• Asian-Australasian Journal of Animal Sciences
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• v.20 no.5
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• pp.622-626
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• 2007

Using multi-trait animal model BLUP, selection was conducted over seven generations for growth rate (DG), real-time ultrasound loin-eye muscle area (LEA), backfat thickness (BF), and intramuscular fat content (IMF) to develop a new line of purebred Duroc pigs with enhanced meat production and meat quality. This study was intended to investigate the relationship between restriction fragment length polymorphism (RFLP) of a heart fatty acid-binding protein (H-FABP) gene and intramuscular fat content (IMF) of this Duroc purebred population. The present experiment examined the RFLP of 499 slaughtered pigs. The DNA was separated from the blood or ear tissue of the pigs, which were slaughtered at 105 kg of body weight. Intramuscular fat content of the longissimus muscle was measured using chemical analysis. A significant difference was detected in the breeding value of IMF among the H-FABP PCR RFLP genotypes. The AA genotype has a significantly larger positive effect on the IMF breeding value than do the Aa and aa genotypes for the MspI RFLP. In addition, the DD genotype has a significantly greater positive effect on IMF breeding value than the Dd and dd genotypes for the HaeIII RFLP. For the HinfI RFLP, the hh genotype has a significantly larger positive effect on IMF breeding value than the HH genotype. Multiple regression analysis was performed using the IMF breeding values as the dependent variable and the three H-FABP genotypes as independent variables. Results revealed that the contribution of the genotypes to variation in IMF breeding values was approximately 40%. These results demonstrated that H-FABP RFLPs affect IMF in this Duroc population.

• Journal of Microbiology and Biotechnology
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• v.22 no.6
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• pp.729-735
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• 2012

The PCR-RFLP method has been useful for detection of known genes and identification of novel genes. In the present study, degenerate primers were designed from five groups of cry1 genes for PCR-RFLP analysis. Bacillus thuringiensis (Bt) isolates from different regions were evaluated for PCR amplification of various cry1 genes using newly designed primers and cry2 genes using reported primers. PCR analysis showed an abundance of cry1A genes and especially cry1Ac genes in isolates from all regions. RFLP analysis revealed the presence of multiple cry1A genes in isolates from central and southern regions. Unique digestion patterns of cry1A genes were observed in isolates from each region. Few of the isolates represented a digestion pattern of cry1A genes that did match to any of the known cry1A genes. RFLP analysis suggested an abundance of cry2Ab along with a novel cry2 gene in Bt isolates from different regions of India. Sequence analysis of the novel cry2 gene revealed 95% sequence identity to cry2Ab and cry2Ah genes. Phylogenetic analysis revealed that the novel cry2 gene could have diverged earlier than the other cry2 genes. Our results encourage finding of more diverse cry2 genes in Bt isolates. Rarefaction analysis was used to compare cry1A gene diversity in isolates from different soil types. It showed a higher degree of cry1A gene diversity in isolates from central region. In the present study, we propose the use of novel degenerate primers for cry1 genes and the PCR-RFLP method using a single enzyme to distinguish multiple cry1A and cry2 genes as well as identify novel genes.

• Korean Journal of Plant Taxonomy
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• v.34 no.1
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• pp.43-61
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• 2004

Molecular taxonomic studies were conducted to evaluate interspecific relationships in Korean Viola 34 taxa including two Japanese populations using RAPD(randornly amplified polymorphic DNA), ISSR(inter simple sequence repeat) and PCR-RFLP(restriction fragment length polymorphism) analysis. Only six and four primers out of 40 arbitrary and 12 ISSR primers were screened for 34 taxa, and were revealed 70 (98.6%) and 28 (96.6%) polymorphic bands, respectively. Fifteen restriction endonucleases produced 80 restriction sites and size variations from the large single copy region of cpDNA, 16 (20%) of which were polymorphic. The separate analyses from the RAPD, ISSR and PCR-RFLP data were incongruent in the relationships among 34 taxa, but combined data was in accordance with previous infrageneric classification system based on morphological characters, especially the subsection and series level. Section Chamaemelanium placed between subsect. Patellares and Vagimtae of section Nomimium was not formed as a distinct group. Viola alb ida complex including three very closely related taxa was recognized independent group within subsect. Patellares in combined data tree. This result strongly suggested that they should be treated to series Pinmtae. RAPD analysis was very useful to clarify the interspecific relationships among the species of Korean Viola than ISSH and PCR-RFLP analyses.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.275-283
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• 2012

