Publications by authors named "Sukchan Lee"

113 Publications

Adaptation and Codon-Usage Preference of Apple and Pear-Infecting Apple Stem Grooving Viruses.

Microorganisms 2021 May 21;9(6). Epub 2021 May 21.

Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea.

Apple stem grooving virus (ASGV; genus ) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates-13 isolates from apple ( L.) and 11 isolates from pear ( L.)-from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.
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http://dx.doi.org/10.3390/microorganisms9061111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8223792PMC
May 2021

Broad-Spectrum Antiviral Activity of 3D8, a Nucleic Acid-Hydrolyzing Single-Chain Variable Fragment (scFv), Targeting SARS-CoV-2 and Multiple Coronaviruses In Vitro.

Viruses 2021 04 9;13(4). Epub 2021 Apr 9.

Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Korea.

The virus behind the current pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the etiology of novel coronavirus disease (COVID-19) and poses a critical public health threat worldwide. Effective therapeutics and vaccines against multiple coronaviruses remain unavailable. Single-chain variable fragment (scFv), a recombinant antibody, exhibits broad-spectrum antiviral activity against DNA and RNA viruses owing to its nucleic acid-hydrolyzing property. The antiviral activity of 3D8 scFv against SARS-CoV-2 and other coronaviruses was evaluated in Vero E6 cell cultures. Viral growth was quantified with quantitative RT-qPCR and plaque assay. The nucleic acid-hydrolyzing activity of 3D8 was assessed through abzyme assays of in vitro viral transcripts and cell viability was determined by MTT assay. We found that 3D8 inhibited the replication of SARS-CoV-2, human coronavirus OC43 (HCoV-OC43), and porcine epidemic diarrhea virus (PEDV). Our results revealed the prophylactic and therapeutic effects of 3D8 scFv against SARS-CoV-2 in Vero E6 cells. Immunoblot and plaque assays showed the reduction of coronavirus nucleoproteins and infectious particles, respectively, in 3D8 scFv-treated cells. These data demonstrate the broad-spectrum antiviral activity of 3D8 against SARS-CoV-2 and other coronaviruses. Thus, it could be considered a potential antiviral countermeasure against SARS-CoV-2 and zoonotic coronaviruses.
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http://dx.doi.org/10.3390/v13040650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068894PMC
April 2021

Transcriptome Assembly of Two Fern Species Identifies Enzymes Required for Two Upstream Pathways of Phytoecdysteroids.

Int J Mol Sci 2021 Feb 19;22(4). Epub 2021 Feb 19.

Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea.

species produce a high amount of phytoecdysteroids (PEs), which are widely used in traditional medicine in the Pacific islands. The PEs in two different species, (MP) and (MS), were examined using high-performance liquid chromatography (HPLC). In particular, MS produces a high amount of 20-hydroxyecdysone, which is the main active compound in PEs. To identify genes for PE biosynthesis, we generated reference transcriptomes from sterile frond tissues using the NovaSeq 6000 system. De novo transcriptome assembly after deleting contaminants resulted in 57,252 and 54,618 clean transcripts for MP and MS, respectively. The clean transcripts for each species were annotated according to gene ontology terms, UniProt pathways, and the clusters of the orthologous group protein database using the MEGAN6 and Sma3s programs. In total, 1852 and 1980 transcription factors were identified for MP and MS, respectively. We obtained transcripts encoding for 38 and 32 enzymes for MP and MS, respectively, potentially involved in mevalonate and sterol biosynthetic pathways, which produce precursors for PE biosynthesis. Phylogenetic analyses revealed many redundant and unique enzymes between the two species. Overall, this study provides two reference transcriptomes that might be useful for further studies regarding PE biosynthesis in species.
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http://dx.doi.org/10.3390/ijms22042085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7923240PMC
February 2021

Nanovirus Disease Complexes: An Emerging Threat in the Modern Era.

Front Plant Sci 2020 19;11:558403. Epub 2020 Nov 19.

Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea.

Multipartite viruses package their genomic segments independently and mainly infect plants; few target animals. is a family of multipartite single-stranded DNA plant viruses that individually encapsidate single-stranded DNAs of approximately 1 kb and transmit them through aphids without replication in the aphid vectors, thereby causing important diseases of leguminous crops and banana. Significant findings regarding nanoviruses have recently been made on important features, such as their multicellular way of life, the transmission of distinct encapsidated genome segments through the vector body, evolutionary ambiguities, mode of infection, host range and geographical distribution. This review deals with all the above-mentioned features in view of recent advances with special emphasis on the emergence of new species and recognition of new host range of nanoviruses and aims to shed light on the evolutionary linkages, the potentially devastating impact on the world economy, and the future challenges imposed by nanoviruses.
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http://dx.doi.org/10.3389/fpls.2020.558403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710663PMC
November 2020

Zooming on dynamics of marine microbial communities in the phycosphere of Akashiwo sanguinea (Dinophyta) blooms.

