. Therefore, the Kmr plasmids of DKI anit GMM strains in LH were intactly transferred and other plasmitls were variously rearranged. but Km' gene of DKC600 in FW water was integrated into the chromosorn: without regards to the temperature and pH of the water.

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Genes of Wild Rice (Oryza grandiglumis) Induced by Wounding and Yeast Extract (상처와 효모추출물 처리조건에서 유발되는 야생벼 유전자 스크린)

  • Shin, Sang-Hyun;Im, Hyun-Hee;Lee, Jai-Heon;Kim, Doh-Hoon;Chung, Won-Bok;Kang, Kyung-Ho;Cho, Sung-Ki;Shin, Jeong-Sheop;Chung, Young-Soo
    • Journal of Life Science
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    • v.14 no.4
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    • pp.650-656
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    • 2004
  • Oryza grandiglumis (CCDD, 2n=48), one of the wild rice species, has been known to possess fungal-,bacterial-, and insect-resistance against sheath blight, rice blast, bacterial leaf blight and brown plant hopper (Nilaparvata lugens). To rapidly isolate differentially expressed genes responding to fungal and wounding stress, wounding and yeast extract were treated to O. grandiglumis for 24 hrs. Suppression subtractive hybridization (SSH) method was used to obtain differentially expressed genes from yeast extract and wounding treated plants. Seven hundreds and seventy six clones were obtained by subcloning PCR product, and colony array and screening were carried out using radio-isotope labeled cDNA probes prepared from the wounding and yeast extract treated plants. One hundred and fifteen colonies were confirmed as true positive ones. Average insert size of the clones were ranged from 400 bp to 700 bp and all the inserts were sequenced. To decide the identity of those clones, sequences were analyzed by sequence homology via GenBank database. The homology search result showed that 68 clones were matched to the genes with known function; 16 were related to primary metabolism, 5 to plant retrotransposons, 5 to defense related metallothionein-like genes. In addition to that, others were matched to various genes with known function in amino acid synthesis and processing, membrane transport, and signal transduction, so on. In northern blot analysis, induced expressions of ogwfi-161, ogwfi-646, ogwfi-663, and ogwfi-695 by wounding and yeast extract treatments were confirmed. The result indicates that SSH method is very efficient for rapid screening of differentially expressed genes.

Amino Acid Biosynthesis and Gene Regulation in Seed (종자내 아미노산 합성 조절 유전자에 관한 연구)

