Publications by authors named "Wonseok Shin"

25 Publications

  • Page 1 of 1

High-accuracy quantitative principle of a new compact digital PCR equipment: Lab On An Array.

Genomics Inform 2021 Sep 30;19(3):e34. Epub 2021 Sep 30.

Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea.

Digital PCR (dPCR) is the third-generation PCR that enables real-time absolute quantification without reference materials. Recently, global diagnosis companies have developed new dPCR equipment. In line with the development, the Lab On An Array (LOAA) dPCR analyzer (Optolane) was launched last year. The LOAA dPCR is a semiconductor chip-based separation PCR type equipment. The LOAA dPCR includes Micro Electro Mechanical System that can be injected by partitioning the target gene into 56 to 20,000 wells. The amount of target gene per wells is digitized to 0 or 1 as the number of well gradually increases to 20,000 wells because its principle follows Poisson distribution, which allows the LOAA dPCR to perform precise absolute quantification. LOAA determined region of interest first prior to dPCR operation. To exclude invalid wells for the quantification, the LOAA dPCR has applied various filtering methods using brightness, slope, baseline, and noise filters. As the coronavirus disease 2019 has now spread around the world, needs for diagnostic equipment of point of care testing (POCT) are increasing. The LOAA dPCR is expected to be suitable for POCT diagnosis due to its compact size and high accuracy. Here, we describe the quantitative principle of the LOAA dPCR and suggest that it can be applied to various fields.
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http://dx.doi.org/10.5808/gi.21035DOI Listing
September 2021

Diagnostic evaluation of qRT-PCR-based kit and dPCR-based kit for COVID-19.

Genes Genomics 2021 11 15;43(11):1277-1288. Epub 2021 Sep 15.

Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea.

Background: Coronavirus disease of 2019 (COVID-19) is well known as a fatal disease, first discovered at Wuhan in China, ranging from mild to death, such as shortness of breath and fever. Early diagnosis of COVID-19 is a crucial point in preventing global prevalence.

Objective: We aimed to evaluate the diagnostic competency and efficiency with the Allplex™ 2019-nCoV Assay kit and the Dr. PCR 20 K COVID-19 Detection kit, designed based on the qRT-PCR and dPCR technologies, respectively.

Methods: A total of 30 negative and 20 COVID-19 positive specimens were assigned to the diagnostic test by using different COVID-19 diagnosis kits. Diagnostic accuracy was measured by statistical testing with sensitivity, specificity, and co-efficiency calculations.

Results: Comparing both diagnostic kits, we confirmed that the diagnostic results of 30 negative and 20 positive cases were the same pre-diagnostic results. The diagnostic statistics test results were perfectly matched with value (1). Cohen's Kappa coefficient was demonstrated that the given kits in two different ways were "almost perfect" with value (1). In evaluating the detection capability, the dilutional linearity experiments substantiate that the Dr. PCR 20 K COVID-19 Detection kit could detect SARS-CoV-2 viral load at a concentration ten times lower than that of the Allplex™ 2019-nCoV Assay kit.

Conclusions: In this study, we propose that the dPCR diagnosis using LOAA dPCR could be a powerful method for COVID-19 point-of-care tests requiring immediate diagnosis in a limited time and space through the advantages of relatively low sample concentration and small equipment size compared to conventional qRT-PCR.
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http://dx.doi.org/10.1007/s13258-021-01162-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8441239PMC
November 2021

Post-vaccination Monitoring to Assess Foot-and-Mouth Disease Immunity at Population Level in Korea.

Front Vet Sci 2021 4;8:673820. Epub 2021 Aug 4.

Foot and Mouth Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon-si, South Korea.

