• BMB Reports
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• v.52 no.9
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• pp.540-547
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• 2019

Immune repertoire is a collection of enormously diverse adaptive immune cells within an individual. As the repertoire shapes and represents immunological conditions, identification of clones and characterization of diversity are critical for understanding how to protect ourselves against various illness such as infectious diseases and cancers. Over the past several years, fast growing technologies for high throughput sequencing have facilitated rapid advancement of repertoire research, enabling us to observe the diversity of repertoire at an unprecedented level. Here, we focus on B cell receptor (BCR) repertoire and review approaches to B cell isolation and sequencing library construction. These experiments should be carefully designed according to BCR regions to be interrogated, such as heavy chain full length, complementarity determining regions, and isotypes. We also highlight preprocessing steps to remove sequencing and PCR errors with unique molecular index and bioinformatics techniques. Due to the nature of massive sequence variation in BCR, caution is warranted when interpreting repertoire diversity from error-prone sequencing data. Furthermore, we provide a summary of statistical frameworks and bioinformatics tools for clonal evolution and diversity. Finally, we discuss limitations of current BCR-seq technologies and future perspectives on advances in repertoire sequencing.

• Korean Journal of Environmental Biology
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• v.39 no.2
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• pp.160-168
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• 2021

Doublesex and mab-3 related transcription factor(dmrt) play crucial roles in sex determination and sex differentiation in vertebrates and invertebrates. Although dmrt genes have been identified in vertebrates, little is known about aquatic invertebrates. In this study, two dmrt genes, namely, Dc_dmrt93B and Dc_dmrt99B, were identified from brackish water flea, Diaphanosoma celebensis. Transcriptional changes were observed in the dmrt genes when the flea was exposed to bisphenol(BP), an endocrine disruptor. Sequence and phylogenetic analyses showed that both dmrt genes contained two conserved domains, namely, DM and DMA, closely clustered with those of Daphnia spp. Additionally, a significant increase in the Dc_dmrt99B mRNA expression level was observed upon exposure to intermediate concentrations of BP (bisphenol A>bisphenol S=bisphenol F, p<0.05), while the expression of Dc_dmrt93B mRNA was slightly modulated. These findings imply that the two dmrt genes may be involved in sex differentiation of D. celebensis. Furthermore, it was found that the ability of BP to modulate dmrt genes could affect development and reproduction. This study provides a basis for understanding the function of the dmrt genes and the molecular mode of action of BP in small crustaceans.

• Molecular & Cellular Toxicology
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• v.1 no.2
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• pp.73-77
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• 2005

Nickel is the one of potent environmental, the occupational pollutants and the classified human carcinogens. It is a serious hazard to human health, when the metal exposure. To prevent human diseases from the heavy metals, it is seemingly important that understanding of how nickel exerts their toxicity and carcinogenic effect at a molecular and a genomic level. The process of nickel absorption has been demonstrated as phagocytosis, iron channel and diffusion. Uptaked nickel has been suggested to induce carcinogenesis via two pathways, a direct DNA damaging pathway and an indirect DNA damaging pathway. The former was originated from the ability of metal to generate Reactive Oxygen Species (ROS) and the reactive intermediates to interact with DNA directly. Ni-generated ROS or Nickel itself, interacts with DNAs and histones to cause DNA damage and chromosomal abnormality. The latter was originated from an indirect DNA damage via inhibition of DNA repair, or condensation and methylation of DNA. Cells have ability to protect from the genotoxic stresses by changing gene expression. Microarray analysis of the cells treated with nickel or nickel compounds, show the specific altered gene expression profile. For example, HIF-I (Hypoxia-Inducible Factor I) and p53 were well known as transcription factors, which are upregulated in response to stress and activated by both soluble and insoluble nickel compounds. The induction of these important transcription factors exert potent selective pressure and leading to cell transformation. Genes of metallothionein and family of heat shock proteins which have been known to play role in protection and damage control, were also induced by nickel treatment. These gene expressions may give us a clue to understand of the carcinogenesis mechanism of nickel. Further discussions on molecular and genomic, are need in order to understand the specific mechanism of nickel toxicity and carcinogenicity.