Mol Ecol 2021 01 14;30(1):207-221. Epub 2020 Nov 14.

Risk Assessment Research Center, Korea Institute of Ocean Science & Technology, Geoje, Korea.

Characterizing ecological relationships between viruses, bacteria and phytoplankton in the ocean is critical to understanding the ecosystem; however, these relationships are infrequently investigated together. To understand the dynamics of microbial communities and environmental factors in harmful algal blooms (HABs), we examined the environmental factors and microbial communities during Akashiwo sanguinea HABs in the Jangmok coastal waters of South Korea by metagenomics. Specific bacterial species showed complex synergistic and antagonistic relationships with the A. sanguinea bloom. The endoparasitic dinoflagellate Amoebophrya sp. 1 controlled the bloom dynamics and correlated with HAB decline. Among nucleocytoplasmic large DNA viruses (NCLDVs), two Pandoraviruses and six Phycodnaviruses were strongly and positively correlated with the HABs. Operational taxonomic units of microbial communities and environmental factors associated with A. sanguinea were visualized by network analysis: A. sanguinea-Amoebophrya sp. 1 (r = .59, time lag: 2 days) and A. sanguinea-Ectocarpus siliculosus virus 1 in Phycodnaviridae (0.50, 4 days) relationships showed close associations. The relationship between A. sanguinea and dissolved inorganic phosphorus relationship also showed a very close correlation (0.74, 0 day). Microbial communities and the environment changed dynamically during the A. sanguinea bloom, and the rapid turnover of microorganisms responded to ecological interactions. A. sanguinea bloom dramatically changes the environments by exuding dissolved carbohydrates via autotrophic processes, followed by changes in microbial communities involving host-specific viruses, bacteria and parasitoids. Thus, the microbial communities in HAB are composed of various organisms that interact in a complex manner.
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http://dx.doi.org/10.1111/mec.15714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7839783PMC
January 2021

Inclusion of Lactobacillus salivarius strain revealed a positive effect on improving growth performance, fecal microbiota and immunological responses in chicken.

Arch Microbiol 2021 Mar 17;203(2):847-853. Epub 2020 Oct 17.

Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, 1500, Wanju-gun, 441-706, Republic of Korea.

Probiotics are defined as live microorganisms that when administered in an appropriate amount, provide health benefits to the host. This study aimed to evaluate the effect of the oral administration of Lactobacillus salivarius (L. salivarius) on growth performance, immunological responses, fecal microbial flora and intestinal mucosal morphology in chickens. Chickens were fed with 10 colony-forming units (CFUs) of wild-type (WT) L. salivarius or phosphate-buffered saline (PBS) for 5 weeks. Chickens body weight was significantly increased by administration of L. salivarius groups compared than control group. The microbial taxonomy in the small intestine and cecum was identified via the chicken feces sample. A total of 286,331 bacterial species were obtained from the chicken fecal samples in overall experimental group. From these, 145,012 bacterial species were obtained from oral administration of L. salivarius treatment group, while 141,319 bacterial species were obtained from control group. Almost 98% of all 16S rRNA sequences from the chicken fecal sample of the two groups were classified into known phyla. Firmicutes, Cyanobacteria, Proteobacteria, Bacteroidetes and Actinobacteria were highly abundant in both groups. Compared with the control birds, the chickens orally administered L. salivarius showed no significant differences in villus length and crypt length. Serum concentrations of the cytokines IL-8, TNF-α, IFN-γ, and IL-4 were markedly reduced in the L. salivarius group. In summary, our findings reveal that L. salivarius can act as a potential probiotic to improve performance and overall gut health in of chickens.
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http://dx.doi.org/10.1007/s00203-020-02088-3DOI Listing
March 2021

Rapid diagnosis of two marine viruses, red sea bream iridovirus and viral hemorrhagic septicemia virus by PCR combined with lateral flow assay.

Virusdisease 2020 Sep 31;31(3):251-256. Epub 2020 Mar 31.

College of Biotechnology and Bioengineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419 Korea.

