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Search Results: 1 - 10 of 38265 matches for " Han-Seong Kim "
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Simple and Versatile Molecular Method of Copy-Number Measurement Using Cloned Competitors
Hyun-Kyoung Kim, Hai-Li Hwang, Seong-Yeol Park, Kwang Man Lee, Won Cheol Park, Han-Seong Kim, Tae-Hyun Um, Young Jun Hong, Jin Kyung Lee, Sun-Young Joo, Ju-Young Seoh, Yeong-Wook Song, Soo-Youl Kim, Yong-Nyun Kim, Kyeong-Man Hong
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0069414
Abstract: Variations and alterations of copy numbers (CNVs and CNAs) carry disease susceptibility and drug responsiveness implications. Although there are many molecular methods to measure copy numbers, sensitivity, reproducibility, cost, and time issues remain. In the present study, we were able to solve those problems utilizing our modified real competitive PCR method with cloned competitors (mrcPCR). First, the mrcPCR for ERBB2 copy number was established, and the results were comparable to current standard methods but with a shorter assay time and a lower cost. Second, the mrcPCR assays for 24 drug-target genes were established, and the results in a panel of NCI-60 cells were comparable to those from real-time PCR and microarray. Third, the mrcPCR results for FCGR3A and the FCGR3B CNVs were comparable to those by the paralog ratio test (PRT), but without PRT's limitations. These results suggest that mrcPCR is comparable to the currently available standard or the most sensitive methods. In addition, mrcPCR would be invaluable for measurement of CNVs in genes with variants of similar structures, because combination of the other methods is not necessary, along with its other advantages such as short assay time, small sample amount requirement, and applicability to all sequences and genes.
Chromatin CKAP2, a New Proliferation Marker, as Independent Prognostic Indicator in Breast Cancer
Han-Seong Kim, Jae-Soo Koh, Yong-Bock Choi, Jungsil Ro, Hyun-Kyoung Kim, Mi-Kyung Kim, Byung-Ho Nam, Kyung-Tae Kim, Vishal Chandra, Hye-Sil Seol, Woo-Chul Noh, Eun-Kyu Kim, Joobae Park, Chang-Dae Bae, Kyeong-Man Hong
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0098160
Abstract: Background The level of proliferation activity is a strong prognostic or predictive indicator in breast cancer, but its optimal measurement is still in debate, necessitating new proliferation markers. In the present study, the prognostic significance of the CKAP2-positive cell count (CPCC), a new proliferation marker, was evaluated, and the results were compared with those for the mitotic activity index (MAI). Methods This study included 375 early-stage breast cancer samples collected from two institutions between 2000 and 2006. Immunohistochemical staining was performed using a CKAP2 monoclonal antibody. Cox proportional hazard regression models were fitted to determine the association between the CPCC and relapse-free survival (RFS) amongst three groups formed on the basis of the CPCC or MAI value: groups 2 and 3 showing the middle and highest values, respectively, and group 1 the lowest. Results After adjustment for age, T stage, N stage, HER2 status, estrogen receptor status, progesterone receptor status, institution, and year of surgical resection, the CPCC was associated with a significantly worse RFS {hazard ratio [HR] = 4.10 (95% CI: 1.64–10.29) for group 2; HR = 4.35 (95% CI: 2.04–10.35) for group 3}. Moreover, its prognostic significance was similar to or higher than that based on the MAI {HR = 2.05 (95% CI: 0.94–4.65) for group 2; HR = 2.35 (95% CI: 1.09–5.10) for group 3}. In subgroup analyses, the CPCC showed a prognostic significance in the luminal A and triple-negative subgroups, but not in the HER2-positive subgroup. Conclusions Chromatin CKAP2 is an independent prognostic marker for RFS in early-stage breast cancer, and could potentially replace the MAI in clinical evaluation of proliferation activity. Additionally, our study results suggest that the prognostic significance of proliferation activity differs among the various subgroups of breast cancer.
