• BMB Reports
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• v.45 no.6
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• pp.342-347
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• 2012

Plant mitochondria possess alternative respiratory pathways mediated by the type II NAD(P)H dehydrogenases and alternative oxidases. Here, E3 SUMO ligase was shown to regulate alternative respiratory pathways and to participate in the maintenance of carbon and nitrogen balance in Arabidopsis. The transcript abundance of the type II NAD(P)H dehydrogenases NDA2 and NDB2 and alternative oxidases AOX1a and AOX1d genes was low in siz1-2 mutants compared to that in wild-type. The addition of nitrate or ammonium resulted in a decrease or an increase in the expression of the same gene families, respectively, in both wild-type and siz1-2 mutants. The amount of free sugar (glucose, fructose and sucrose) was lower in siz1-2 mutants than that in wild-type. These results indicate that low nitrate reductase activity due to the AtSIZ1 mutation is correlated with an overall decrease in alternative respiration and with a low carbohydrate content to maintain the carbon to nitrogen ratio in siz1-2 mutants.

• Molecules and Cells
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• v.41 no.1
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• pp.50-54
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• 2018

Atg5 and Atg7 have long been considered as essential molecules for autophagy. However, we found that cells lacking these molecules still form autophagic vacuoles and perform autophagic protein degradation when subjected to certain stressors. During this unconventional autophagy pathway, autophagosomes appeared to be generated in a Rab9-dependent manner by the fusion of vesicles derived from the trans-Golgi and late endosomes. Therefore, mammalian autophagy can occur via at least two different pathways; the Atg5/Atg7-dependent conventional pathway and an Atg5/Atg7-independent alternative pathway.

• Genomics & Informatics
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• v.7 no.3
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• pp.171-174
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• 2009

The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in two- and a-half dimensions (2.5D) as an alternative to three-dimensional (3D) visualizations. Such visualization allows user to display different groups of clustered nodes, in different parallel planes, and to see a detailed view of a group of objects in focus and its place in the context of the whole system. This tool is an extended version of J2dPathway.

• Proceedings of the Zoological Society Korea Conference
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• 1998.10b
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• pp.97-97
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• 1998

No Abstract, See Full Text

• Toxicological Research
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• v.32 no.3
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• pp.259-267
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• 2016

Animal testing was used traditionally in the cosmetics industry to confirm product safety, but has begun to be banned; alternative methods to replace animal experiments are either in development, or are being validated, worldwide. Research data related to test substances are critical for developing novel alternative tests. Moreover, safety information on cosmetic materials has neither been collected in a database nor shared among researchers. Therefore, it is imperative to build and share a database of safety information on toxicological mechanisms and pathways collected through in vivo, in vitro, and in silico methods. We developed the CAMSEC database (named after the research team; the Consortium of Alternative Methods for Safety Evaluation of Cosmetics) to fulfill this purpose. On the same website, our aim is to provide updates on current alternative research methods in Korea. The database will not be used directly to conduct safety evaluations, but researchers or regulatory individuals can use it to facilitate their work in formulating safety evaluations for cosmetic materials. We hope this database will help establish new alternative research methods to conduct efficient safety evaluations of cosmetic materials.

• The Korean Journal of Physiology and Pharmacology
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• v.16 no.2
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• pp.139-144
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• 2012

It has been reported that activation of metabotropic glutamate receptor 1 (mGluR1) can mediate endocannabinoid-induced short-term depression of synaptic transmission in cerebellar parallel fiber (PF)-Purkinje cell (PC) synapse. mGluR1 has signaling pathways involved in intracellular calcium increase which may contribute to endocannabinoid release. Two major mGluR1-evoked calcium signaling pathways are known: (1) slow-kinetic inward current carried by transient receptor potential canonical (TRPC) channel which is permeable to $Ca^{2+}$; (2) $IP_3$-induced calcium release from intracellular calcium store. However, it is unclear how much each calcium source contributes to endocannabinoid signaling. Here, we investigated whether calcium influx through mGluR1-evoked TRPC channel contributes to endocannabinoid signaling in cerebellar Purkinje cells. At first, we applied SKF96365 to inhibit TRPC, which blocked endocannabinoid-induced short-term depression completely. However, an alternative TRP channel inhibitor, BTP2 did not affect endocannabinoid-induced short-term depression although it blocked mGluR1-evoked TRPC currents. Endocannabinoid signaling occurred normally even though the TRPC current was mostly blocked by BTP2. Our data imply that TRPC current does not play an important role in endocannabinoid signaling. We also suggest precaution in applying SKF96365 to inhibit TRP channels and propose BTP2 as an alternative TRPC inhibitor.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.5 no.1
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• pp.76-87
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• 2005

