• 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.

• ALGAE
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• v.29 no.4
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• pp.279-288
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• 2014

Red algal parasites are common within red algae and are mostly closely related to their hosts, but have a reduced habit. In the past, red algal parasites, due to their reduced morphology, have been given distinct generic names, even though they are often phylogenetically nested in their host's genus. This is a problem nomenclaturally for maintenance of a taxonomy based on monophyly. This study investigates the morphology, genetic variation and distribution of an undescribed red algal parasite growing on its host Rhodophyllis membranacea, widely distributed throughout New Zealand. Microscopy, molecular markers (plastid, mitochondrial, nuclear), and herbarium investigation were used to investigate this species. The parasite is widely distributed throughout New Zealand. All molecular markers clearly show that the parasite is almost identical to the host, even though morphologically quite distinct from members of the host genus. We believe that to maintain monophyly of Rhodophyllis the parasite should be described as a new species of Rhodophyllis, Rhodophyllis parasitica sp. nov. We also recommend that in order to maintain generic monophyly most red algal parasite genera should also be transferred to their host genus.

• Journal of Soil and Groundwater Environment
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• v.17 no.6
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• pp.23-32
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• 2012

This study was conducted to monitor microbial species dynamics within the aquifer due to long term operation of geothermal heat pump system. The species were identified by molecular biological methods of 16S rDNA. Groundwater sample was collected from both open (S region) and closed geothermal recovery system (J region) along with the control. J measured and control as well as S measured found Ralstonia pickettii as dominant species at year 2010. In contrast, Rhodoferax ferrireducens was dominantly observed for the control of S. In 2011, Sediminibacterium sp. was universely identified as the dominant species regardless of the monitoring places and type of sample, i.e., measured or control. The difference in the dynamics between the measured and the control was not critically observed, but annual variation was more strikingly found. It reveals that possible environmental changes (e.g. ORP and DO) due to the operation of geothermal heat recovery system in aquifer could be more exceedingly preceded to differentiate annual variation of microbial species rather than positional differences.

• Korean Journal of Biological Psychiatry
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• v.13 no.3
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• pp.152-161
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• 2006

Objective : The relationship between the total daily dose of clozapine given and the plasma concentrations of clozapine and its metabolites(N-desmethylclozapine and clozapine N-oxide) and the effect of Glu158Lys (wild-type : Glu, 'H' ; variant : Lys, 'h') and Glu308Gly(wild-type : Glu, 'D' ; variant : Lys, 'd') variation in FMO3 gene on plasma concentrations of clozapine and its metabolites was studied in schizophrenic patients. Methods : Trough plasma concentrations of clozapine and its metabolites were measured in 34 schizophrenic patients receiving clozapine. The genetic variation of 'h' and 'd' in FMO3 were analyzed in 21 among 34 patients. Results : A linear relationship between the total daily dose of clozapine given(mg/kg body weight per day) and the plasma concentrations(nM) of clozapine was revealed by regression analysis(p<0.001) in the 23 patients receiving a constant daily dose of clozapine for 8 days. The plasma molar concentration ratios of clozapine N-oxide/clozapine in 8 subjects with 'hh' or 'Hh' alleles were not different from those in 6 subjects with 'HH' alleles and the plasma molar concentration ratios in 6 subjects with 'dd' or 'Dd' alleles were not different from those in 8 subjects with 'DD' alleles. Conclusion : The effect of Glu158Lys and Glu308Gly variation in FMO3 gene on clozapine metabolism could not be shown.

• Journal of Ginseng Research
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• v.35 no.3
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• pp.368-374
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• 2011

American ginseng (Panax quinquefolius L.) is grown in some regions of the USA and Canada and marketed for its health promoting attributes. While cultivation of this plant species has taken place in North America for over 100 years, there are many challenges that need to be addressed. In this article, the current production method used by growers is described and the challenges and opportunities for research on this valuable plant are discussed. These include studies on pharmacological activity, genetic diversity within the species, genetic improvement of currently grown plants, molecular characterization of gene expression, and management of diseases affecting plant productivity. The current research developments in these areas are reviewed and areas requiring further work are summarized. Additional research should shed light on the nature of the bioactive compounds and their clinical effects, and the molecular basis of active ingredient biosynthesis, and provide more uniform genetic material as well as improved plant growth, and potentially reduce losses due to pathogens.