Functional neural differentiation of human adipose tissue-derived stem cells using bFGF and forskolin
Sujeong Jang, Hyong-Ho Cho, Yong-Bum Cho, Jong-Seong Park, Han-Seong Jeong
BMC Cell Biology , 2010, DOI: 10.1186/1471-2121-11-25
Abstract: Human ADSCs from earlobe fat maintained self-renewing capacity and differentiated into adipocytes, osteoblasts, or chondrocytes under specific culture conditions. Following neural induction with bFGF and forskolin, hADSCs were differentiated into various types of neural cells including neurons and glia in vitro. In neural differentiated-hADSCs (NI-hADSCs), the immunoreactivities for neural stem cell marker (nestin), neuronal markers (Tuj1, MAP2, NFL, NFM, NFH, NSE, and NeuN), astrocyte marker (GFAP), and oligodendrocyte marker (CNPase) were significantly increased than in the primary hADSCs. RT-PCR analysis demonstrated that the mRNA levels encoding for ABCG2, nestin, Tuj1, MAP2, NFL, NFM, NSE, GAP43, SNAP25, GFAP, and CNPase were also highly increased in NI-hADSCs. Moreover, NI-hADSCs acquired neuron-like functions characterized by the display of voltage-dependent tetrodotoxin (TTX)-sensitive sodium currents, outward potassium currents, and prominent negative resting membrane potentials under whole-cell patch clamp recordings. Further examination by RT-PCR showed that NI-hADSCs expressed high level of ionic channel genes for sodium (SCN5A), potassium (MaxiK, Kv4.2, and EAG2), and calcium channels (CACNA1C and CACNA1G), which were expressed constitutively in the primary hADSCs. In addition, we demonstrated that Kv4.3 and Eag1, potassium channel genes, and NE-Na, a TTX-sensitive sodium channel gene, were highly induced following neural differentiation.These combined results indicate that hADSCs have the same self-renewing capacity and multipotency as stem cells, and can be differentiated into functional neurons using bFGF and forskolin.Stem cell-based therapies for the repair and regeneration of various tissues and organs offer a paradigm shift that may lead to alternative therapeutic solutions for a number of diseases. The emerging field of regenerative medicine requires reliable sources of stem cells, biomaterial scaffolds and cytokine growth factors. A stem cell i
Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks
Inhae Kim,Heetak Lee,Seong Kyu Han,Sanguk Kim
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003881
Abstract: The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.
Developing Stable Cultivar through Microspore Mutagenesis in ×Brassicoraphanus koranhort, Inter-Generic Allopolyploid between Brassica rapa and Raphanus sativus  [PDF]
Soo-Seong Lee, Byoung Ho Hwang, Tae Yoon Kim, Jeongmin Yang, Na Rae Han, Jongkee Kim, Hyun Hee Kim, Hadassah Roa Belandres
American Journal of Plant Sciences (AJPS) , 2017, DOI: 10.4236/ajps.2017.86091
Abstract: A stable progeny was developed through induced mutation, using microspore culture, of the hybrid (F1F1) produced by crossing a newly synthesized, unstable allopolyploid (F1) and a stable cultivar, BB#1(F1) in xBrassicoraphanus. An F1F1 plant was subjected to the induced mutation system established during production of BB#1. Morphological characteristics of the progeny such as color, and leaf number and length, differed from those of BB#1. The bolting time of the progeny in spring cropping was very late compared to BB#1, allowing it to be grown to an adult plant in spring. Genomic in situ hybridization analysis of pollen mother cells at prophase I identified 19 bivalents, 10 from Brassica rapa and 9 from Raphanus sativus. The glucoraphenin content was almost identical to that of BB#1. Two cultivars are available in the baemoochae crop now. These results indicate that induced mutation using microspore culture is a viable method of stabilizing intergeneric allopolyploids between B. rapa and R. sativus.