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.155-162
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• 2009

A cultivation-based approach was employed to compare the culturable bacterial diversity associated with two phylogenetically closely related marine sponges, Spirastrella abata and Spirastrella panis, which have geologically overlapping distribution patterns. The bacteria associated with sponge were cultivated using MA medium supplemented with 3% sponge extracts. Community structures of the culturable bacteria of the two sponge species were analyzed with PCR-RFLP (restriction fragment length polymorphism) based on 16S rDNA sequences. The RFLP fingerprinting of 16S rDNA digested with HaeIII and MspI, revealed 24 independent RFLP types, in which 1-5 representative strains from each type were partially sequenced. The sequence analysis showed >98.4% similarity to known bacterial species in public databases. Overall, the microbial populations of two sponges investigated were found to be the members of the classes; Alphaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. The Alphaproteobacteria were predominant in the bacterial communities of the two sponges. Gammaproteobacteria represented 38.5% of bacterial community in S. abata. Whereas only 1.6% of this class was present in S. panis. Bacillus species were dominat in S. panis. Bacillus species were found to be 44.3% of bacterial species in S. panis, while they were only 9.7% in S. abata. It is interesting to note that Planococcus maritimus (8.1%, phylum Firmicutes) and Psychrobacter nivimaris (28.9%, phylum Gammaproteobacteria) were found only in S. abata. This result revealed that profiles of bacterial communities from the sponges with a close phylogenetic relationship were highly species-specific.

• Korean Journal of Microbiology
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• v.46 no.4
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• pp.366-374
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• 2010

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Spirastrella abata. A total of 164 bacterial strains associated with the sponge were cultivated using Zobell and Natural sea salt media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 95% similarities compared with known bacterial species, and the isolates belonged to four phyla, Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteriodetes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge- derived total gDNA showed five major DGGE bands, and their sequences showed more than 96% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of four phyla, including Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Spirochetes, and Chloroflexi. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with S. abata by both RFLP and DGGE methods; however, overall bacterial community in the sponge differed depending on the analysis methods.

• Korean Journal of Microbiology
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• v.33 no.2
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• pp.149-156
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• 1997

We have employed comparative RFL,P(Restriction Fragment Ixngth Pol~iniorphism) analysis and molecular phylogenetic techniques to investigate the diversity of uncultured microorganisms associated with the anaerobic PCP degradation in PCP-adapted enrichment cultures inoculated by samples from anaerobic cewage sludgc(Jangrim, Pusan) and leachate of landfill site(Kimhae). 16s rDNA cloncs were obtairted by PCR amplification of mixed population DNAs extracted directly from the nonactive and active stage ol each PCP-adapted culture. After three rounds of comparative RFLP analyses. two RFLP types. designated as Ala and Hld, were found prevalent and common in both active stage samples. Thc analysis of phylogenctic diversity bawd on the 5'-terminal 180 nt of sequences from whole clones of the Ala and Bld RFLP types showed close similarity among themselves. In case of Bld clones, 7XQ of them shared identical sequences. Thcse resuliq suggest that the clones of both RFLP types wcre originated from highly affiliated microorganisms which are e~iriched as a result of metabolic activity to PCP. The full-length 16s rRNA sequence of each representative clone from both RFLP types was determined. and an Ala clone w i n found to he related to Clo.strrdiurn ulfutzac~(Genk~ank No. Z69203) and a Bld clone to Thermobacteroides proteolyticus(Genbank No. X09335), with sequence similarities of 89%' and 97%. respectively.

