• Journal of fish pathology
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• v.24 no.3
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• pp.269-278
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• 2011

Gene expression of two glyceraldehyde-3-phosphate dehydrogenase (GAPDH) paralogs was examined during Edwardsiella tarda challenge and heavy metal exposures in mud loach (Misgurnus mizolepis; Cypriniformes) kidney and spleen. Transcription of the two mud loach GAPDH paralogs (mlGAPDH-1 and mlGAPDH-2) was significantly modulated by these stimulatory challenges in an isoform-dependent manner. Based on the real-time RT-PCR analysis, the mlGAPDH-2 transcripts were more preferentially induced by E. tarda challenge, whereas the mlGAPDH-1 transcripts were proven to show more inducibility in response to heavy metal exposure using Cd, Cu, Mn and Zn at $5{\mu}M$. Their isoform-specific response patterns were closely in accordance with the TF binding profiles in promoter and intron-1 of the two mlGAPDH isoforms, in which the mlGAPDH-2 has more binding sites for immune-related transcription factors than mlGAPDH-1 while the mlGAPDH-1 possesses exclusively metal responsive elements in its intron. Collectively, the mlGAPDHs are potentially involved in cellular pathways independent of glycolysis and the two GAPDH paralogs might undergo functional diversification or subfunctionalization at least at the transcription level.

• Mycobiology
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• v.48 no.1
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• pp.44-50
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• 2020

Calonectria pseudonaviculata and C. henricotiae are two closely related fungal species responsible for boxwood blight disease of ornamental shrubs (Buxus spp.) in the U.S. and Europe. A previous study has shown isolates of the latter species, which is restricted to Europe, to be less sensitive to tetraconazole, an azole fungicide. In this study, we have analyzed the CYP51 paralogs for polymorphism in 26 genomes, representing geographically disparate populations of C. pseudonaviculata (n = 19) and C. henricotiae (n = 7), from the U.S., Europe, Asia, and New Zealand. The presence of a CYP51A pseudogene and lack of a functional CYP51A paralog in all C. pseudonaviculata genomes examined is a novel discovery for fungi and could have implications for the evolution of resistance to antifungal chemicals.

• Fisheries and Aquatic Sciences
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• v.14 no.2
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• pp.93-104
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• 2011

Two hepcidin paralogs (ojhamp1 and ojhamp2) were isolated and characterized from a euryhaline Javanese ricefish (Oryzias javanicus: Beloniformes). The ojhamp1 cDNA encoded 90 or 91 amino acids (aa) of a typical HAMP1 preproprotein. This preproprotein is believed to cleave and yield the 66 or 67 aa-proprotein, followed by the 26 aa-mature peptide, composed of 8 conserved cysteine residues and the QSHL amino terminal motif. The ojhamp2 cDNA encoded 89 aa of HAMP2 preproprotein, cleaved to yield a 65 aa proprotein, and subsequently the 25 aa-mature peptide. The mature OJHAMP1 possessed a cationic isoelectric point (pI), whereas OJHAMP2 had an anionic charge. At the genomic level, both ojhamp1 and ojhamp2 share a conserved tripartite structure (three exons interrupted by two introns) with other vertebrate hepcidin genes. However, the ojhamp1 was shown to exist as two distinct mRNA species, encoding 90 or 91 aa, due to alternative splicing at the junction site between intron I and exon II. Both ojhamp1 and ojhamp2 transcripts were detected in a wide range of tissue types with varying levels of basal expression, although the highest expression was observed in the liver for both isoforms. Transcriptional response to bacterial challenge using Edwardsiella tarda showed that ojhamp1 was moderately upregulated in the liver but remained unchanged in the kidney. However, the ojhamp2 was significantly suppressed in both the kidney and liver, suggesting a potential diversification between the two paralogs.