  • ;;;;;Fumio Takaiwa
    • Proceedings of the Botanical Society of Korea Conference
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    • 1996.07a
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    • pp.61-74
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    • 1996
  • Human and monogastric animals can not synthesize 10 out of the 20 amino asids and therefor need to obtain these from their diet. The plant seed is a major source of dietary protein. It is particular important in their study to increase nutritional quality of the seed storage proteins. The low contents of lysine, asparagine and threonenein various cereal seeds and of cystein and methionine. In legume seeds is due to the low proportions of these amino acids in the major storage proteins, we have tried to apply the three strategies; (1) mutagenesis and selection of specific amino acid analogue resistance, (2) cloning and expression study of lysine biosynthesis related gene, (3) transfomation of lysine rich soybean glycinin gene. The 5-methyltryptophan (5MT) resistant cell lines, SAR1, SAR2 and SAR3 were selected from anther derived callus of rice (Oryza sativa L. "Sasanishiki"). Among these selected cell lines, two (SAR1 and SAR3) were able to grow stably at 200 mg/L of 5MT. Analysis of the freed amino acids in callus shows that 5MT resistant cells (SAR3) accumulated free tryptophan at least up to 50 times higher than those that of the higher than of SAS. These results indicated that the 5MT resistant cell lines are useful in studies of amino acid biosynthesis. Tr75, a rice (Oryza sativa L., var. Sasanishiki) mutant resistant to 5MT was segregated from the progenies of its initial mutant line, TR1. The 5MT resistant of TR75 was inherited in the M8 generations as a single dominant nuclear gene. The content of free amino acids in the TR75 homozygous seeds increased approximately 1.5 to 2.0 fold compared to wild-type seeds. Especially, the contents of tryptophan, phenylalanine and aspartic acid were 5.0, 5.3 and 2.7 times higher than those of wild-type seeds, respectively. The content of lysine is significantly low in rice. The lysine is synthesized by a complex pathway that is predominantly regulated by feedback inhibition of several enzymes including asparginase, aspatate kinase, dihydrodipicolinat synthase, etc. For understanding the regulation mechanism of lysine synthesis in rice, we try to clone the lysine biosynthetic metabolism related gene, DHPS and asparaginase, from rice. We have isolated a rice DHPS genomic clone which contains an ORF of 1044 nucleotides (347 amino acids, Mr. 38, 381 daltons), an intron of 587 nucleotides and 5'and 3'-flanking regions by screening of rice genomic DNA library. Deduced amino acid sequence of mature peptide domain of GDHPS clone is highly conserved in monocot and dicot plants whereas that of transit peptide domain is extremely different depending on plant specie. Southern blot analysis indicated that GDHPS is located two copy gene in rice genome. The transcripts of a rice GDHPS were expressed in leaves and roots but not detected in callus tissues. The transcription level of GDHPS is much higher in leaves indicating enormous chloroplast development than roots. Genomic DNA clones for asparaginase genes were screened from the rice genomic library by using plaque hybridization technique. Twelve different genomic clones were isolated from first and second screening, and 8 of 12 clones were analyzed by restriction patterns and identified by Southern Blotting, Restriction enzyme digestion patterns and Southern blot analysis of 8 clones show the different pattern for asparaginase gene. Genomic Southern blot analysis from rice were done. It is estimated that rice has at least 2-3 copy of asparaginase gene. One of 8 positive clones was subcloned into the pBluescript SK(+) vector, and was constructed the physical map. For transformation of lysine rich storage protein into tobacco, soybean glycinin genes are transformed into tobacco. To examine whether glycinin could be stably accumulated in endosperm tissue, the glycinin cDNA was transcriptionally fused to an endosperm-specific promotor of the rice storage protein glutelin gene and then introduced into tobacco genomic via Agrobacterium-mediated transformation. Consequently the glycinin gene was expressed in a seed-and developmentally-specific manner in transgenic tobacco seeds. Glycinin were targeted to vacuole-derived protein bodies in the endosperm tissue and highly accumulated in the matrix region of many transgenic plant (1-4% of total seed proteins). Synthesized glycinin was processed into mature form, and assembled into a hexamer in a similar manner as the glycinin in soybean seed. Modified glycinin, in which 4 contiguous methionine residues were inserted at the variable regions corresponding to the C - teminal regions of the acidic and basic polypeptides, were also found to be accumulated similarly as in the normal glycinin. There was no apparent difference in the expression level, processing and targeting to protein bodies, or accumulation level between normal and modified glycinin. glycinin.

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Rapid prenatal diagnosis of Down syndrome and Edward syndrome by fluorescence In situ hybridization : Clinical experience with 309 cases (FISH를 이용한 다운증후군과 에드워드증후군의 신속한 산전확인 : 309예의 임상적 고찰)

  • Kang, Jin-Hee;Lee, Sook-Hwan;Park, Sang-Hee;Park, Ji-Hyun;Kim, Ji-Youn;Han, Won-Bo;Kim, In-Hyun;Park, Sang-Won;Jang, Jin-Beum;Lee, Kyoung-Jin;Park, Hee-Jin;Jun, Hye-Sun;Lee, Kyung-Ju;Shin, Joong-Sik;Cha, Dong-Hyun
    • Journal of Genetic Medicine
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    • v.4 no.1
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    • pp.64-71
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    • 2007
  • Purpose : The purpose of this study was to evaluate the clinical utility of rapid detection of Down syndrome and Edward syndrome by Interphase Fluorescence in Situ Hybridization (FISH) analysis. Methods : Aretrospective study in 309 cases of amniotic fluid samples, analysed by interphase FISH with DNA probes specific to chromosome 18 and 21, was performed. All FISH results w ere compared with conventional cytogenetic karyotypings. Results : The results were considered as informative and they were obtained within 48 hrs. A case of Down syndrome and a case of Edward syndrome were diagnosed by FISH and confirmed by subsequent cytogenetic analysis. In 12 cases with normal FISH results, the cytogenetic analysis showed a case of partial trisomy 22, three cases of sex chromosomal aneuploidy, two cases of mosaicism, two cases of microdeletion, and four cases of structural rearrangement. Conclusion : FISH is a rapid and effective diagnostic method, which can be used as an adjunctive test to cytogenetic analysis, for prenatal identification of chromosome aneuploidies. For the more genome-wide screening with variety of probes, the technique of FISH is both expensive and labor-intensive.

