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

• IMMUNE NETWORK
• /
• v.3 no.3
• /
• pp.227-234
• /
• 2003

Background: Immunoglobulin (Ig) light chain repertoire has been implicated as a critical determinant in regulation of autoreactive B cells and production of pathogenic anti-DNA antibodies in systemic lupus erythematosus (SLE). We analyzed the impact of Ig ${\lambda}$ chain repertoire on development of autoimmunity in patients with SLE. Methods: We obtained genomic DNA from individual peripheral CD19+ B cells of 3 untreated active SLE patients, and amplified $V{\lambda}$ rearrangements from each single cell by polymerase chain reaction. Results: A total number of 208 $V{\lambda}J{\lambda}$ rearrangements were analyzed. Analyzed sequences included 158 productive rearrangements and 50 nonproductive rearrangements. The differences in $V{\lambda}$ gene usage in the productive and nonproductive repertoire of SLE patients were found compared to the non-autoimmune individuals. $V{\lambda}$ gene, 9A was significantly overrepresented in nonproducative repertoire of SLE patients (P=0.016). In the productive repertoire, $V{\lambda}$ genes, 3L and 1E were found more often in the SLE patients (P=0.001, P=0.043). When the productive and the nonproductive repertoires were compared, 9A was found significantly less in the productive repertoire in the SLE patients (P=0.000). There were no significant differences in the $J{\lambda}$ gene usage between SLE patients and non-autoimmune individuals, but $J{\lambda}2/3$ gene was the most frequently used in SLE, whereas $J{\lambda}7$ gene was the most frequently used in the normal subjects. In the productive SLE $V{\lambda}$ repertoire, 9.4% of the total sequences employed identical CDR3. It was particularly striking to find 7 identical versions of the 1G-$J{\lambda}2/3$ $V{\lambda}J{\lambda}$ rearrangements from one patient and 3 of the same sequence from another patient. Notably, identical $V{\lambda}$ junctions in the SLE patients utilized significantly more homologous joining compared to $V{\lambda}$ junctions of the normal adults (P=0.044). Conclusion: These data demonstrate regulation of ${\lambda}$ light chain expression in the SLE patients by selection of unique $V{\lambda}$ genes. Also, biased selection and clonal expansion of particular $V{\lambda}$ rearrangements are apparent in the SLE ${\lambda}$ repertoire.

• Journal of Korean Neurosurgical Society
• /
• v.64 no.4
• /
• pp.505-513
• /
• 2021

Objective : The adaptive immune response following subarachnoid hemorrhage (SAH) is not well understood. We evaluated and compared the T cell receptor (TCR) immune repertoire of good-grade and poor-grade SAH patients to elucidate the T cell immunology after ictus. Methods : Peripheral blood from six SAH patients was collected at two different times, admission and at the 7-day follow-up. Composition and variation of the TCR β-chain (TCRB) complimentary determining regions (CDR) 3 repertoire was examined using high-throughput sequencing; the analysis was based on sampling time and disease severity (good vs. poor-grade SAH). Results : Clonality at admission and follow-up were 0.059 (0.037-0.038) and 0.027 (0.014-0.082) (median, 25th-75th percentile). Poor-grade SAH (0.025 [0.011-0.038]) was associated with significantly lower clonality than good-grade SAH (0.095 [0.079-0.101]). Poor-grade SAH patients had higher diversity scores than good-grade SAH patients. CDR length was shorter in good-grade SAH vs. poor-grade SAH. Differences in clonotype distribution were more prominent in TCRBV gene segments than TCRBJ segments. TCRBV19-01/TCRBJ02-04 and TCRBV28-01/TCRBJ02-04 were the most increased and the most decreased V-J pairs in the 7-day follow-up compared to admission in good-grade SAH. The most increased and decreased V-J pairs in poor-grade SAH patients were TCRBV28-01/TCRBJ02-06 and TCRBV30-01/TCRBJ02-04, respectively. Conclusion : The TCRB repertoire is dynamic in nature following SAH. TCRB repertoire may facilitate our understanding of adaptive immune response according to SAH severity.

• Animal cells and systems
• /
• v.9 no.2
• /
• pp.47-55
• /
• 2005

Avian vocalization has been main topics in studying animal communication. The structure and usage as well as development and function of vocalization vary enormously among species and even among populations, and thus we reviewed the general patterns of song learning and the consequences of song communication in birds at the behavioural level: first, we compared the different learning phenomena between non-songbird and songbird, and we investigated the learning process of songbird both in the field and in the lab, which are needed to fully understand vocal communication. Second, we discussed a recent trend of sexual selection hypothesis explaining the structural and functional diversity of song in songbirds with repertoire and presented how the repertoire is actually used between neighbours based on individual recognition.

• Animal cells and systems
• /
• v.13 no.1
• /
• pp.91-96
• /
• 2009

The size of song repertoires mainly provides evidence for explaining sexual selection for female choice as well as male-male competition. We investigated the role of oriental great reed warbler songs (Acrocephalus orientalis) of breeding territorial males. Early arrived males possessed larger song repertoires, paired earlier, and tended to become polygynous. No correlation was found between arrival date and territory size, but polygynous males significantly occupied larger territories than non polygynous males. Song sharing was low among males and the degree of similarity did not relate with spatial distance. Our results suggest that song repertoire of the oriental great reed warbler males play a role in female choice, where territory quality may affect male pairing success.

