• 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.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2000.07a
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• pp.67-70
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• 2000

In this paper, all SCR recombination currents including setback and graded layer's recombination currents are analytically introduced for the first time. Different emitter-base structures are tested to prove the validity of the model. In 1995, the analytical equations of electric field, electrostatic potential, and junction capacitance for abrupt and linearly graded heterojunctions with or without a setback layer was derived. But setback layer and linearly graded layer's recombination current was considered numerically. In this paper, recombination current model included setback layer and graded layer is proposed. New recombination current model also includes abrupt heterojunction's recombination current model. In this paper, new recombination current model analytically explains effects of setback layer and graded layer.

• Microbiology and Biotechnology Letters
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• v.23 no.6
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• pp.784-788
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• 1995

The lambda Integrase (Int) carries out site-specific recombination between the two partner DNA sequences, attachment P (attP) and attachment B (attB). In order to study the recombination mechanism, a large quantity of pure integrase is required. Then, we constructed an int gene inserted recombinant plasmid (pNYL3) by using the pQE31 HIS-Tag vector, and produced the fusion protein, 6xHIS-Int from the E. coli TG1 strain carrying the pNYL3 plasmid. The recombinant protein produced was purified by phosphocellulose and Ni$^{++}$-NTA affinity column chromatographies. The result of the in vitro recombination assay using the standard reaction mixture containing 6xHIS-Int and partially purified integration host factor (IHF) showed that the 6xHIS-Int tagged recombination Integrase had the full recombination activity.

• Molecules and Cells
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• v.40 no.11
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• pp.814-822
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• 2017

Meiotic homologous recombination generates new combinations of preexisting genetic variation and is a crucial process in plant breeding. Within the last decade, our understanding of plant meiotic recombination and genome diversity has advanced considerably. Innovation in DNA sequencing technology has led to the exploration of high-resolution genetic and epigenetic information in plant genomes, which has helped to accelerate plant breeding practices via high-throughput genotyping, and linkage and association mapping. In addition, great advances toward understanding the genetic and epigenetic control mechanisms of meiotic recombination have enabled the expansion of breeding programs and the unlocking of genetic diversity that can be used for crop improvement. This review highlights the recent literature on plant meiotic recombination and discusses the translation of this knowledge to the manipulation of meiotic recombination frequency and location with regards to crop plant breeding.

• BMB Reports
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• v.40 no.3
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• pp.432-438
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• 2007

V(D)J recombination, a site-specific gene rearrangement process occurring during the lymphocyte development, begins with DNA double strand breaks by two recombination activating gene products (RAG1/2) and finishes with the repair process by several proteins including DNA-dependent protein kinase (DNA-PK). In this report, we found that RAG2 was specifically phosphorylated by DNA-PK at the $365^{th}$ serine residue, and this phosphorylated RAG2 affected the V(D)J recombination activity in cells in the GFP expression-based assay. While the V(D)J recombination activity between wild-type RAG2 and mutant S365A RAG2 in the assay using a signal joint substrate was undistinguishable in DNA-PK deficient cells (M059J), the activity with wild-type RAG2 was largely increased in DNA-PK proficient cells (M059K) in comparison with mutant RAG2, suggesting that RAG2 phosphorylation by DNA-PK plays a crucial role in the signal joint formation during V(D)J recombination.

• Proceedings of the Microbiological Society of Korea Conference
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• 1991.04a
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• pp.82-96
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• 1991

To understand the mechanism of illegitimate recombination in mammalian cells, we have examined the recombination role of DNA topoisomerase II (Topo II ). We found that purified calf thymus Topo II mediates recombination between two phage $\lambda$ DNA molecules in an in vitro system. The enzyme mainly produced a linear monomer recombinant DNA that can be packaged in vitro. Novobiocin and anti-calf thymus Topo II antibody inhibit this ATP-dependent recombination. The recombinant molecules contain duplications or deletion, and most crossovers take place between nonhomologous sequences of $\lambda$ DNA, as judged by the sequences of recombination junctions. In order to study the effects of Topo II on illegitimate recombination in mammalian cells, we have developed a new shuttle vector, pNKl, which contains three bacterial genes, amp(APR), galK and neo($Km^R$). Using this system, we have shown that a Topo II inhibitor, VM26, stimulated deletion formation in pNK1 DNA in monkey COS1 cells. Both in vitro and in vivo results suggest that Topo II participates in illegitimate recombination in mammalian cells.