In South Korea, domestic cattle, pigs, and goats were subjected to mandatory foot-and-mouth disease (FMD) vaccination and year-round serosurveillance since 2011. In 2020, approximately USD 95 million was spent solely for FMD vaccine purchase for 59 million livestock, and 1.25 million samples were tested to estimate the population immunity and demonstrate the absence of virus circulation. As the FMD vaccination program was revised in 2018, the post-vaccination monitoring (PVM) was designed to evaluate the effectiveness of the vaccine program of three vaccines approved for routine use. To this end, monitoring post-vaccination immunity has been conducted by collecting 35,626 serum samples at 28 days post-vaccination following regular national vaccinations, which were carried out in April and in October in 2020. The design of the serological test for PVM was specially targeted at particular livestock groups, including dairy cattle, goats, and beef cattle aged 6-12 months, which were generally estimated to have a low expected seroprevalence. The risk factors had also been identified, considering the increased likelihood of infection in a particular location, herd size, and husbandry system applied in a targeted sample collection. Serum sample collection and SP-O and NSP antibody tests were performed by local veterinary laboratories using commercially available ELISAs. The current FMD vaccination program, which was performed twice a year following the regimen of primary vaccination and boost, resulted in over 80% population immunity. The seroprevalence monitored after the vaccination in fall was higher than the one studied in spring except in pigs. It was demonstrated that the seroprevalence of risk-based targeted samples ranged from 93.8 to 100% in cattle, 63.2 to 100% in pigs, and 20.0 to 100% in goats. Of note is the area near the North Korean borders which showed a relatively low seroprevalence among the targeted regions, and no NSP sero-positive reactor was detected in this region. When subpopulation immunity at the individual level was assessed, the seroprevalence in young cattle stock was slightly lower (95.8%) than that of adults (98.4%). In conclusion, the FMD vaccination campaign has been successfully implemented in Korea, and the PVM can be a supplementary program for massive routine surveillance in terms of providing timely information needed both to estimate population immunity and to properly target "risk-based surveillance."
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http://dx.doi.org/10.3389/fvets.2021.673820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371437PMC
August 2021

Differential expressions of L1-chimeric transcripts in normal and matched-cancer tissues.

Anal Biochem 2020 07 8;600:113769. Epub 2020 May 8.

Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea; NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea; Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. Electronic address:

L1s are a cis-regulatory elements and contain bidirectional internal promoters within the 5' untranslated region (UTR). L1s provide bidirectional promoters that generate alternative transcripts and affect differential expressions in the human genome. In particular, L1 antisense promoters (L1ASPs) could produce aberrant transcripts in cancer tissues compared to normal tissues. In this study, we identified the L1-chimeric transcripts derived from L1ASPs and analyzed relative expression of L1-chimeric transcripts between normal and matched-cancer tissues. First, we collected 425 L1-chimeric transcripts by referring to previous studies. Through the manual inspection, we identified 144 L1-chimeric transcripts derived from 44 L1 antisense promoters, suggesting that the antisense promoter acted as an alternative promoter. We analyzed relative gene expression levels of 16 L1-chimeric transcripts between matched cancer-normal tissue pair (lung, liver, gastric, kidney, thyroid, breast, ovary, uterus, and prostate) using real-time quantitative PCR (RT-qPCR) and investigated putative transcription factor binding motifs to determine activity of L1ASPs. Taken together, we propose that L1ASPs could contribute to the differential gene expression between normal and cancer tissues.
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http://dx.doi.org/10.1016/j.ab.2020.113769DOI Listing
July 2020

Quantitative evaluation of the molecular marker using droplet digital PCR.

Genomics Inform 2020 Mar 31;18(1):e4. Epub 2020 Mar 31.

Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea.

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE-association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.
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http://dx.doi.org/10.5808/GI.2020.18.1.e4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120350PMC
March 2020

Application of NanoString technologies in angioimmunoblastic T cell lymphoma.

Genes Genomics 2020 04 7;42(4):485-494. Epub 2020 Mar 7.

Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Background: Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive disease. Most cancer diagnoses are determined by anatomical histology. Therefore, many samples are stored in FFPE blocks for H&E staining. However, RNAs extracted from the FFPE block have a high level of fragmentation, making it difficult to perform accurate DEG analysis using RNA sequencing.

Objective: To overcome fragmented RNA's drawback in NGS application, we applied the NanoString nCounter technique of hybridization method that can be used for DEG analysis without PCR amplification.