Enhancement of Th1-biased protective immunity against avian influenza H9N2 virus via oral co-administration of attenuated Salmonella enterica serovar Typhimurium expressing chicken interferon-α and interleukin-18 along with an inactivated vaccine
Md Rahman, Erdenebileg Uyangaa, Young Han, Seong Kim, Jin Kim, Jin Choi, Seong Eo
BMC Veterinary Research , 2012, DOI: 10.1186/1746-6148-8-105
Abstract: Oral co-administration of S. enterica serovar Typhimurium expressing chIFN-α and chIL-18, prior to vaccination with inactivated AI H9N2 vaccine, modulated the immune response of chickens against the vaccine antigen through enhanced humoral and Th1-biased cell-mediated immunity, compared to chickens that received single administration of S. enterica serovar Typhimurium expressing either chIFN-α or chIL-18. To further test the protective efficacy of this improved vaccination regimen, immunized chickens were intra-tracheally challenged with a high dose of LPAI H9N2 virus. Combined administration of S. enterica serovar Typhimurium expressing chIFN-α and chIL-18 showed markedly enhanced protection compared to single administration of the construct, as determined by mortality, clinical severity, and feed and water intake. This enhancement of protective immunity was further confirmed by reduced rectal shedding and replication of AIV H9N2 in different tissues of challenged chickens.Our results indicate the value of combined administration of chIFN-α and chIL-18 using a Salmonella vaccine strain to generate an effective immunization strategy in chickens against LPAI H9N2.Avian influenza viruses (AIV) of the H9N2 subtype are classified as low-pathogenicity viruses both by molecular characterization and pathotyping. Among low-pathogenicity avian influenza (LPAI) viruses, this particular subtype has attracted great concern due to its wide host range [1], chance of genetic reassortment [2] and possible avian-to-human transmission [3]. Thus, circulation of H9N2 viruses in poultry not only causes industrial losses, but also poses a potential threat to human health. Although the vaccine has been proved to be highly immunogenic in laboratory trials [4] and can prevent clinical disease and reduce viral shedding in field conditions, it cannot prevent vaccinated poultry from becoming infected and from shedding wild viruses in farm settings [5]. Therefore, an improved vaccination strate
A case of native valve endocarditis caused by Burkholderia cepacia without predisposing factors
Hyun Ki, Sung Kim, Seong Han, Hae Cheong
BMC Infectious Diseases , 2011, DOI: 10.1186/1471-2334-11-114
Abstract: Here, we report the case of a patient who developed Burkholderia cepacia-induced native valve endocarditis with consequent cerebral involvement without any predisposing factors; she was successfully treated by antimicrobial agents only.In this report, we also present literature review of relevant cases.Burkholderia cepacia is a gram-negative bacillus. It is important nosocomial pathogen that particularly infects patients with cystic fibrosis [1] and chronic granulomatous diseases[2] and is known to be resistant to many anti-bacterial agents.Burkholderia cepacia rarely causes endocarditis in community settings, but it is known to cause infective endocarditis particularly in intravenous heroin users, and in patients with prosthetic valve replacement [3]. However, infective endocarditis caused by Burkholderia cepacia in patients without predisposing factors is rare [4-6].The treatment of Burkholderia cepacia endocarditis could be conservative, i.e., administration of antibacterial agents, and/or surgical modality [4-13]. According to the previous reports, most patients were prescribed trimethoprim-sulfamethoxazole and underwent valve surgery. Notwithstanding, the mortality in cases of infective endocarditis patients is not low despite the aggressive treatment of infective endocarditis [3].Here, we report the case of a patient with Burkholderia cepacia endocarditis and cerebral involvement who had no predisposing factors, and the infection was successfully managed only by antimicrobial treatment. Along with this case, we also present a literature review.A 77-year-old woman was transferred to our hospital from a local hospital for loss of consciousness and disorientation. She had experienced a fall 2 weeks before admission to our hospital. Plain spine radiography had revealed a spine compression fracture. Two days earlier, she was admitted to a local hospital for relief from back pain. However, during her stay at the hospital, she developed low grade fever, aphasia, and
Atomistic Mechanisms of Codoping-Induced p- to n-Type Conversion in Nitrogen-Doped Graphene
Hyo Seok Kim,Han Seul Kim,Seong Sik Kim,Yong-Hoon Kim
Physics , 2014, DOI: 10.1039/c4nr05024j
Abstract: It was recently shown that nitrogen-doped graphene (NG) can exhibit both p- and n-type characters depending on the C-N bonding nature, which represents a significant bottleneck for the development of graphene-based electronics. Based on first-principles calculations, we herein scrutinise the correlations between atomic and electronic structures of NG, and particularly explore the feasibility of converting p-type NG with pyridinic, pyrrolic, and nitrilic N into n- or bipolar type by introducing an additional dopant atom. Out of the nine candidates, B, C, O, F, Al, Si, P, S, and Cl, we find that the B-, Al-, and P-codoping can anneal even relatively large vacancy defects in p-type NG. It will be also shown that, while the NG with pyridinic N can be converted into n-type via codoping, only the bipolar type conversion can be achieved for the NG with nitrilic or pyrrolic N. The amount of work function reduction was up to 0.64 eV for the pyridinic N next to a monovacancy. The atomistic origin of such diverse type changes is analysed based on Mulliken and crystal orbital Hamiltonian populations, which provide us with a framework to connect the local bonding chemistry with macroscopic electronic structure in doped and/or defective graphene. Moreover, we demonstrate that the proposed codoping scheme can recover the excellent charge transport properties of pristine graphene. Both the type conversion and conductance recovery in codoped NG should have significant implications for the electronic and energy device applications.