• MALSORI
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• no.63
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• pp.125-137
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• 2007

Recently, many techniques have been proposed to improve the noise robustness for speaker verification. In this paper, we consider the feature recombination technique in multi-band approach. In the conventional feature recombination for speaker verification, to compute the likelihoods of speaker models or universal background model, whole feature components are used. This computation method is not effective in a view point of multi-band approach. To deal with non-effectiveness of the conventional feature recombination technique, we introduce a subband likelihood computation, and propose a modified feature recombination using subband likelihoods. In decision step of speaker verification system in noise environments, a few very low likelihood scores of a speaker model or universal background model cause speaker verification system to make wrong decision. To overcome this problem, a reliable feature selection method is proposed. The low likelihood scores of unreliable feature are substituted by likelihood scores of the adaptive noise model. In here, this adaptive noise model is estimated by maximum a posteriori adaptation technique using noise features directly obtained from noisy test speech. The proposed method using subband-based reliable feature selection obtains better performance than conventional feature recombination system. The error reduction rate is more than 31 % compared with the feature recombination-based speaker verification system.

• JSTS:Journal of Semiconductor Technology and Science
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• v.15 no.2
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• pp.232-242
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• 2015

Analytical study of surface recombination at the $Si/SiO_2$ interface is carried out in order to set the optimum surface conditions that result in minimum dark base current and maximum open circuit voltage in silicon solar cells. Recombination centers are assumed to form a continuum rather than to be at a single energy level in the energy gap. It is shown that the presence of a hump in the dark I-V characteristics of high efficiency PERL cells is due to the dark current transition from a high surface recombination regime at low voltage to a low surface recombination regime at high voltage. Successful fitting of reported dark I-V characteristics of a typical PERL cell is obtained with several possible combinations of surface parameters including equal electron and hole capture cross sections.

• Journal of Industrial Technology
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• v.43 no.1
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• pp.33-41
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• 2023

This paper provides a general overview of surface catalytic recombination in hypersonic flow. The surface catalytic recombination phenomena is elaborated in terms of its general overview and numerical modeling associated with it. The general overview of the surface catalytic recombination phenomena describes the elementary surface reactions for the surface catalytic and the role of the surface catalytic recombination efficiency in the heat transfer determination. In the numerical modeling, the surface catalytic recombination is described based on the stagnation-point boundary layer analysis, and finite-rate surface reaction modeling. Throughout this overview manuscript, a general understanding of this phenomena is obtained and can be used as foundation for deeper application with the numerical computational fluid dynamics (CFD) flow solver to estimate the surface heat transfer in the hypersonic vehicles.

• Journal of Microbiology and Biotechnology
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• v.18 no.3
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• pp.585-590
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• 2008

Human tropic Porcine Endogenous Retroviruses (PERVs) are the major concern in zoonosis for xenotransplantation because PERVs cannot be eliminated by specific pathogen-free breeding. Recently, a PERV A/C recombinant with PERV-C bearing PERV-A gp70 showed a higher infectivity (approximately 500-fold) to human cells than PERV-A. Additionally, the chance of recombination between PERVs and HERVs is frequently stated as another risk of xenografting. Overcoming zoonotic barriers in xenotransplantation is more complicated by recombination. To achieve successful xenotransplantation, studies on the recombination in PERVs are important. Here, we cloned and sequenced proviral PERV env sequences from pig gDNAs to analyze natural recombination. The envelope is the most important element in retroviruses as a pivotal determinant of host tropisms. As a result, a total of 164 PERV envelope genes were cloned from pigs (four conventional pigs and two miniature pigs). Distribution analysis and recombination analysis of PERVs were performed. Among them, five A/B recombinant clones were identified. Based on our analysis, we determined the minimum natural recombination frequency among PERVs to be 3%. Although a functional recombinant envelope clone was not found, our data evidently show that the recombination event among PERVs may occur naturally in pigs with a rather high possibility.