Methods: We characterized the gene expression profiling of AITLs though transcriptome analysis based on the nCounter PanCancer IO 360™ Panel and NanoString platform. To perform the analysis of differential expression gene (DEG) profiles in AITLs, we compared the NanoString data from eight AITL patients with a healthy control donor.

Results: Ninety-one genes were up-regulated and six genes were down-regulated in AITLs compared to control. The Gene Ontology (GO) analysis of 97-DEGs revealed that they were closely related to cytokine, MAPK cascade, leukocyte differentiation, and immune response, suggesting that this affect the immune system. In addition, KEGG analysis revealed that AITL DEGs were found to be highly involved in cytokine-cytokine receptor interaction and PI3K-Akt signaling pathway.

Conclusion: We believe that comprehensive multiplex studies, along with NanoString analysis, may be helpful to understand the molecular mechanisms of AITL, including mutations, gene expression, and protein expression studies.
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http://dx.doi.org/10.1007/s13258-020-00919-7DOI Listing
April 2020

Impact of Sleep Disorder as a Risk Factor for Dementia in Men and Women.

Biomol Ther (Seoul) 2020 Jan;28(1):58-73

College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea.

Sleep is an essential physiological process, especially for proper brain function through the formation of new pathways and processing information and cognition. Therefore, when sleep is insufficient, this can result in pathophysiologic conditions. Sleep deficiency is a risk factor for various conditions, including dementia, diabetes, and obesity. Recent studies have shown that there are differences in the prevalence of sleep disorders between genders. Insomnia, the most common type of sleep disorder, has been reported to have a higher incidence in females than in males. However, sex/gender differences in other sleep disorder subtypes are not thoroughly understood. Currently, increasing evidence suggests that gender issues should be considered important when prescribing medicine. Therefore, an investigation of the gender-dependent differences in sleep disorders is required. In this review, we first describe sex/gender differences not only in the prevalence of sleep disorders by category but in the efficacy of sleep medications. In addition, we summarize sex/gender differences in the impact of sleep disorders on incident dementia. This may help understand gender-dependent pathogenesis of sleep disorders and develop therapeutic strategies in men and women.
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http://dx.doi.org/10.4062/biomolther.2019.192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939686PMC
January 2020

Comparison of library construction kits for mRNA sequencing in the Illumina platform.

Genes Genomics 2019 10 26;41(10):1233-1240. Epub 2019 Jul 26.

Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Background: The emergence of next-generation sequencing (NGS) technologies has made a tremendous contribution to the deciphering and significance of transcriptome analysis in biological fields. Since the advent of NGS technology in 2007, Illumina, Inc. has provided one of the most widely used sequencing platforms for NGS analysis.

Objective: Although reagents and protocols provided by Illumina are adequately performed in transcriptome sequencing, recently, alternative reagents and protocols which are relatively cost effective are accessible. However, the kits derived from various manufacturers have advantages and disadvantages when researchers carry out the transcriptome library construction.

Methods: We compared them using a variety of protocols to produce Illumina-compatible libraries based on transcriptome. Three different mRNA sequencing kits were selected for this study: TruSeq RNA Sample Preparation V2 (Illumina, Inc., USA), Universal Plus mRNA-Seq (NuGEN, Ltd., UK), and NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ltd., USA). We compared them focusing on cost, experimental time, and data output.

Results: The quality and quantity of sequencing data obtained through the NGS technique were strongly influenced by the type of the sequencing library kits. It suggests that for transcriptome studies, researchers should select a suitable library construction kit according to the goal and resources of experiments.

Conclusion: The present work will help researchers to choose the right sequencing library construction kit for transcriptome analyses.
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http://dx.doi.org/10.1007/s13258-019-00853-3DOI Listing
October 2019

Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method.

Mol Cells 2019 Jan 6;42(1):87-95. Epub 2018 Dec 6.

Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea.

Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.
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http://dx.doi.org/10.14348/molcells.2018.0351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354063PMC
January 2019

Inverse design of large-area metasurfaces.