• BMB Reports
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• v.56 no.3
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• pp.172-177
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• 2023

BEST family is a class of Ca²⁺-activated Cl- channels evolutionary well conserved from bacteria to human. The human BEST paralogs (BEST1-BEST4) share significant amino acid sequence homology in the N-terminal region, which forms the transmembrane helicases and contains the direct calcium-binding site, Ca²⁺-clasp. But the cytosolic C-terminal region is less conserved in the paralogs. Interestingly, this domain-specific sequence conservation is also found in the BEST1 orthologs. However, the functional role of the C-terminal region in the BEST channels is still poorly understood. Thus, we aimed to understand the functional role of the C-terminal region in the human and mouse BEST1 channels by using electrophysiological recordings. We found that the calcium-dependent activation of BEST1 channels can be modulated by the C-terminal region. The C-terminal deletion hBEST1 reduced the Ca²⁺-dependent current activation and the hBEST1-mBEST1 chimera showed a significantly reduced calcium sensitivity to hBEST1 in the HEK293 cells. And the C-terminal domain could regulate cellular expression and plasma membrane targeting of BEST1 channels. Our results can provide a basis for understanding the C-terminal roles in the structure-function of BEST family proteins.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.156-160
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• 2005

We introduce a fully automatic clustering method to classier candidate paralog clusters from a set of protein sequences within one genome. A set of protein sequences is represented as a set of nodes, each represented by the amino acid sequence for a protein with the sequence similarities among them constituting a set of edges in a graph of protein relationships. We use graph-based clustering methods to identify structurally consistent sets of nodes which are strongly connected with each other. Our results are consistent with those from current leading systems such as COG/KOG and KEGG based on manual curation. All the results are viewable at http://www.cs.rutgers.edu/${\sim}$seabee.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.109-112
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• 2005

Identifying orthologous paralogenes is a fundamental problem in comparative genomics and can facilitate the study of evolutionary history of the species. Existing approaches for locating paralogs make use of local alignment based algorithms such as BLAST. However, there are cases that genes with high alignment scores are not paralogenes. On the other hand, whole genome alignment tools are designed to locate orthologs. Most of these tools are based on some unique substrings (called anchors) in the corresponding orthologous pair to identify them. Intuitively, these tools may not be useful in identifying orthologous paralogenes as paralogenes are very similar and there may not be enough unique anchors. However, our study shows that this is not true. Paralogenes although are similar, they have undergone different mutations. So, there are enough unique anchors for identifying them. Our contributions include the followings. Based on this counter-intuitive finding, we propose to employ the whole genome alignment tools to help verifying paralogenes. Our experiments on five pairs of human-mouse chromosomes show that our approach is effective and can identify most of the mis-classified paralog groups (more than 80%). We verify our finding that whole genome alignment tools are able to locate orthologous paralogenes through a simulation study. The result from the study confirms our finding.

• Development and Reproduction
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• v.27 no.3
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• pp.137-147
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• 2023

Pharyngeal pouches are an important epithelial structure controlling facial skeletal development in vertebrates. A series of pouches arise sequentially in the pharyngeal endoderm through collective cell migration followed by rearrangement of pouch-forming cells. While crucial transcription factors and signaling molecules have been identified in pouch formation, a role for Neuropilins (Nrps) in pouch development has not yet been analyzed in any vertebrates. Nrps are cell surface receptors essential for angiogenesis and axon guidance. In all vertebrates, the two Nrp family members, Nrp1 and Nrp2, are conserved in the genome, with two paralogs for Nrp1 (Nrp1a and Nrp1b) and Nrp2 (Nrp2a and Nrp2b) being identified in zebrafish. Here, I report a potential requirement of Nrp signaling in pouch development in zebrafish. nrp1a and nrp2b were expressed in the developing pouches, with sema3d, a ligand for Nrps, being expressed in the pouches. Knocking down Nrps signaling in the pharyngeal endoderm led to severe defects in pouches and facial cartilages. In addition, blocking Mitogen-activated protein kinase (MAPK) activities, a downstream effector of Nrp signaling, in the pharyngeal endoderm caused similar defects in pouches and facial skeleton to those by knocking down Nrps signaling. My results suggest that Nrp signaling acts for pouch formation through MAPK.

