• Molecules and Cells
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• v.37 no.4
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• pp.307-313
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• 2014

Cell migration requires a defined cell polarity which is formed by diverse cytoskeletal components differentially localized to the poles of cells to extracellular signals. Rap-GAP3 transiently and rapidly translocates to the cell cortex in response to chemoattractant stimulation and localizes to the leading edge of migrating cells. Here, we examined localization of truncated RapGAP3 proteins and found that the I/LWEQ domain in the central region of RapGAP3 was sufficient for posterior localization in migrating cells, as opposed to leading-edge localization of full-length Rap-GAP3. All truncated proteins accumulated at the leading edge of migrating cells exhibited clear translocation to the cell cortex in response to stimulation, whereas proteins localized to the posterior in migrating cells displayed no translocation to the cortex. The I/LWEQ domain appears to passively accumulate at the posterior region in migrating cells due to exclusion from the extended front region in response to chemoattractant stimulation rather than actively being localized to the back of cells. Our results suggest that posterior localization of the I/LWEQ domain of RapGAP3 is likely related to F-actin, which has probably different properties compared to newly formed F-actin at the leading edge of migrating cells, at the lateral and posterior regions of the cell.

• Molecules and Cells
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• v.24 no.1
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• pp.76-82
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• 2007

By combining in situ hybridization (ISH) and immunocytochemistry (IC), microscopic topological localization of mRNAs and proteins can be determined. Although this technique can be applied to a variety of tissues, it is particularly important for use on neuronal cells which are morphologically complex and in which specific mRNAs and proteins are located in distinct subcellular domains such as dendrites and dendritic spines. One common technical problem for combined ISH and IC is that the signal for immunocytochemical localization of proteins often becomes much weaker after conducting ISH. In this manuscript, we report a simplified but robust protocol that allows immunocytochemical localization of proteins after ISH. In this protocol, we fix cultured cortical or hippocampal neurons with 4% paraformaldehyde (PFA), rinse briefly in PBS, and then further fix the cells with $-20^{\circ}C$ methanol. Our method has several major advantages over previously described ones in that (1) it is simple, as it is just consecutive routine fixation procedures, (2) it does not require any special alteration to the fixation procedures such as changes in salt concentration, and (3) it can be used with antibodies that are compatible with either methanol (MeOH-) or PFA-fixed target proteins. To our best knowledge, we are the first to employ this fixation method for fluorescence ISH + IC.

• Molecules and Cells
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• v.21 no.1
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• pp.34-41
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• 2006

The neuronal localization of alpha-amino-3-hydroxyl-5-methyl-4-isoxazole propionic acid (AMPA) glutamate receptor (GluR) subunits is vital as they play key roles in the regulation of calcium permeability. We have examined the distribution of the calcium permeable AMPA glutamate receptor subunit GluR1 in the mouse visual cortex immunocytochemically. We compared this distribution to that of the calcium-binding proteins calbindin D28K, calretinin, and parvalbumin, and of GABA. The highest density of GluR1-immunoreactive (IR) neurons was found in layers II/III. Enucleation appeared to have no effect on the distribution of GluR1-IR neurons. The labeled neurons varied in morphology; the majority were round or oval and no pyramidal cells were labeled by the antibody. Two-color immunofluorescence revealed that 26.27%, 10.65%, and 40.31% of the GluR1-IR cells also contained, respectively, calbindin D28K, calretinin, and parvalbumin. 20.74% of the GluR1-IR neurons also expressed GABA. These results indicate that many neurons that express calcium-permeable GluR1 also express calcium binding proteins. They also demonstrate that one fifth of the GluR1-IR neurons in the mouse visual cortex are GABAergic interneurons.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.237-242
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• 2005

Predicting the cellular location of an unknown protein gives a 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 for predicting subcellular localization of proteins.

• Journal of Microbiology and Biotechnology
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• v.10 no.5
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• pp.606-611
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• 2000

Dimorphic yeast Candida albicans reversibly switches between the form of yeast and hyphae depending on external conditions. We investigated possible roles of the myosin family in the growth and dimorphic switches of C. albicans with a general myosin ATPase inhibitor, 2,3-butanedione-2-monoxime (BDM). Transition to hyphae as well as proliferation by budding was completely inhibited by BDM at 16 mM. Presence of 16 mM BDM did not affect hyphae-to-bud transition but it blocked budding. The effects of BDM on yeast growth and dimorphic switches were reversible. More than 70% of the BDM-treated cells demonstrated defects in the amount and the polarized localization of F-actin as well as in the shape and migration of the nucleus, suggesting that myosin activities are needed in these cellular processes of C. albicans.