Opt Express 2018 Dec;26(26):33732-33747

We present a computational framework for efficient optimization-based "inverse design" of large-area "metasurfaces" (subwavelength-patterned surfaces) for applications such as multi-wavelength/multi-angle optimizations, and demultiplexers. To optimize surfaces that can be thousands of wavelengths in diameter, with thousands (or millions) of parameters, the key is a fast approximate solver for the scattered field. We employ a "locally periodic" approximation in which the scattering problem is approximated by a composition of periodic scattering problems from each unit cell of the surface, and validate it against brute-force Maxwell solutions. This is an extension of ideas in previous metasurface designs, but with greatly increased flexibility, e.g. to automatically balance tradeoffs between multiple frequencies or to optimize a photonic device given only partial information about the desired field. Our approach even extends beyond the metasurface regime to non-subwavelength structures where additional diffracted orders must be included (but the period is not large enough to apply scalar diffraction theory).
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http://dx.doi.org/10.1364/OE.26.033732DOI Listing
December 2018

Investigation of Hanwoo-specific structural variations using whole-genome sequencing data.

Genes Genomics 2019 02 8;41(2):233-240. Epub 2018 Dec 8.

Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Background: The total length of the cattle genome is approximately ~ 3 billion base pairs. About half of the bovine genome (46.5%) is composed of transposable elements (TEs). The TEs could be a major source of genomic structural variations (SVs) between cattle breeds. These SVs have led to genomic fluidity and rearrangements between interspecies.

Objective: TE-mediated insertion and deletion events could have a strong influence on the bovine genome. This study aimed to investigate TE-mediated deletion events that are common to 12 Hanwoo genome resequencing data.

Results: We compared 12 Hanwoo genome resequencing data with the cattle reference genome (Bos taurus_UMD_3.1.1) and six other open source data (2 Jersey, 2 Holstein, 2 Angus). By using BreakDancer program, the common SVs to the 12 Hanwoo genomes were detected. A total of 299 Hanwoo-specific SV candidates were detected. Among them, 56 Hanwoo-specific TE-mediated deletion candidate loci were validated by PCR and Sanger sequencing. Finally, we identified one locus, DEL_96, which is an authentic Hanwoo-specific deletion. The DEL_96 event occurred by nonallelic homologous end-joining between LINE (BovB) and unique sequence with 1 bp microhomology. The 370 bp deletion event appeared to be only in the Hanwoo individuals after the divergence of Hanwoo and Holstein lineages.

Conclusion: Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein.
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http://dx.doi.org/10.1007/s13258-018-0772-3DOI Listing
February 2019

A Simple Guideline to Assess the Characteristics of RNA-Seq Data.

Biomed Res Int 2018 4;2018:2906292. Epub 2018 Nov 4.

Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea.

Next-generation sequencing (NGS) techniques have been used to generate various molecular maps including genomes, epigenomes, and transcriptomes. Transcriptomes from a given cell population can be profiled via RNA-seq. However, there is no simple way to assess the characteristics of RNA-seq data systematically. In this study, we provide a simple method that can intuitively evaluate RNA-seq data using two different principal component analysis (PCA) plots. The gene expression PCA plot provides insights into the association between samples, while the transcript integrity number (TIN) score plot provides a quality map of given RNA-seq data. With this approach, we found that RNA-seq datasets deposited in public repositories often contain a few low-quality RNA-seq data that can lead to misinterpretations. The effect of sampling errors for differentially expressed gene (DEG) analysis was evaluated with ten RNA-seq data from invasive ductal carcinoma tissues and three RNA-seq data from adjacent normal tissues taken from a Korean breast cancer patient. The evaluation demonstrated that sampling errors, which select samples that do not represent a given population, can lead to different interpretations when conducting the DEG analysis. Therefore, the proposed approach can be used to avoid sampling errors prior to RNA-seq data analysis.
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http://dx.doi.org/10.1155/2018/2906292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6241233PMC
March 2019

Predicting Walking Intentions using sEMG and Mechanical sensors for various environment.

