• Proceedings of the Korean Information Science Society Conference
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• 2005.07b
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• pp.226-228
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• 2005

Predicting the cellular location of an unknown protein gives valuable information for inferring the possible function of the protein. For more accurate Prediction system, we need a good feature extraction method that transforms the raw sequence data into the numerical feature vector, minimizing information loss. In this paper we propose new methods of extracting underlying features only from the sequence data by computing pairwise sequence alignment scores. In addition, we use composition based features to improve prediction accuracy. To construct an SVM ensemble from separately trained SVM classifiers, we propose specificity based weighted majority voting . The overall prediction accuracy evaluated by the 5-fold cross-validation reached $88.53\%$ for the eukaryotic animal data set. By comparing the prediction accuracy of various feature extraction methods, we could get the biological insight on the location of targeting information. Our numerical experiments confirm that our new feature extraction methods are very useful forpredicting subcellular localization of proteins.

• Genomics & Informatics
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• v.17 no.1
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• pp.2.1-2.12
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• 2019

Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

• YAKHAK HOEJI
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• v.50 no.2
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• pp.93-98
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• 2006

Human foamy virus (HFV) integrase mediates integration of viral c-DNA into cellular DNA. In this process, HFV prointegration complex (PIC) in which integrase is a key component moves to nuclei of the infected cells and leads to integration of viral DNA to the cellular genome, which is essential in viral life cycle. In general nuclear localization signals (NLS) have been suggested to be involved in localizing retroviral PIC to nuclei, but the mechanisms for nuclear localization of the HFV PIC remains unclear. To functionally identify the NLS of HFV integrase, various subdomains of the protein were expressed as GFP fusions and their subcellular locations were analyzed with confocal laser scanning microscopy. Wild type HFV integrase was karyophilic by targeting the fusion protein to nuclei of the COS-1 and 293T cells. Our results showed that strong NLS of HFV integrase was mapped to the C-terminal regions. In addition the karyophilic properties of N-terminal and central regions are not individually strong enough to direct localization of the fusion proteins to nuclei, but their cooperative activity for nuclear import was confirmed.

• Molecules and Cells
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• v.37 no.7
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• pp.554-561
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• 2014

Lysophosphatidic acid (LPA) is a lipid growth factor that exerts diverse biological effects through its cognate receptors ($LPA_1-LPA_6$). $LPA_1$, which is predominantly expressed in the brain, plays a pivotal role in brain development. However, the role of $LPA_1$ in neuronal migration has not yet been fully elucidated. Here, we delivered $LPA_1$ to mouse cerebral cortex using in utero electroporation. We demonstrated that neuronal migration in the cerebral cortex was not affected by the overexpression of $LPA_1$. Moreover, these results can be applied to the identification of the localization of $LPA_1$. The subcellular localization of $LPA_1$ was endogenously present in the perinuclear area, and overexpressed $LPA_1$ was located in the plasma membrane. Furthermore, $LPA_1$ in developing mouse cerebral cortex was mainly expressed in the ventricular zone and the cortical plate. In summary, the overexpression of $LPA_1$ did not affect neuronal migration, and the protein expression of $LPA_1$ was mainly located in the ventricular zone and cortical plate within the developing mouse cerebral cortex. These studies have provided information on the role of $LPA_1$ in brain development and on the technical advantages of in utero electroporation.

• Molecules and Cells
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• v.24 no.3
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• pp.378-387
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• 2007

The Bcl-2 family of proteins interacts at the mitochondria to regulate apoptosis. However, the anti-apoptotic Bcl-2 and $Bcl-X_L$ are not completely localized to the mitochondria. In an attempt to generate Bcl-2 and $Bcl-X_L$ chimeras that are constitutively localized to the mitochondria, we substituted their C-terminal transmembrane tail or both the C-terminal transmembrane tail and the adjacent loop with the equivalent regions from Bak or Bax mutant (BaxS184V) as these regions determine the mitochondrial localization of Bak and Bax. The effects of these substitutions on subcellular localization and their activities were assessed following expression in HeLa and CHO K1 cells. The substitution of the C-terminal tail or the C-terminal tail and the adjacent loop of Bcl-2 with the equivalent regions from Bak or the Bax mutant resulted in its association with the mitochondria. This change in subcellular localization of Bcl-2 chimeras triggered cells to undergo apoptotic-like cell death. The localization of this Bcl-2 chimera to the mitochondria may be associated with the disruption of mitochondrial membrane potential. Unlike Bcl-2, the loop structure adjacent to the C-terminal tail in $Bcl-X_L$ is crucial for its localization. To localize the $Bcl-X_L$ chimeras to the mitochondria, the loop structure next to the C-terminal tail in $Bcl-X_L$ protein must remain intact and cannot be substituted by the loop from Bax or Bak. The chimeric $Bcl-X_L$ with both its C-terminal tail and the loop structure replaced by the equivalent regions of Bak or Bax mutant localized throughout the entire cytosol. The $Bcl-X_L$ chimeras that are targeted to the mitochondria and the wild type $Bcl-X_L$ provided same protection against cell death under several death inducing conditions.

