• Microbiology and Biotechnology Letters
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• v.31 no.4
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• pp.322-328
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• 2003

The Transformation-Associated Recombination (TAR) cloning technique allows selective isolation of chromosomal regions and genes from complex genomes. The procedure requires knowledge of relatively small genomic sequences that reside adjacent to the chromosomal region of interest. This technique involves homologous recombination during yeast spheroplast transformation between genomic DNA and a TAR vector that has 5'and 3' gene targeting sequences. In this study, we examined the minimum size of specific hooks required for a single-copy gene isolation and compared the utility of different TAR vectors, radial and unique vectors, by cloning the same single-copy gene. The efficiency of TAR cloning of the hHPRT gene was same using hooks varying from 750 to 63 bp. The number of transformants decreased approximately 20-fold when the TAR vector contained two unique hooks versus using a radial vector, but the percentage of positive recombinants increased over 2-fold when a unique TAR vector was used. Therefore, we suggest that the two-unique TAR vector is suitable for general TAR cloning given its high selectivity, and the radial TAR vector is more suitable when genomic DNA is in limited quantity, for example, DNA isolated from pathological specimens. Moreover, we confirm the minimal length of a unique sequence in a TAR vector is approximately 60 bp for a single-copy gene isolation.

• Genomics & Informatics
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• v.21 no.2
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• pp.27.1-27.7
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• 2023

Recombination events complicate the evolutionary history of populations and species and have a significant impact on the inference of isolation-with-migration (IM) models. However, several existing methods have been developed, assuming no recombination within a locus and free recombination between loci. In this study, we investigated the effect of recombination on the estimation of IM models using genomic data. We conducted a simulation study to evaluate the consistency of the parameter estimators with up to 1,000 loci and analyze true gene trees to examine the sources of errors in estimating the IM model parameters. The results showed that the presence of recombination led to biased estimates of the IM model parameters, with population sizes being more overestimated and migration rates being more underestimated as the number of loci increased. The magnitude of the biases tended to increase with the recombination rates when using 100 or more loci. On the other hand, the estimation of splitting times remained consistent as the number of loci increased. In the absence of recombination, the estimators of the IM model parameters remained consistent.

• Journal of the Korea Organic Resources Recycling Association
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• v.26 no.3
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• pp.39-46
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• 2018

Two domestic earthworm populations used in vermicomposting in different lacalities were collected. The one was from Hongcheon (Kangwon province) and the other was from Youngdong (Chungcheong province). Reproductive capacities and the degree of reproductive isolation of two population were investigated. CO I gene sequences were also compared. There was no difference in their reproductive capacities. And there was no reproductive isolation between two populations. Two populations were identified as Eisenia andrei or Eisenia fetida by CO I gene biomarkers. Phylogenetic tree formulated by CO I gene sequence strongly suggested that two populations were just the same species.

• Genomics & Informatics
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• v.17 no.4
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• pp.37.1-37.8
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• 2019

Isolation-with-migration (IM) models have become popular for explaining population divergence in the presence of migrations. Bayesian methods are commonly used to estimate IM models, but they are limited to small data analysis or simple model inference. Recently three methods, IMa3, MIST, and AIM, resolved these limitations. Here, we describe the major problems addressed by these three software and compare differences among their inference methods, despite their use of the same standard likelihood function.

• Microbiology and Biotechnology Letters
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• v.23 no.6
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• pp.781-783
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• 1995

A method is described for the rapid and simple isolation of genomic DNA from 3 ml culture of Bifidobacterium. The method is expected to be used in gene manipulation of Bifidobacterium spp. The isolated DNA using this method is shown to be an excellent substrate for restriction endonuclease digestion and ligation with T4 DNA ligase.

• Journal of Ecology and Environment
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• v.31 no.4
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• pp.255-260
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• 2008

A commonly held view in studies of character displacement is that character states of both species are shifted in areas of sympatry. This view has been confirmed in an overwhelming number of cases for ecological character displacement. Excluding species pairs in which one of the two interacting species is found only within the distribution of the other species and species displaying gynogenesis, the pattern of reproductive character displacement is asymmetrical in that the shift in character states between areas of symaptry and allopatry occurs in only one of the two interacting species. Hypotheses for the reasons behind this asymmetry in reproductive character displacement include (1) homogenization by gene flow, (2) other mechanisms of reproductive isolation, and (3) sufficient reproductive isolation being provided by one of the interacting species exhibiting a pattern of reproductive character displacement. Because reproductive isolation can be achieved by divergence at any point in a sequence of premating reproductive behaviors and postmating developments, it is necessary to understand the mechanisms of reproductive isolation of two interacting taxa in areas of sympatry and allopatry and to analyze the relative contributions of potential factors to reproductive isolation to disentangle hypotheses for the patterns of asymmetry.

• Korean Journal of Microbiology
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• v.39 no.3
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• pp.128-134
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• 2003

Transformation-associated recombination (TAR) cloning is based on co-penetration into yeast spheroplasts of genomic DNA along with TAR vector DNA that contains 5'- and 3'-sequences (hooks) specific for a gene of interest, followed by recombination between the vector and the human genomic DNA to establish a circular YAC. Typically, the frequency of recombinant insert capture is 0.01-1% for single-copy genes by TAR cloning. To further refine the TAR cloning technology, we determined the effect of GC content on target hooks required for gene isolation utilizing the $Tg\cdot\AC$ mouse transgene as the targeted region. For this purpose, a set of vectors containing a B1 repeated hook and Tg AC-specific hooks of variable GC content (from 18 to 45%) was constructed and checked for efficiency of transgene isolation by radial TAR cloning. Efficiency of cloning decreased approximately 2-fold when the TAR vector contained a hook with a GC content ～${\leq}23$% versus ～40%. Thus, the optimal GC content of hook sequences required for gene isolation by TAR is approximately 40%. We also analyzed how the distribution of high GC content (65%) within the hook affects gene capture, but no dramatic differences for gene capturing were observed.

• The Korea Genome Conference
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• 2002.08a
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• pp.50.1-50.1
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• 2002

• Proceedings of the Zoological Society Korea Conference
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• 1994.10a
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• pp.243.2-243
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• 1994

No Abstract, See Full Text

• Proceedings of the Zoological Society Korea Conference
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• 1995.10b
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• pp.336.1-336
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• 1995

No Abstract, See Full Text