Annu Int Conf IEEE Eng Med Biol Soc 2018 Jul;2018:4414-4417

Predicting the motion intentions of a user is very challenging when controlling an exoskeleton robot. When only a mechanical sensor is used, a change in the motion is detected during the user's movement. An electromyographic (EMG) signal, which is a biological signal, is detected by the activation of the muscles before the actual movement of a person. Using the EMG signal, the motion intention can be identified before the actual movement, and the delay in time in controlling the exoskeletal robot can be shortened to reduce the resistance felt by the user. In this paper, the surface electromyographic (sEMG) signal is used together with a mechanical sensor to identify the walking environment according to the walking gait cycle. In the classification, the combination of sensors was varied, and information from one leg and two legs was analyzed by the different gait periods before and after heel contact and toe off. As a result of the classification into three sensor combinations, sEMG, kinetic, and kinematic sensors, at the pre heel contact time before walking, a 96.8% and 98.6% accuracy was obtained for information from one and two legs, respectively. In the same gait environment, it was shown that the gait prediction can be performed based on the time unit by dividing the time interval before starting the gait. An average accuracy of 84.4% was obtained when the time was divided by the environment in intervals of 100ms before heel contact, and the average was 90.9% when it was divided by an interval of 200ms before heel contact.
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http://dx.doi.org/10.1109/EMBC.2018.8513322DOI Listing
July 2018

Accelerating convergence of an iterative solution of finite difference frequency domain problems via schur complement domain decomposition.

Opt Express 2018 Jun;26(13):16925-16939

We show that iterative solution of Maxwell's equations using the finite-difference frequency-domain method can be significantly accelerated by using a Schur complement domain decomposition method. We account for the improvement by analyzing the spectral properties of the linear systems resulting from the use of the domain decomposition method.
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http://dx.doi.org/10.1364/OE.26.016925DOI Listing
June 2018

A case of interdigitating dendritic cell sarcoma studied by whole-exome sequencing.

Genes Genomics 2018 12 11;40(12):1279-1285. Epub 2018 Aug 11.

Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of IDCS by sequencing the protein-coding regions of IDCS. We performed whole-exome sequencing with genomic DNA from blood and sarcoma tissue of the IDCS patient using the Illumina Hiseq 2500 platform. After that, we conducted Sanger sequencing for validation of sarcoma-specific variants and gene ontology analysis using DAVID bioinformatics resources. Through comparing sequencing data of sarcoma with normal blood, we obtained 15 nonsynonymous single nucleotide polymorphisms (SNPs) as sarcoma-specific variants. Although the 15 SNPs were not validated by Sanger sequencing due to tumor heterogeneity and low sensitivity of Sanger sequencing, we examined the function of the genes in which each SNP is located. Based on previous studies and gene ontology database, we found that POLQ encoding DNA polymerase theta enzyme and FNIP1 encoding tumor suppressor folliculin-interacting protein might have contributed to the IDCS. Our study provides potential causative genetic factors of IDCS and plays a role in advancing the understanding of IDCS pathogenesis.
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http://dx.doi.org/10.1007/s13258-018-0724-yDOI Listing
December 2018

The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum).

Genome Biol Evol 2017 06;9(6):1487-1498

Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea.

The manila clam, Ruditapes philippinarum, is an important bivalve species in worldwide aquaculture including Korea. The aquaculture production of R. philippinarum is under threat from diverse environmental factors including viruses, microorganisms, parasites, and water conditions with subsequently declining production. In spite of its importance as a marine resource, the reference genome of R. philippinarum for comprehensive genetic studies is largely unexplored. Here, we report the de novo whole-genome and transcriptome assembly of R. philippinarum across three different tissues (foot, gill, and adductor muscle), and provide the basic data for advanced studies in selective breeding and disease control in order to obtain successful aquaculture systems. An approximately 2.56 Gb high quality whole-genome was assembled with various library construction methods. A total of 108,034 protein coding gene models were predicted and repetitive elements including simple sequence repeats and noncoding RNAs were identified to further understanding of the genetic background of R. philippinarum for genomics-assisted breeding. Comparative analysis with the bivalve marine invertebrates uncover that the gene family related to complement C1q was enriched. Furthermore, we performed transcriptome analysis with three different tissues in order to support genome annotation and then identified 41,275 transcripts which were annotated. The R. philippinarum genome resource will markedly advance a wide range of potential genetic studies, a reference genome for comparative analysis of bivalve species and unraveling mechanisms of biological processes in molluscs. We believe that the R. philippinarum genome will serve as an initial platform for breeding better-quality clams using a genomic approach.
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http://dx.doi.org/10.1093/gbe/evx096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499747PMC
June 2017

Metal-insulator-metal waveguides for particle trapping and separation.