• The Journal of Society for e-Business Studies
• /
• v.26 no.4
• /
• pp.133-154
• /
• 2021

Today smart phone is the most common media with a vehicle called 'application'. In order to understand how media users select applications and build their repertoire, this study conducted two-step approach using big data from smart phone log for 4 weeks in November 2019, and finally classified 8 media repertoire groups. Each of the eight media repertoire groups showed differences in time spent of mobile application category compared to other groups, and also showed differences between groups in demographic distribution. In addition to the academic contribution of identifying the mobile application repertoire with large scale behavioral data, this study also has significance in proposing a two-step approach that overcomes 'outlier issue' in behavioral data by extracting prototype vectors using SOM (Sefl-Organized Map) and applying it to k-means clustering for optimization of the classification. The study is also meaningful in that it categorizes customers using e-commerce services, identifies customer structure based on behavioral data, and provides practical guides to e-commerce communities that execute appropriate services or marketing decisions for each customer group.

• The Journal of the Korea Contents Association
• /
• v.15 no.2
• /
• pp.196-207
• /
• 2015

This study introduced the concept of 'Media-content repertoire', which indicates the set of favorite media-content combinations of media users and extracted five media user types based on those combinations. We used the range of media(i.e., smartphone, tablet, PC, and TV) and entertainment content(i.e., movie, broadcasting, music, and game) for the analysis. Also, we investigated the differences between those types including demographic variables, individual characteristics, and content buying behavior and we found that statistically significant differences exist among them. Those include 'non-user'(i.e., lower level of media use), 'screen user'(i.e., 50s, TV-centered media use), 'variety seeker'(i.e., 20s. heavy public transport user), 'selective focus'(i.e., 20,30s, movie&broadcasting-centered media use), and 'heavy user'(i.e., high level of media use and consumption). The results provide both academic implications(e.g., extension of media repertoire concept) and practical implications(e.g., direction to the target marketing for each user type).

• The Journal of the Korea Contents Association
• /
• v.18 no.11
• /
• pp.13-29
• /
• 2018

An increasing number of people in their lifes have used personal web-casting services as a new type of broadcasting, whose power has grown in the broadcasting market and industry. Nevertheless, limited research concerning personal web-casting has been conducted so far. This research explored consumption structures of personal web-casting users in terms of their genre usage based on the theoretical concept of genre repertoire. And it also examined what determinants have influences on these structures by focusing on as an representative case in South Korea. The findings showed that sensation seeking, motivation for getting information and social presence affect genre repertoire of personal web-casting users. They also indicated that there is a moderating effect of social presence in the relationship between motivation for joy and genre repertoire.

• ALGAE
• /
• v.35 no.2
• /
• pp.133-144
• /
• 2020

Pythium porphyrae is responsible for devastating outbreaks in seaweed farms of Pyropia, the most valuable cultivated seaweed worldwide. While the genus Pythium contains many well studied pathogens, the genome of P. porphyrae has yet to be sequenced. Here we report the first available gene repertoire of P. porphyrae and a preliminary analysis of pathogenicity-related genes. Using ab initio detection strategies, similarity based and manual annotation, we found that the P. porphyrae gene repertoire is similar to classical phytopathogenic Pythium species. This includes the absence of expanded RxLR effector family and the detection of classical pathogenicity-related genes like crinklers, glycoside hydrolases, cellulose-binding elicitor lectin-like proteins and elicitins. We additionally compared this dataset to the proteomes of 8 selected Pythium species. While 34% of the predicted proteome appeared specific to P. porphyrae, we could not attribute specific enzymes to the degradation of red algal biomass. Conversely, we detected several cellulases and a cutinase conserved with plant-pathogenic Pythium species. Together with the recent report of P. porphyrae triggering disease symptoms on several plant species in lab-controlled conditions, our findings add weight to the hypothesis that P. porphyrae is a reformed plant pathogen.

• Clinical and Experimental Vaccine Research
• /
• v.13 no.1
• /
• pp.1-9
• /
• 2024

Since the 1950s decade, it has been suggested that a naturally produced or induced repertoire of immunoglobulin G (IgG) idiotypes may exert some immunoregulatory functions. In the last decades, some more advanced theories have suggested that the repertoire of IgG idiotypes may influence the development or control of some atopic diseases. In atopic dermatitis (AD), some evidence indicated that the IgG repertoire obtained from these patients could effectively mediate regulatory functions on thymic and peripheral CD4+ and CD8+ T cells. Furthermore, some recent clinical trials have corroborated the hypothesis that IgG from AD patients can exert regulatory functions in vivo. Here, we revised some historical aspects that yield current approaches developed in vitro and in vivo to elucidate a recently proposed theory termed "hooks without bait" that can strengthen the broad spectrum of research about evaluating different sets of IgG idiotypes and determine their immunological effects.