• Molecules and Cells
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• v.39 no.6
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• pp.447-459
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• 2016

Many studies have been conducted to understand plant stress responses to salinity because irrigation-dependent salt accumulation compromises crop productivity and also to understand the mechanism through which some plants thrive under saline conditions. As mechanistic understanding has increased during the last decades, discovery-oriented approaches have begun to identify genetic determinants of salt tolerance. In addition to osmolytes, osmoprotectants, radical detoxification, ion transport systems, and changes in hormone levels and hormone-guided communications, the Salt Overly Sensitive (SOS) pathway has emerged to be a major defense mechanism. However, the mechanism by which the components of the SOS pathway are integrated to ultimately orchestrate plant-wide tolerance to salinity stress remains unclear. A higher-level control mechanism has recently emerged as a result of recognizing the involvement of GIGANTEA (GI), a protein involved in maintaining the plant circadian clock and control switch in flowering. The loss of GI function confers high tolerance to salt stress via its interaction with the components of the SOS pathway. The mechanism underlying this observation indicates the association between GI and the SOS pathway and thus, given the key influence of the circadian clock and the pathway on photoperiodic flowering, the association between GI and SOS can regulate growth and stress tolerance. In this review, we will analyze the components of the SOS pathways, with emphasis on the integration of components recognized as hallmarks of a halophytic lifestyle.

• Journal of The Korean Association For Science Education
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• v.18 no.2
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• pp.161-171
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• 1998

The effects of computer-assisted instruction (CAl) using molecular-level animation upon students' conceptions, attitudes toward science instruction, and learning motivation were investigated. Treatment and control groups (2 classes) were selected from a girls middle school in Seoul, and taught about the motion of molecule for 5 class hours. Before instruction, the short-version Group Assessment of Logical Thinking (GALT) and the Patterns of Adaptive Survey were administered, and the grade for the previous science course was obtained. The GALT score was used as a blocking variable, and the others as covariates. After the instructions, the researcher-made conceptions test, the test of attitudes toward science instruction, and the motivation questionnaire were administered. The perception questionnaire of CAl was also administered to the treatment group. Although more students in the CAl group had sound understanding about the motion of molecule, the scores of the conceptions test for the two groups were not significantly different at .05 level of significance. The students in the CAl group, however, were found to have more positive attitudes toward science instruction and learning motivation. In the perception questionnaire of CAl, most students in the treatment group exhibited positive attitudes toward the CAl. However, some students mentioned that they were disturbed by noisy environments, and that they could not understand some content presented. Educational implications are discussed.

• International Journal of Stem Cells
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• v.16 no.3
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• pp.342-355
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• 2023

Background and Objectives: Osteoblasts are derived from bone marrow mesenchymal stem cells (BMMSCs) and play important role in bone remodeling. While our previous studies have investigated the cell subtypes and heterogeneity in osteoblasts and BMMSCs separately, cell-to-cell communications between osteoblasts and BMMSCs in vivo in humans have not been characterized. The aim of this study was to investigate the cellular communication between human primary osteoblasts and bone marrow mesenchymal stem cells. Methods and Results: To investigate the cell-to-cell communications between osteoblasts and BMMSCs and identify new cell subtypes, we performed a systematic integration analysis with our single-cell RNA sequencing (scRNA-seq) transcriptomes data from BMMSCs and osteoblasts. We successfully identified a novel preosteoblasts subtype which highly expressed ATF3, CCL2, CXCL2 and IRF1. Biological functional annotations of the transcriptomes suggested that the novel preosteoblasts subtype may inhibit osteoblasts differentiation, maintain cells to a less differentiated status and recruit osteoclasts. Ligand-receptor interaction analysis showed strong interaction between mature osteoblasts and BMMSCs. Meanwhile, we found FZD1 was highly expressed in BMMSCs of osteogenic differentiation direction. WIF1 and SFRP4, which were highly expressed in mature osteoblasts were reported to inhibit osteogenic differentiation. We speculated that WIF1 and sFRP4 expressed in mature osteoblasts inhibited the binding of FZD1 to Wnt ligand in BMMSCs, thereby further inhibiting osteogenic differentiation of BMMSCs. Conclusions: Our study provided a more systematic and comprehensive understanding of the heterogeneity of osteogenic cells. At the single cell level, this study provided insights into the cell-to-cell communications between BMMSCs and osteoblasts and mature osteoblasts may mediate negative feedback regulation of osteogenesis process.