Conductance recovery and spin polarization in boron and nitrogen codoped graphene nanoribbons
Seong Sik Kim,Han Seul Kim,Hyo Seok Kim,Yong-Hoon Kim
Physics , 2014,
Abstract: We present an ab initio study of the structural, electronic, and quantum transport properties of B-N-complex edge-doped graphene nanoribbons (GNRs). We find that the B-N edge codop-ing is energetically a very favorable process and furthermore can achieve novel doping effects that are absent for the single B or N doping. The compensation effect between B and N is predicted to generally recover the excellent electronic transport properties of pristine GNRs. For the zigzag GNRs, however, the spatially localized B-N defect states selectively destroy the doped-side spin-polarized GNR edge currents at the valence and conduction band edges. We show that the energetically and spatially spin-polarized currents survive even in the fully ferromagnetic metallic state and heterojunction configurations. This suggests a simple yet ef-ficient scheme to achieve effectively smooth GNR edges and graphene-based spintronic de-vices.
Deep RNA Sequencing Reveals Novel Cardiac Transcriptomic Signatures for Physiological and Pathological Hypertrophy
Hong Ki Song, Seong-Eui Hong, Taeyong Kim, Do Han Kim
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035552
Abstract: Although both physiological hypertrophy (PHH) and pathological hypertrophy (PAH) of the heart have similar morphological appearances, only PAH leads to fatal heart failure. In the present study, we used RNA sequencing (RNA-Seq) to determine the transcriptomic signatures for both PHH and PAH. Approximately 13–20 million reads were obtained for both models, among which PAH showed more differentially expressed genes (DEGs) (2,041) than PHH (245). The expression of 417 genes was barely detectable in the normal heart but was suddenly activated in PAH. Among them, Foxm1 and Plk1 are of particular interest, since Ingenuity Pathway Analysis (IPA) using DEGs and upstream motif analysis showed that they are essential hub proteins that regulate the expression of downstream proteins associated with PAH. Meanwhile, 52 genes related to collagen, chemokines, and actin showed opposite expression patterns between PHH and PAH. MAZ-binding motifs were enriched in the upstream region of the participating genes. Alternative splicing (AS) of exon variants was also examined using RNA-Seq data for PAH and PHH. We found 317 and 196 exon inclusions and exon exclusions, respectively, for PAH, and 242 and 172 exon inclusions and exclusions, respectively for PHH. The AS pattern was mostly related to gains or losses of domains, changes in activity, and localization of the encoded proteins. The splicing variants of 8 genes (i.e., Fhl1, Rcan1, Ndrg2, Synpo, Ttll1, Cxxc5, Egfl7, and Tmpo) were experimentally confirmed. Multilateral pathway analysis showed that the patterns of quantitative (DEG) and qualitative (AS) changes differ depending on the type of pathway in PAH and PHH. One of the most significant changes in PHH is the severe downregulation of autoimmune pathways accompanied by significant AS. These findings revealed the unique transcriptomic signatures of PAH and PHH and also provided a more comprehensive understanding at both the quantitative and qualitative levels.
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