• Journal of Sensor Science and Technology
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• v.21 no.5
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• pp.359-366
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• 2012

Nanopore DNA sequencing is an emerging and promising technique that can potentially realize the goal of a low-cost and high-throughput method for analyzing human genome. Especially, solid-state nanopores have relatively high mechanical stability, simple surface modification, and facile fabrication process without the need for labeling or amplification of PCR (polymerized chain reaction) in DNA sequencing. For these advantages of solid-sate nanopores, the use of solid-state nanopores has been extensively considered for developing a next generation DNA sequencing technology. Solid-state nanopore sequencing technique can determine and count charged molecules such as single-stranded DNA, double-stranded DNA, or RNA when they are driven to pass through a membrane nanopore between two electrolytes of cis-trans chambers with applied bias voltage by measuring the ionic current which varies due to the existence of the charged particles in the nanopore. Recently, many researchers have suggested that nanopore-based sensors can be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000.

• The Plant Pathology Journal
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• v.38 no.5
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• pp.503-512
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• 2022

Lilies (Lilium spp.) are one of the most important ornamental flower crops grown in Korea. Most viral diseases in lilies are transmitted by infected bulbs, which cause serious economic losses due to reduced yields. Various diagnostic techniques and high-throughput sequencing methods have been used to detect lily viruses. According to Oxford Nanopore Technologies (ONT), MinION is a compact and portable sequencing device. In this study, three plant viruses, lily mottle, lily symptomless, and plantago asiatica mosaic virus, were detected in lily samples using the ONT platform. As a result of genome assembly of reads obtained through ONT, 100% coverage and 90.3-93.4% identity were obtained. Thus, we show that the ONT platform is a promising tool for the diagnosis and characterization of viruses that infect crops.

• The Plant Pathology Journal
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• v.39 no.3
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• pp.303-308
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• 2023

The global climate change and international trade have facilitated the movement of plants across borders, increasing the risk of introducing novel plant viruses in new territories. Ixora coccinea exhibited virus-like foliar symptoms, including mosaic and mild mottle. An Oxford Nanopore Technologies-based compact and portable MinION platform was used to identify the causal viral pathogen. The complete genome sequence of jasmine virus H (JaVH; 3867 nt, JaVH-CNU) was determined and found to share 88.4-90.3% nucleotide identity with that of Jasminum sambac JaVH isolate in China. Phylogenetic analysis based on the complete amino acid sequences of RNA-dependent RNA polymerase and coat protein revealed that JaVH-CNU was grouped separately with other JaVH isolates. This is the first report of a natural JaVH infection of I. coccinea. The application of rapid nanopore sequencing for plant virus identification was demonstrated and is expected to provide accurate and rapid diagnosis for virus surveillance.

• Journal of Veterinary Science
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• v.25 no.3
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• pp.44.1-44.13
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• 2024

Importance: The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics. Objective: This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia. Methods: Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder. Results: Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%. Conclusions and Relevance: The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.

• Genomics & Informatics
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• v.16 no.4
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• pp.30.1-30.6
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• 2018

There is urgent need for effective and cost-efficient data storage, as the worldwide requirement for data storage is rapidly growing. DNA has introduced a new tool for storing digital information. Recent studies have successfully stored digital information, such as text and gif animation. Previous studies tackled technical hurdles due to errors from DNA synthesis and sequencing. Studies also have focused on a strategy that makes use of 100-150-bp read sizes in both synthesis and sequencing. In this paper, we a suggest novel data encoding/decoding scheme that makes use of long-read DNA (~1,000 bp). This enables accurate recovery of stored digital information with a smaller number of reads than the previous approach. Also, this approach reduces sequencing time.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.188-199
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• 2018