• Animal cells and systems
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• v.5 no.3
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• pp.225-229
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• 2001

Nek2 is a mammalian protein kinase that is structurally homologous to NIMA, a mitotic regulator in Aspergillus nidulans. To understand cellular processes in which Nek2 participates during mammalian development, we investigated the expression and subcellular localization of Nek2 in vivo. The Nek2 protein was detected in spermatocytes and in a fraction of actively dividing ovarian follicle cells and of embryonic tissues. We also observed that Nek2 was localized in both the nucleus and centrosome in embryonic cells. Such localization pattern supports the proposal that Nek2 is a mitotic regulator that is involved in multiple cell cycle events during mammalian development.

• Biomedical Science Letters
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• v.12 no.3
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• pp.201-208
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• 2006

PI3-kinase activity through p85, the regulatory subunit of class IA PI3-kinase, is indispensable for the growth, differentiation, and survival of skeletal muscle cells, but little is known about the function of other regulatory subunits such as p55 and p50. We examined the subcellular localization and the expression of the regulatory subunits of class IA PI3-kinase in L6 myoblasts. Both p55 and p50 as well as p85 were expressed in L6 myoblasts. Whereas p85 was localized at both cytosolic and nuclear tractions, p55 and p50 were localized at only the nuclear traction. During the differentiation of L6 myoblasts, the protein concentrations of both p55 and p50 were decreased but that of p85 was not significantly changed. Menadione-induced oxidative stress induced the translocation of p85 from cytosol to nucleus and the increase of p55 expression. These results suggest that the regulatory subunits of class IA PI3-kinase play an important role in L6 myoblasts.

• Journal of Physiology & Pathology in Korean Medicine
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• v.22 no.2
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• pp.315-320
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• 2008

This study investigated the signaling mechanisms contributed to the vasodilatory effects of HMC05, a herbal prescription. HMC05 acted in an endothelium-independent manner. To elucidate the fundamental mechanisms of its vascular actions, we focused on the signaling molecules involved in actin-myosin filament regulation including 20 kDa myosin light chains (LC20), Rho-associated kinase (ROCK), PKC, JNK and extracellular signal-regulated protein kinase (ERK) in the endothelium-denuded thoracic aorta or isolated smooth muscle cells (SMCs). It lowered the phosphorylation level of LC20 and showed that ROCK, ERK, JNK and $PKC{\alpha}$ pathways played important roles in the effects, as confirmed by the observations with a specific inhibition or activation, and with the activity and the subcellular localization of these molecules. In particular, HMC05 dramatically inhibited the activity of ERK and the downstream signaling of ROCK. It also changed the subcellular localization of the phophorylated $PKC{\alpha}$ as well as the amount of phosphorylation. Taken together, these data indicate that the vascular relaxation effects of HMC05 are attributed to the regulation of these signaling mechanisms.

• BMB Reports
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• v.40 no.5
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• pp.617-624
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• 2007

Protein arginine methylation is a posttranslational modification involved in various cellular functions including cell signaling, protein subcellular localization and transcriptional regulation. We analyze the protein arginine methyltransferases (PRMTs) that catalyze the formation of methylarginines in porcine brain. We fractionated the brain extracts and determined the PRMT activities as well as the distribution of different PRMT proteins in subcellular fractions of porcine brain. The majority of the type I methyltransferase activities that catalyze the formation of asymmetric dimethylarginines was in the cytosolic S3 fraction. High specific activity of the methyltransferase was detected in the S4 fraction (high-salt stripping of the ultracentrifugation precipitant P3 fraction), indicating that part of the PRMT was peripherally associated with membrane and ribosomal fractions. The amount and distribution of PRMT1 are consistent with the catalytic activity. The elution patterns from gel filtration and anion exchange chromatography also indicate that the type I activity in S3 and S4 are mostly from PRMT1. Our results suggest that part of the type I arginine methyltransferases in brains, mainly PRMT1, are sequestered in an inactive form as they associated with membranes or large subcellular complexes. Our biochemical analyses confirmed the complex distribution of different PRMTs and implicate their regulation and catalytic activities in brain.

• BMB Reports
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• v.40 no.2
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• pp.270-276
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• 2007

We have cloned a novel mouse zinc finger protein gene Znf313 by rapid amplification of cDNA ends (RACE) according to the homologue of human ZNF313 gene. The cDNA is 2,163 base pairs (bp) in length and encodes a 229 amino acids (aa) protein with a $C_3HC_4$ ring finger domain and three $C_2H_2$ domains. 89% and 93% nucleotide (nt) and aa sequence identity is observed with its human homologue. Revealed by Northern blot and RT-PCR, full mRNA consists of 2.16 kb and widely expresses in tissues as a single transcript, most abundantly in heart, liver, kidney and testis. The expression of Znf313 in testis is detected in all development stages. Western blot analysis also reveals that Znf313 is expressed in the tissues. Immunohistochemical staining and subcellular localization demonstrate that Znf313 is expressed both in the cytoplasm and nucleus whereas predominantly localized in the nucleus. Present data suggests that Znf313 gene might play a fundamental role in gene transcription and regulation in organism and relates to spermatogenesis.