• BMB Reports
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• v.46 no.2
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• pp.65-72
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• 2013

In situ detection of RNAs is becoming increasingly important for analysis of gene expression within and between intact cells in tissues. International genomics efforts are now cataloging patterns of RNA transcription that play roles in cell function, differentiation, and disease formation, and they are demon-strating the importance of coding and noncoding RNA transcripts in these processes. However, these techniques typically provide ensemble averages of transcription across many cells. In situ hybridization-based analysis methods complement these studies by providing information about how expression levels change between cells within normal and diseased tissues, and they provide information about the localization of transcripts within cells, which is important in understanding mechanisms of gene regulation. Multi-color, single-molecule fluorescence in situ hybridization (smFISH) is particularly useful since it enables analysis of several different transcripts simultaneously. Combining smFISH with immunofluorescent protein detection provides additional information about the association between transcription level, cellular localization, and protein expression in individual cells.

• 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.

• Journal of Life Science
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• v.27 no.11
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• pp.1369-1375
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• 2017

The purpose of this study was to investigate the cellular characterization of phospholipase C-${\delta}1$ in olive flounders (Paralichthys olivaceus). In general, phospholipase C signaling pathways are distributed in nuclei at plasma membranes and in cytoplasms, although the pathways' nuclear localization mechanisms are unclear. P. olivaceus duplicates type-A PoPLC-${\delta}1$ (PoPLC-${\delta}1A$), which has a high similarity to the human isoform PLC-${\delta}$; type-B PoPLC-${\delta}1$ (PoPLC-${\delta}1B$ [Sf]), which has a low similarity to the human isoform PLC-${\delta}$ and the alternative splice variant PoPLC-${\delta}1B$ (Lf), which has a nuclear localization signal (NLS) and a nuclear export signal (NES) for nuclear imports and exports, respectively. This study confirmed the effects of the cellular localization and translocation of GFP-tagged PoPLC-${\delta}1A$, PoPLC-${\delta}1B$ (Sf) and PoPLC-${\delta}1B$ (Lf). It administered treatments of $Ca^{2+}$ ionophore ionomycin and endoplasmic reticulum (ER)-$Ca^{2+}$ pump inhibitor thapsigargin to hirame natural-embryo (HINAE) cells. A laser-scanning confocal microscope was used. GFP-tagged PoPLC-${\delta}1A$ was distributed to the cellular organelles, rather than to the cytoplasms and cytomembranes, when PoPLC-${\delta}1B$ (Lf) and PoPLC-${\delta}1B$ (Sf) were localized at the plasma membranes. The treatments of ionomycin and thapsigargin showed the accumulation of PoPLC-${\delta}1A$ in the nuclei when PoPLC-${\delta}1B$ (Lf) nucleocytoplasmic shuttling and PoPLC-${\delta}1B$ (Sf) nucleocytoplasmic shuttling were not observed. The results were the first evidence that PoPLC-${\delta}1A$, which contains functional, intact NES sequences, has a main role in nucleocytoplasmic shuttling and translocation in fish.

• Analytical Science and Technology
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• v.29 no.1
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• pp.10-18
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• 2016

Phosphodiesterase (PDE) plays an important role in cAMP-mediated signaling within cells. We previously showed that the long-form of Aplysia PDE4 (ApPDE4) was localized in the plasma membrane and the presynaptic terminal in Aplysia sensory neurons, and the 16 N-terminal amino acid was sufficient for this targeting process. In this study, we characterized the cellular localization of various ApPDE4 mutants. We first identified the roles of each amino acid within the group of 16 N-terminal amino acids of long-form ApPDE4. As a result, we were able to identify various mutants that were localized to both the plasma membrane and the Golgi complex, Golgi only, or both the endoplasmic reticulum (ER) and the Golgi complex. To examine the role of palmitoylation on the cellular localization of ApPDE4 mutants, 2-bromo palmitate (2-BR) was used as a treatment. As a result, in the presence of 2-BR, the plasma membrane targeting of many mutants was impaired, indicating that palmitoylation was involved in the plasma membrane targeting of the mutants. We also found that PI4P play crucial roles in the Golgi targeting of (N16,C3S/VV/G)-mRFP, L(N16,C3S/LFS/R)-mRFP, and L(N16,EPL/R)-mRFP.

• BMB Reports
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• v.43 no.5
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• pp.344-348
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• 2010

Messenger ribonucleoprotein particles (mRNPs) are used to transport mRNAs along neuronal dendrites to their site of translation. Staufen2 is an mRNA-binding protein expressed in the cell bodies and cellular processes of different brain cells. It is notably involved in the transport of dendritic mRNAs along microtubules. Its knockdown expression was shown to change spine morphology and impair synaptic functions. However, the identity of Staufen2-bound mRNAs in brain cells is still completely unknown. As a mean to identify these mRNAs, we immunoprecipitated Staufen2-containing mRNPs from embryonic rat brains and used a genome wide approach to identify Staufen2-associated mRNAs. The genome wide approach identified 1780 mRNAs in Staufen2-containing mRNPs that code for proteins involved in cellular processes such as post-translational protein modifications, RNA metabolism, intracellular transport and translation. These results represent an additional and important step in the characterization of Staufen2- mediated neuronal functions in rat brains.