• Molecules and Cells
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• v.27 no.5
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• pp.539-546
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• 2009

In Saccharomyces cerevisiae, ribosomal protein L7, one of the ~46 ribosomal proteins of the 60S subunit, is encoded by paralogous RPL7A and RPL7B genes. The amino acid sequence identity between RPl7a and RPl7b is 97 percent; they differ by only 5 amino acid residues. Interestingly, despite the high sequence homology, Rpl7b is detected in both the cytoplasm and the nucleolus, whereas Rpl7a is detected exclusively in the cytoplasm. A site-directed mutagenesis experiment revealed that the change in the amino acid sequence of Rpl7b does not influence its subcellular localization. In addition, introns of RPL7A and RPL7B did not affect the subcellular localization of Rpl7a and Rpl7b. Remarkably, Rpl7b was detected exclusively in the cytoplasm in rpl7a knockout mutant, and overexpression of Rpl7a resulted in its accumulation in the nucleolus, indicating that the subcellular localization of Rpl7a and Rpl7b is influenced by the intracellular level of Rpl7a. Rpl7b showed a wide range of localization patterns, from exclusively cytoplasmic to exclusively nucleolar, in knockout mutants for some rRNA-processing factors, nuclear pore proteins, and large ribosomal subunit assembly factors. Rpl7a, however, was detected exclusively in the cytoplasm in these mutants. Taken together, these results suggest that although Rpl7a and Rpl7b are paralogous and functionally replaceable with each other, their precise physiological roles may not be identical.

• Molecules and Cells
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• v.39 no.5
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• pp.395-402
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• 2016

Identifying Hoxc8 target genes is at the crux of understanding the Hoxc8-mediated regulatory networks underlying its roles during development. However, identification of these genes remains difficult due to intrinsic factors of Hoxc8, such as low DNA binding specificity, context-dependent regulation, and unknown cofactors. Therefore, as an alternative, the present study attempted to test whether the roles of Hoxc8 could be inferred by simply analyzing genes frequently coexpressed with Hoxc8, and whether these genes include putative target genes. Using archived gene expression datasets in which Hoxc8 was differentially expressed, we identified a total of 567 genes that were positively coexpressed with Hoxc8 in at least four out of eight datasets. Among these, 23 genes were coexpressed in six datasets. Gene sets associated with extracellular matrix and cell adhesion were most significantly enriched, followed by gene sets for skeletal system development, morphogenesis, cell motility, and transcriptional regulation. In particular, transcriptional regulators, including paralogs of Hoxc8, known Hox co-factors, and transcriptional remodeling factors were enriched. We randomly selected Adam19, Ptpn13, Prkd1, Tgfbi, and Aldh1a3, and validated their coexpression in mouse embryonic tissues and cell lines following $TGF-{\beta}2$ treatment or ectopic Hoxc8 expression. Except for Aldh1a3, all genes showed concordant expression with that of Hoxc8, suggesting that the coexpressed genes might include direct or indirect target genes. Collectively, we suggest that the coexpressed genes provide a resource for constructing Hoxc8-mediated regulatory networks.

• Journal of KIISE:Databases
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• v.35 no.2
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• pp.125-131
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• 2008

It is very useful to predict orthologs for new genome annotation and research on genome evolution. We showed that the previous work can be extended to construct OCs(Ortholog Clusters) automatically from multiple complete-genomes. The proposed method also has the quality of production of InParanoid, which produces orthologs from just two genomes. On the other hand, in order to predict more exactly the function of a newly sequenced gene it can be an important issue to prevent unwanted inclusion of paralogs into the OCs. We have, here, investigated how well it is possible to construct a functionally purer OCs with score cut-offs. Our OCs were generated from the datasets of 20 procaryotes. The similarity with both COG(Clusters of Orthologous Group) and KO(Kegg Orthology) against our OCs has about 90% and inclines to increase with the growth of score cut-offs.