• Genomics & Informatics
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• v.1 no.2
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• pp.94-100
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• 2003

Motivation: Many have observed a nonlinear relationship between the signal intensity and the transcript abundance in microarray data. The first step in analyzing the data is to normalize it properly, and this should include a correction for the nonlinearity. The commonly used linear normalization schemes do not address this problem. Results: Nonlinearity is present in both cDNA and oligonucleotide arrays, but we concentrate on the latter in this paper. Across a set of chips, we identify those genes whose within-chip ranks are relatively constant compared to other genes of similar intensity. For each gene, we compute the sum of the squares of the differences in its within-chip ranks between every pair of chips as our statistic and we select a small fraction of the genes with the minimal changes in ranks at each intensity level. These genes are most likely to be non-differentially expressed and are subsequently used in the normalization procedure. This method is a generalization of the rank-invariant normalization (Li and Wong, 2001), using all available chips rather than two at a time to gather more information, while using the chip that is least likely to be affected by nonlinear effects as the reference chip. The assumption in our method is that there are at least a small number of non­differentially expressed genes across the intensity range. The normalized expression values can be substantially different from the unnormalized values and may result in altered down-stream analysis.

• Proceedings of the Microbiological Society of Korea Conference
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• 2000.10a
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• pp.15-23
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• 2000

The subcellular localization of the SopB protein, which is encoded by the Escherichia coli F plasmid and is involved in the partition of the single-copy plasmid, was directly visualized through the expression of the protein fused to the jellyfish green fluorescent protein (GFP). The fusion protein was found to localize to positions close but not at the poles of exponentially growing cells. Examination of derivatives of the fusion protein lacking various regions of SopB suggests that the signal for the cellular localization of SopB resides in a region close to its N terminus. Overexpression of SopB led to silencing of genes linked to, but well-separated from, a cluster of SopB-binding sites termed sopC. In this SopB-mediated repression of sopC-linked genes, all but the N-terminal 82 amino acids of SopB can be replaced by the DNA-binding domain of a sequence-specific DNA -binding protein, provided that the sopC locus is also replaced by the recognition sequence of the DNA-binding domain. These results suggest a mechanism of gene silencing: patches of closely packed DNA-binding protein is localized to specific cellular sites; such a patch can capture a DNA carrying the recognition site of the DNA -binding domain and sequestrate genes adjacent to the recognition site through nonspecific binding of DNA.

• Molecules and Cells
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• v.38 no.8
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• pp.697-704
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• 2015

Deleted in breast cancer-1 (DBC1) contributes to the regulation of cell survival and apoptosis. Recent studies demonstrated that DBC is phosphorylated at Thr454 by ATM/ATR kinases in response to DNA damage, which is a critical event for p53 activation and apoptosis. However, how DBC1 phosphorylation is regulated has not been studied. Here we show that protein phosphatase 4 (PP4) dephosphorylates DBC1, regulating its role in DNA damage response. PP4R2, a regulatory subunit of PP4, mediates the interaction between DBC1 and PP4C, a catalytic subunit. PP4C efficiently dephosphorylates pThr454 on DBC1 in vitro, and the depletion of PP4C/PP4R2 in cells alters the kinetics of DBC1 phosphorylation and p53 activation, and increases apoptosis in response to DNA damage, which are compatible with the expression of the phosphomimetic DBC-1 mutant (T454E). These suggest that the PP4-mediated dephosphorylation of DBC1 is necessary for efficient damage responses in cells.

• Journal of Species Research
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• v.10 no.2
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• pp.164-167
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• 2021

According to Article 9.3 of the International Code of Nomenclature for algae, fungi, and plants(Shenzhen Code), a lectotype may be selected as the nomenclatural type from the original material, if the name was published without a holotype. While reviewing the genus Scrophularia collected in Northeast Asia, we found that two species, S. alata A. Gray and S. kakudensis Franch., were still untypified. S. alata has three specimens considered as syntypes in two herbaria, Harvard University and the Smithsonian Institution. For S. kakudensis, two specimens considered as syntypes at the Muséum National d'Histoire Naturelle, Paris were classified as normal specimens, not type specimens. Therefore, two species of Scrophularia L. namely, S. alata A. Gray and S. kakudensis Franch., are lectotypified. The lectotypes are kept in the Harvard University and the Muséum National d'Histoire Naturelle, Paris, respectively. Furthermore, some nomenclatural issues related to these names are discussed, and the photographs of the selected lectotypes are provided.

• Journal of The Korean Astronomical Society
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• v.49 no.3
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• pp.73-81
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• 2016

We report the characterization of a massive (m_p = 3.9±1.4M_jup) microlensing planet (OGLE-2015-BLG-0954Lb) orbiting an M dwarf host (M = 0.33 ± 0.12M_⊙) at a distance toward the Galactic bulge of $0.6^{+0.4}_{-0.2}kpc$, which is extremely nearby by microlensing standards. The planet-host projected separation is a⊥ ~ 1.2AU. The characterization was made possible by the wide-field (4 deg²) high cadence (Γ = 6 hr^–1) monitoring of the Korea Microlensing Telescope Network (KMTNet), which had two of its three telescopes in commissioning operations at the time of the planetary anomaly. The source crossing time t_* = 16 min is among the shortest ever published. The high-cadence, wide-field observations that are the hallmark of KMTNet are the only way to routinely capture such short crossings. High-cadence resolution of short caustic crossings will preferentially lead to mass and distance measurements for the lens. This is because the short crossing time typically implies a nearby lens, which enables the measurement of additional effects (bright lens and/or microlens parallax). When combined with the measured crossing time, these effects can yield planet/host masses and distance.

• Publications of The Korean Astronomical Society
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• v.30 no.2
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• pp.665-669
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• 2015

The Kepler mission has shown that small planets are extremely common. It is likely that nearly every star in the sky hosts at least one rocky planet. We just need to look hard enough-but this requires vast amounts of telescope time. MINERVA (MINiature Exoplanet Radial Velocity Array) is a dedicated exoplanet observatory with the primary goal of discovering rocky, Earth-like planets orbiting in the habitable zone of bright, nearby stars. The MINERVA team is a collaboration among UNSW Australia, Harvard-Smithsonian Center for Astrophysics, Penn State University, University of Montana, and the California Institute of Technology. The four-telescope MINERVA array will be sited at the F.L. Whipple Observatory on Mt Hopkins in Arizona, USA. Full science operations will begin in mid-2015 with all four telescopes and a stabilised spectrograph capable of high-precision Doppler velocity measurements. We will observe ~100 of the nearest, brightest, Sun-like stars every night for at least five years. Detailed simulations of the target list and survey strategy lead us to expect $15{\pm}4$ new low-mass planets.

• 대한생식의학회:학술대회논문집
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• 2003.12a
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• pp.114-115
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• 2003

• Journal of Microbiology and Biotechnology
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• v.32 no.12
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• pp.1632-1632
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• 2022

• Proceedings of the Korea Air Pollution Research Association Conference
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• 2005.11a
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• pp.129-130
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• 2005

• 대한예방의학회:학술대회논문집
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• 2000.10a
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• pp.316-317
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• 2000