Lab Chip 2016 06 24;16(12):2302-8. Epub 2016 May 24.

Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA.

Optical particle trapping and separation are essential techniques in the fields of biology and chemistry. In many applications, it is important to identify passive separation techniques that only rely on intrinsic forces in a system with a fixed device geometry. We present a dual-waveguide sorter that utilizes the loss of metal-insulator-metal (MIM) waveguides for completely passive particle trapping and separation and is created using a unique angle sidewall deposition process. Our experiments show that an inner Au-Si3N4-Au waveguide is able to trap particles within the propagation distance of its dominant modes and release the particles into an outer Au-H2O-Au waveguide. The outer waveguide then propels the particles and separates them by size. The separation results are accurately modeled by a first-principles, analytical model.
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http://dx.doi.org/10.1039/c6lc00366dDOI Listing
June 2016

Plasmonic coaxial waveguide-cavity devices.

Opt Express 2015 Aug;23(16):20549-62

We theoretically investigate three-dimensional plasmonic waveguide-cavity structures, built by side-coupling stub resonators that consist of plasmonic coaxial waveguides of finite length, to a plasmonic coaxial waveguide. The resonators are terminated either in a short or an open circuit. We show that the properties of these waveguide-cavity systems can be accurately described using a single-mode scattering matrix theory. We also show that, with proper choice of their design parameters, three-dimensional plasmonic coaxial waveguide-cavity devices and two-dimensional metal-dielectric-metal devices can have nearly identical transmission spectra. Thus, three-dimensional plasmonic coaxial waveguides offer a platform for practical implementation of two-dimensional metal-dielectric-metal device designs.
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http://dx.doi.org/10.1364/OE.23.020549DOI Listing
August 2015

Dislocated double-layer metal gratings: an efficient unidirectional coupler.

Nano Lett 2014 Jul 18;14(7):3848-54. Epub 2014 Jun 18.

State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-sen University , Guangzhou 510275, China.

We propose theoretically and demonstrate experimentally a dislocated double-layer metal grating structure, which operates as a unidirectional coupler capable of launching surface plasmon polaritons in a desired direction under normal illumination. The structure consists of a slanted dielectric grating sandwiched between two gold gratings. The upper gold grating has a nonzero lateral relative displacement with respect to the lower one. Numerical simulations show that a grating structure with 7 periods can convert 49% of normally incident light into surface plasmons with a contrast ratio of 78 between the powers of the surface plasmons launched in two opposite directions. We explain the unidirectional coupling phenomenon by the dislocation-induced interference of the diffracted waves from the upper and lower gold gratings. Furthermore, we developed a simple and cost-effective technique to fabricate the structure via tilted two-beam interference lithography and subsequent shadow deposition of gold. The experimental results demonstrate a coupling efficiency of 36% and a contrast ratio of 43. The relatively simple periodic nature of our structure lends itself to large-scale low-cost fabrication and simple theoretical analysis. Also, unlike the previous unidirectional couplers based on aperiodic structures, the design parameters of our unidirectional coupler can be determined analytically. Therefore, this structure can be an important component for surface-plasmon-based nanophotonic circuits by providing an efficient interface between free-space and surface plasmon waves.
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http://dx.doi.org/10.1021/nl501007dDOI Listing
July 2014

Accelerated solution of the frequency-domain Maxwell's equations by engineering the eigenvalue distribution of the operator.