• BMB Reports
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• v.48 no.6
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• pp.301-302
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• 2015

Hypoxia is associated with many pathological conditions as well as the normal physiology of metazoans. We identified a lactate-dependent signaling pathway in hypoxia, mediated by the oxygen- and lactate-regulated protein NDRG family member 3 (NDRG3). Oxygen negatively regulates NDRG3 expression at the protein level via the PHD2/VHL system, whereas lactate, produced in excess under prolonged hypoxia, blocks its proteasomal degradation by binding to NDRG3. We also found that the stabilized NDRG3 protein promotes angiogenesis and cell growth under hypoxia by activating the Raf-ERK pathway. Inhibiting cellular lactate production abolishes NDRG3-mediated hypoxia responses. The NDRG3-Raf-ERK axis therefore provides the genetic basis for lactate-induced hypoxia signaling, which can be exploited for the development of therapies targeting hypoxia-induced diseases in addition to advancing our understanding of the normal physiology of hypoxia responses. [BMB Reports 2015; 48(6): 301-302]

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.82-85
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• 2005

Doxorubicin is a highly-valuable anthracycline-family polyketide drug with a very potent anticancer activity, typically produced by a Gram-positive soil bacterium called Streptomyces peucetius. Thanks to the recent development of Streptomyces genomics-based technologies, the random mutagenesis approach for Streptomyces strain improvement has been switched toward the genomics-based technologies including the application of DNA microarray systems. In order to identify and characterize the genomics-driven potential target genes critical for doxorubincin overproduction, three different types of doxorubicin overproducing strains, a dnrI(doxorubicin-specific positive regulatory gene)-overexpressor, a doxA (gene involved in the conversion from daunorubicin to doxorubicin)-overexpressor, and a recursively-mutated industrial strain, were generated and examined their genomic transcription profiles using Streptomyces DNA microarray systems. The DNA microarray results revealed several potential target genes in S. peucetius genome, whose expressions were significantly either up- or down-regulated comparing with the wild-type strain. A systematic understanding of doxorubicin overproduction at the genomic level presented in this research should lead us a rational design of molecular genetic strain improvement strategy.

• Genomics & Informatics
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• v.14 no.4
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• pp.234-240
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• 2016

Different mechanisms, including transcriptional and post transcriptional processes, regulate tissue specific expression of genes. In this study, we report differences in gene/protein compositional features between apoptosis involved genes selectively expressed in human tissues. We found some correlations between codon/amino acid usage and tissue specific expression level of genes. The findings can be significant for understanding the translational selection on these features. The selection may play an important role in the differentiation of human tissues and can be considered for future studies in diagnosis of some diseases such as cancer.

• BMB Reports
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• v.42 no.11
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• pp.705-712
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• 2009

Our understanding of the relationships between genes, brains, and behaviors has changed a lot since the first behavioral mutants were isolated in the fly bottles of the Benzer lab at Caltech (1), but Drosophila is still an excellent model system for studying the neurobiology of behavior. Recent advances provide an unprecedented level of control over fly neural circuits. Efforts are underway to add to existing GAL4-driver lines that permit exogenous expression of genetic tools in small populations of neurons. Combining these driver lines with a variety of inducible UAS lines permits the visualization of neuronal morphology, connectivity, and activity. These driver lines also make it possible to specifically ablate, inhibit, or activate subsets of neurons and assess their roles in the generation of behavioral responses. Here, I will briefly review the extensive arsenal now available to drosophilists for investigating the neuronal control of behavior.