• Korean Journal of Plant Resources
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• v.22 no.3
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• pp.242-247
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• 2009

Randomly Amplified Polymorphic DNA (RAPD) was performed to define the genetic variation and relationships of Artemisia capillaris. Fifteen populations by the distributions and habitat were collected to conduct RAPD analysis. RAPD markers were observed mainly between 300bp and 1600bp. Total 72 scorable markers from 7 primers were applied to generate the genetic matrix, and 69 bands were polymorphic and only 3 bands were monomorphic. The genetic dissimilarity matrix by Nei's genetic distance (1972) and UPGMA phenogram were produced from the data matrix. Populations of Artemisia capillaris were clustered with high genetic affinities and cluster patterns were correlated with distributional patterns. Two big groups were clustered as southern area group and middle area group. The closest OTUs were GW2 and GG1 in middle area group, and GB1 from southern area group was clustered with OTUs in middle area group. RAPD data was useful to define the genetic variations and relationships of A. capillaris.

• BMB Reports
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• v.30 no.3
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• pp.216-221
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• 1997

Changes in pathogenicity of old and successively-cultured isolates of Fusarium oxysporum f. sp. niveum have been observed and the concept that such cultures will become attenuated is generally accepted. However, the genetic basis for this phenomenon has not been studied. In an effort to identify a DNA marker closely linked to variations, DNA methylation was investigated both before and after the successive transfers of F. o. f. sp. niveum isolates on artificial media. A sector of mycelium in F. o. f. sp. niveum race 2 isolate (TXXID) which showed variation in pigmentation and colonial morphology occurred after 18 successive weekly transfers on potato dextrose agar (PDA). The sector characteristics were stable and did not change after more successive transfers. It was shown that DNA methylation preexists in ribosomal RNA gene (rDNA) of F. o. f. sp. niveum and that additional changes in DNA methylation occurred during successive culturing.

• BMB Reports
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• v.50 no.1
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• pp.3-4
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• 2017

Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found genetic evidence that genomes represent what animals eat through modifying genes. Highly conserved genetically relevant regions were discovered in genomes at the family level. Also, the Felidae family genomes exhibited low levels of genetic diversity associated with decreased population sizes, presumably because of their strict diet, suggesting their vulnerability and critical conservation status. Our findings can be used for human health enhancement, since we share the same genes as cats with some variation. This is an example how wildlife genomes can be a critical resource for human evolution, providing key genetic marker information for disease treatment.

• The Korean Journal of Nuclear Medicine
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• v.38 no.2
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• pp.143-151
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• 2004

Recent progress in the development of non-invasive imaging technologies continues to strengthen the role of molecular imaging biological research. These tools have been validated recently in variety of research models, and have been shown to provide continuous quantitative monitoring of the location(s), magnitude, and time-variation of gene expression. This article reviews the principles, characteristics, categories and the use of radionuclide reporter gene imaging technologies as they have been used in imaging cell trafficking, imaging gene therapy, imaging endogenous gene expression and imaging molecular interactions. The studios published to date demonstrate that reporter gene imaging technologies will help to accelerate pre-clinical model validation as well as allow for clinical monitoring of human diseases.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.12 no.3
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• pp.225-233
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• 2007

To verify which loop regions of 18S rRNA gene are suitable as species-specific genetic markers in ciliates, we analyzed the genetic variation of 18S rRNA gene among 9 Euplotes species (Hypotrichia : Ciliophora). In our result, no inter-specific variation was detected from V1, V3 and V5 regions, and the length of V7 and V8 are 44 bp and 79 bp, respectively, which are too short to make genetic marker. In contrast, V2 and V4 may be good candidate segments of species-specific diagnostic molecular markers because these two regions are most variable ($1.75{\sim}20.61%$) and showed good inter-specific phylogeny. Furthermore, the sequences of V2 and V4 are 123 bp and 306 bp, respectively in length which are enough to make species-specific marker.