• Journal of Life Science
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• v.31 no.1
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• pp.66-72
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• 2021

This study developed a species identification method for the salted opossum shrimp of Acetes japonicus, A. chinensis (Korea, China), A. indicus (I, II), and Palaemon gravieri based on PCR-RFLP markers. Genomic DNA was extracted from the salted opossum shrimp. The COI gene was used to amplify 519 base pairs (bp) using specific primers. The amplified products were digested by Acc I and Hinf I, and the DNA fragments were separated by automated electrophoresis for RFLP analysis. When the amplified DNA product (519 bp) was digested with Acc I, A. japonicus, A. chinensis (Korea), and A. indius (II) showed two fragments, whereas a single band of 519 bp was detected in A. chinensis (China) and A. indius (I). Also, in the RFLP patterns digested by Hinf I, A. chinensis (Korea) and A. chinensis (China) showed a single band of 519 bp, while two fragments were observed in A. japonicus and A. indius (I) and four fragments in A. indius (II). The PCR amplicon of P. gravieri was digested by Acc I into 3 bands of 271, 202, and 46 bp and by Hinf I into a single band of 519 bp. Therefore, salted opossum shrimp-specific RFLP markers showing distinct differences between four species and two sub-species by PCR-RFLP analysis. Thus, the PCR-RFLP markers developed in this study are a good method for identifying the six types of salted opossum shrimp.

• BMB Reports
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• v.38 no.4
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• pp.491-499
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• 2005

DNA-based molecular markers for differentiation of five penaeid shrimps (Penaeus monodon, P. semisulcatus, Feneropenaeus merguiensis, Litopenaeus vannamei and Marsupenaeus japonicus) were developed based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and single-stranded conformation polymorphism (SSCP) of 16S ribosomal (r) DNA. Differentiation of P. monodon, P. semisulcatus and L. vannamei can be unambiguously carried out by PCR-RFLP of 16S $rDNA_{560}$ whereas P. semisulcatus and M. japonicus shared a BABB mitotype. These shrimps were successfully discriminated by SSCP analysis of 16S $rDNA_{560}$. Nevertheless, the amplification success for L. vannamei and F. merguiensis was not consistent when tested against larger sample sizes. As a result, 16S $rDNA_{560}$ of an individual representing the most common mitotype of each species was cloned and sequenced. The new primer pair was designed and tested against the large sample sizes (312 bp product, N = 185). The amplification success was consistent across all species. PCR-RFLP of 16S $rDNA_{312}$ was as effective as that of 16S $rDNA_{560}$. Differentiation of all shrimp species were successfully carried out by SSCP analysis.

• Journal of The Association for Neo Medicine
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• v.2 no.1
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• pp.25-33
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• 1997

In Sasang medicine, humen are classified into four constitutions which are Taeyang, Soyang. Taeum and Soum. Depending on each different constitution, the clinical and pharmacological application for the same disease might be different. In this study, genomic DNA of different constitutions(Taeum, Soyang and Soum) were analyzed by Restriction Fragment Length Polymorphism(RFLP) to provide scientific and objective references for Sasang classification. The DNA polymorphism for each constitution detected as differences in the length of DNA fragments, after digestion with restriction enzyme Hae III, was investigated using YNH24 as DNA probe. The allele size of Taeum, Soyang and Soum group detected by YNH24 ranged from 1.3 to 3.8 kb, 1.5 to 3.9 kb and 1.3 to 4.6 kb, respectively. However, the allele size distribution of YNH24 loci of different constitutions was shown to be too variable to be classified as 3 different constitution groups investigated. For further study, it is suggested that the number of each constitution samples for RFLP analysis should be increased and statistical analysis of the allele size distribution should be carried out.