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Effect of Dietary Anti-oxidant Supplementation on Telomere Length and Egg Quality in Laying Hens (산란계에 항산화물질 급여가 텔로미어 함량 및 난질에 미치는 영향)

  • Lee, M.H.;Lee, S.H.;Kim, Y.J.;Ko, Y.H.;Jang, I.S.;Moon, Y.S.;Choi, Y.H.;Sohn, S.H.
    • Korean Journal of Poultry Science
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    • v.35 no.3
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    • pp.267-274
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    • 2008
  • There are many kinds of anti-oxidant materials in natural plant resources. The Siberian ginseng and Eucommia are well known as anti-oxidant and medicinal plants. To investigate the effect of their anti-oxidant-like activity on telomere quantity and egg quality, diets containing Siberian ginseng leaf and Eucommia leaf at 0.5% and 1% were given Hyline Brown commercial laying hens during two periods of age: 20 to 30 wks and 60 to 70 wks. The amount of telomere in lymphocyte, liver, ovary, heart and lung was analyzed by quantitative fluorescence in situ hybridization using telomeric DNA probe. Egg weight, albumin height, Haugh unit, egg yolk color, egg shell color, egg shell thickness, egg shell weight and egg shell density were measured to analyze egg quality. The chickens consuming diets Siberian ginseng and Eucommia had higher telomeric DNA in lymphocytes than control chickens in younger layers whereas no significant differences were detected in all target cells analyzed from older layers. Egg quality was increased in younger hens with dietary supplementation as determined by egg weight, albumin height and Haugh unit but there were no effects in older hens. These results imply that dietary supplementation of Siberian ginseng and Eucommia in layers improves bio-activity and egg quality at early laying stage.

The Detection and Diagnosis Methods of Infectious Viroids caused Plant Diseases (식물체에 감염성 질병을 유발하는 바이로이드 검출 및 진단 방법)

  • Lee, Se Hee;Kim, Yang-Hoon;Ahn, Ji-Young
    • Journal of Life Science
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    • v.26 no.5
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    • pp.620-631
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    • 2016
  • Viroids are about 250-400 base pair of short single strand RNA fragments have been associated with economically important plant diseases. Due to the lack of protein expression capacity associated with replication, it is very difficult to diagnosis viroid diseases in serological methods. For detecting viroid at plants, molecular-based techniques such as agarose gel electrophoresis, polyacrylamide gel electrophoresis (PAGE), DNA-hybridization, blotting analysis and conventional RT-PCR are reliable. Real-time RT-PCR methods that grafted on RT-PCR methods with improved confirmation methods have been also utilized. However, they are still labor-intensive, time-consuming, and require personnel with expertise. Loop-mediated Isothermal Amplification (LAMP) method is a nucleic acid amplification method under the isothermal condition. The LAMP methodology has been reported to be simple, rapid, sensitive and field applicable in detecting a variety of pathogens. The results of LAMP method can be colorized by adding a visible material such as SYBR green I, Evagreen, Calcein, Berberine and Hydroxy naphthol blue (HNB) with simple equipment or naked eyes. The combination of LAMP method and nucleic pathogens, viroids, can be used to realize simple diagnosis platform for the genetic point-of care testing system. The aim at this review is to summary viroid-caused diseases and the simple visible approach for diagnosing viroids using Loop-mediated Isothermal Amplification (LAMP) method.