Various disorders cause hyperammonemia during childhood. Amongthem are those caused by inherited defects in urea synthesis and related metabolic pathways. These disorders can be grouped into two types: disorders of the enzymes that comprise the urea cycle, and disorders of the transporters or metabolites of theamino acids related to the urea cycle. Principal clinical features of these disorders are caused by elevated levels of blood ammonium. Additional disease-specific symptoms are related to the particular metabolic defect. These specific clinical manifestations are often due to an excess or lack of specific amino acids. Treatment of urea cycle disorders and related metabolic diseases consists of nutritional restriction of proteins, administration of specific amino acids, and use of alternative pathways for discarding excess nitrogen. Although combinations of these treatments are extensively employed, the prognosis of severe cases remains unsatisfactory. Liver transplantation is one alternative for which a better prognosis is reported.

• BMB Reports
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• v.50 no.4
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• pp.201-207
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• 2017

Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced.

• Biomolecules & Therapeutics
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• v.32 no.5
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• pp.582-600
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• 2024

Tyrosine kinase inhibitors (TKIs) have revolutionized the treatment landscape for chronic myeloid leukemia (CML). However, TKI resistance poses a significant challenge, leading to treatment failure and disease progression. Resistance mechanisms include both BCR::ABL1-dependent and BCR::ABL1-independent pathways. The mechanisms underlying BCR::ABL1 independence remain incompletely understood, with CML cells potentially activating alternative signaling pathways, including the AKT/mTOR and JAK2/STAT5 pathways, to compensate for the loss of BCR::ABL1 kinase activity. This study explored tumoral VISTA (encoded by VSIR) as a contributing factor to TKI resistance in CML patients and identified elevated tumoral VISTA levels as a marker of resistance and poor survival. Through in vitro and in vivo analyses, we demonstrated that VSIR knockdown and the application of NSC-622608, a novel VISTA inhibitor, significantly impeded CML cell proliferation and induced apoptosis by attenuating the AKT/mTOR and JAK2/STAT5 pathways, which are crucial for CML cell survival independent of BCR::ABL1 kinase activity. Moreover, VSIR overexpression promoted TKI resistance in CML cells. Importantly, the synergistic effect of NSC-622608 with TKIs offers a potent therapeutic avenue against both imatinib-sensitive and imatinib-resistant CML cells, including those harboring the challenging T315I mutation. Our findings highlight the role of tumoral VISTA in mediating TKI resistance in CML, suggesting that inhibition of VISTA, particularly in combination with TKIs, is an innovative approach to enhancing treatment outcomes in CML patients, irrespective of BCR::ABL1 mutation status. This study not only identified a new pathway contributing to TKI resistance but also revealed the possibility of targeting tumoral VISTA as a means of overcoming this significant clinical challenge.

• Genomics & Informatics
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• v.19 no.2
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• pp.16.1-16.14
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• 2021

Even in the current age of advanced medicine, the prognosis of malignant peritoneal mesothelioma (MPM) remains abysmal. Molecular mechanisms responsible for the initiation and progression of MPM are still largely not understood. Adopting an integrated bioinformatics approach, this study aims to identify the key genes and pathways responsible for MPM. Genes that are differentially expressed in MPM in comparison with the peritoneum of healthy controls have been identified by analyzing a microarray gene expression dataset. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of these differentially expressed genes (DEG) were conducted to gain a better insight. A protein-protein interaction (PPI) network of the proteins encoded by the DEGs was constructed using STRING and hub genes were detected analyzing this network. Next, the transcription factors and miRNAs that have possible regulatory roles on the hub genes were detected. Finally, survival analyses based on the hub genes were conducted using the GEPIA2 web server. Six hundred six genes were found to be differentially expressed in MPM; 133 are upregulated and 473 are downregulated. Analyzing the STRING generated PPI network, six dense modules and 12 hub genes were identified. Fifteen transcription factors and 10 miRNAs were identified to have the most extensive regulatory functions on the DEGs. Through bioinformatics analyses, this work provides an insight into the potential genes and pathways involved in MPM.