Genomic epidemiology exploits various basic microbial research areas. High-throughput sequencing technologies dramatically have been expanding the number of microbial genome sequences available. Abundant genomic data provide an opportunity to perform strain typing more effectively, helping identify microbial species and strains at a higher resolution than ever before. Genomic epidemiology needs to find antimicrobial resistance genes in addition to standard genome annotations. Strain typing and antimicrobial resistance gene finding are static aspects of genomic epidemiology. Finding which hosts infected which other hosts requires the inference of transient transmission routes among infected hosts. The strain typing, antimicrobial resistance gene finding, and transmission tree inference would allow for better surveillance of microbial infectious diseases, which is one of the ultimate goals of genomic epidemiology. Among several high-throughput sequencing technologies, genomic epidemiology will benefit from the more portability and shorter sequencing time of the Oxford Nanopore Technologies's MinION, the third-generation sequencing technology. Here, this study reviewed computational methods for quantifying antimicrobial resistance genes and inferring disease transmission trees. In addition, the MinION's applications to genomic epidemiology were discussed.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.415.1-415.1
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• 2014

Carrying out first-principles calculations, we study N-doped capped carbon nanotube (CNT) electrodes applied to DNA sequencing. While we obtain for the face-on nucleobase junction configurations a conventional conductance ordering where the largest signal results from guanine according to its high highest occupied molecular orbital (HOMO) level, we extract for the edge-on counterparts a distinct conductance ordering where the low-HOMO thymine provides the largest signal. The edge-on mode is shown to operate based on a novel molecular sensing mechanism that reflects the chemical connectivity between N-doped CNT caps that can act both as electron donors and electron acceptors and DNA functional groups that include the hyperconjugated thymine methyl group[1].

• Mycobiology
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• v.51 no.6
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• pp.452-462
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• 2023

Opportunistic infections due to Cryptococcus neoformans and C. gattii species complexes continue to rise unabated among HIV/AIDS patients, despite improved antifungal therapies. Here, we collected a total of 20 environmental and 25 presumptive clinical cryptococcal isolates from cerebrospinal fluid (CSF) samples of 175 patients enrolled in an ongoing clinical trial Ambition 1 Project (Botswana-Harvard Partnership). Identity confirmation of the isolates was done using MALDI-TOF MS and PCR. We describe the diversity of the isolates by PCR fingerprinting and sequencing (Oxford Nanopore Technology) of the intergenic spacer region. Mating types of the isolates were determined by amplification of the MAT locus. We report an unusual prevalence of 42.1% of C. neoformans × C. deneoformans hybrids Serotype AD (n = 16), followed by 39.5% of C. neoformans Serotype A (n = 15), 5.3% of C. deneoformans, Serotype D (n = 2), 7.9% of C. gattii (n = 3), and 5.3% of C. tetragattii (n = 2) in 38 representative isolates that have been characterized. Mating type-specific PCR performed on 38 representative environmental and clinical isolates revealed that 16 (42.1%) were MATa/MAT𝛼 hybrids, 17 (44.7%) were MAT𝛼, and five (13.2%) possessed MATa mating type. We used conventional and NGS platforms to demonstrate a potential link between environmental and clinical isolates and lay a foundation to further describe mating patterns/history in Botswana.

• Korean Journal of Environmental Biology
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• v.30 no.2
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• pp.77-89
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• 2012

With the advent of the genomics era powered by DNA sequencing technologies, life science is being transformed significantly and biological research and development have been accelerated. Environmental biology concerns the relationships among living organisms and their natural environment, which constitute the global biogeochemical cycle. As sustainability of the ecosystems depends on biodiversity, examining the structure and dynamics of the biotic constituents and fully grasping their genetic and metabolic capabilities are pivotal. The high-speed high-throughput next-generation sequencing can be applied to barcoding organisms either thriving or endangered and to decoding the whole genome information. Furthermore, diversity and the full gene complement of a microbial community can be elucidated and monitored through metagenomic approaches. With regard to human welfare, microbiomes of various human habitats such as gut, skin, mouth, stomach, and vagina, have been and are being scrutinized. To keep pace with the rapid increase of the sequencing capacity, various bioinformatic algorithms and software tools that even utilize supercomputers and cloud computing are being developed for processing and storage of massive data sets. Environmental genomics will be the major force in understanding the structure and function of ecosystems in nature as well as preserving, remediating, and bioprospecting them.

• BMB Reports
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• v.55 no.7
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• pp.305-315
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• 2022

Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of 'Dissociation (Dc) locus' by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.