Opt Express 2013 Sep;21(19):22578-95

We introduce a simple method to accelerate the convergence of iterative solvers of the frequency-domain Maxwell's equations for deep-subwavelength structures. Using the continuity equation, the method eliminates the high multiplicity of near-zero eigenvalues of the operator while leaving the operator nearly positive-definite. The impact of the modified eigenvalue distribution on the accelerated convergence is explained by visualizing residual vectors and residual polynomials.
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http://dx.doi.org/10.1364/OE.21.022578DOI Listing
September 2013

Broadband sharp 90-degree bends and T-splitters in plasmonic coaxial waveguides.

Nano Lett 2013 Oct 4;13(10):4753-8. Epub 2013 Sep 4.

E. L. Ginzton Laboratory, Stanford University , Stanford, California 94305, United States.

We demonstrate numerically that sharp 90° bends and T-splitters can be designed in plasmonic coaxial waveguides at deep-subwavelength scale to operate without reflection and radiation over a broad range of wavelengths, including the telecommunication wavelength of 1.55 μm. We explain the principles of the operation using a transmission line model of the waveguide in the quasi-static limit. The compact bends and T-splitters open up a new avenue for the design of densely integrated optical circuits with minimal crosstalk.
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http://dx.doi.org/10.1021/nl402335xDOI Listing
October 2013

Upper bound on the modal material loss rate in plasmonic and metamaterial systems.

Phys Rev Lett 2013 May 29;110(18):183901. Epub 2013 Apr 29.

Department of Applied Physics, Stanford University, Stanford, California 94305, USA.

A better understanding of optical loss in plasmonic and metamaterial systems is of increasing importance for both basic and applied research in a broad range of topics including sensors, antennas, optical interconnects, and photovoltaics. In this Letter, we use a photonic band formalism for plasmonics to exactly derive a fundamental upper bound on the nonradiative material loss rate of modes in plasmonic, polaritonic, and metamaterial systems. This bound is purely defined by material properties and cannot be overcome by device design. Moreover it is frequency dependent in the presence of multiple Lorentz poles. We numerically verify this bound through direct calculations for a range of plasmonic systems, including optical antennas where the bound places fundamental performance constraints.
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http://dx.doi.org/10.1103/PhysRevLett.110.183901DOI Listing
May 2013

Human-specific HERV-K insertion causes genomic variations in the human genome.

PLoS One 2013 12;8(4):e60605. Epub 2013 Apr 12.

Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan, Republic of Korea.

Human endogenous retroviruses (HERV) sequences account for about 8% of the human genome. Through comparative genomics and literature mining, we identified a total of 29 human-specific HERV-K insertions. We characterized them focusing on their structure and flanking sequence. The results showed that four of the human-specific HERV-K insertions deleted human genomic sequences via non-classical insertion mechanisms. Interestingly, two of the human-specific HERV-K insertion loci contained two HERV-K internals and three LTR elements, a pattern which could be explained by LTR-LTR ectopic recombination or template switching. In addition, we conducted a polymorphic test and observed that twelve out of the 29 elements are polymorphic in the human population. In conclusion, human-specific HERV-K elements have inserted into human genome since the divergence of human and chimpanzee, causing human genomic changes. Thus, we believe that human-specific HERV-K activity has contributed to the genomic divergence between humans and chimpanzees, as well as within the human population.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060605PLOS
October 2013

Elements for plasmonic nanocircuits with three-dimensional slot waveguides.

Adv Mater 2010 Dec;22(45):5120-4

Stanford University, CA 94305, USA.

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http://dx.doi.org/10.1002/adma.201001440DOI Listing
December 2010

Phase front design with metallic pillar arrays.

Opt Lett 2010 Mar;35(6):844-6

E. L. Ginzton Laboratory and Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA.

We demonstrate numerically, using a three-dimensional finite-difference frequency-domain method, the ability to design a phase front using an array of metallic pillars. We show that in such structures, the local phase delay upon transmission can be tuned by local geometry. We apply this knowledge to demonstrate a metallic microlens. The presented design principles apply to a wider range of wavelength-size integrated photonic components.
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http://dx.doi.org/10.1364/OL.35.000844DOI Listing
March 2010
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