Red sea bream iridovirus (RSIV) and Viral hemorrhagic septicemia virus (VHSV are the most important viral marine pathogens in South Korea because RSIV and VHSV infect and cause high mortality rates in major fish species such as and . These viruses can be transmitted both vertically and horizontally, and early diagnosis is imperative. In this research, RSIV and VHSV viral genomes are detected by PCR-lateral flow assay (LFA). PCR-LFA is sensitive, capable of detecting a viral genome at a concentration of 2-200 fg/µL. Development of this detection method is very meaningful because LFA is simple, requiring a minimum of personnel training to perform. Additionally, LFA requires less time than other detection methods and can be an immediate detection tool that is indispensable in preventing rapid viral spread.
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http://dx.doi.org/10.1007/s13337-020-00577-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459051PMC
September 2020

Administration of L. salivarius expressing 3D8 scFv as a feed additive improved the growth performance, immune homeostasis, and gut microbiota of chickens.

Anim Sci J 2020 Jan-Dec;91(1):e13399

Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea.

Probiotics have been defined as live microorganisms that are administered in an appropriate amount to provide health benefits to the host animal. In this study, we investigated the effect of L. salivarius DJ-sa-01 secreting the 3D8 single-chain variable fragment (3D8 scFv) on the growth performance, cytokine secretion, and intestinal microbial flora of chickens. The experiment was divided into the control group and L. salivarius expressing 3D8 scFv experimental group. Chicken was fed 10 colony-forming units (CFUs) of wild-type (WT) L. salivarius or 3D8 scFv-secreting L. salivarius daily for 35 days. The administration of L. salivarius expressing 3D8 scFv significantly improved the body weight of chickens compared with the administration of WT L. salivarius. A 16S ribosomal RNA metagenomic analysis showed that Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in both experimental groups. At the genus level, Lactobacillus was more abundant (22.82%) in the L. salivarius/3D8 group compared with the WT L. salivarius group. The serum levels of cytokines, such as IL-8, TNF-α, IL-1β, IFN-γ, IL-4, and IGF1, were significantly reduced in the L. salivarius/3D8-treated chickens. In summary, our results suggest that L. salivarius expressing 3D8 scFv could be considered a feed additive for improving the growth performance, immune function, and disease resistance of poultry.
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http://dx.doi.org/10.1111/asj.13399DOI Listing
October 2020

Development of novel detection system for sweet potato leaf curl virus using recombinant scFv.

Sci Rep 2020 05 15;10(1):8039. Epub 2020 May 15.

College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.

Sweet potato leaf curl virus (SPLCV) causes yield losses in sweet potato cultivation. Diagnostic techniques such as serological detection have been developed because these plant viruses are difficult to treat. Serological assays have been used extensively with recombinant antibodies such as whole immunoglobulin or single-chain variable fragments (scFv). An scFv consists of variable heavy (V) and variable light (V) chains joined with a short, flexible peptide linker. An scFv can serve as a diagnostic application using various combinations of variable chains. Two SPLCV-specific scFv clones, F7 and G7, were screened by bio-panning process with a yeast cell which expressed coat protein (CP) of SPLCV. The scFv genes were subcloned and expressed in Escherichia coli. The binding affinity and characteristics of the expressed proteins were confirmed by enzyme-linked immunosorbent assay using SPLCV-infected plant leaves. Virus-specific scFv selection by a combination of yeast-surface display and scFv-phage display can be applied to detection of any virus.
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http://dx.doi.org/10.1038/s41598-020-64996-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7228925PMC
May 2020

Seed Transmission of Tomato Leaf Curl New Delhi Virus from Zucchini Squash in Italy.

Plants (Basel) 2020 Apr 29;9(5). Epub 2020 Apr 29.

College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Korea.

(ToLCNDV) is a bipartite begomovirus affecting tomato cultivation on the Indian subcontinent. Recently, however, a new strain of the virus, named ToLCNDV-ES, has spread to Mediterranean countries such as Spain, Italy, and Tunisia, and occurred in Cucurbita crops, causing economic damage. Although ToLCNDV is spread by the sweet potato whitefly (), like other begomoviruses, it has not been clear how ToLCNDV suddenly spread from the Indian subcontinent to the Mediterranean region. In 2017, ToLCNDV was diagnosed in young seedlings germinated naturally from fruits fallen in the prior year on a farm located in Giugliano in Campania, Naples, Italy, suggesting a possible role of the seeds in vertical transmission of the virus. Because sweet potato whiteflies were widespread naturally in that region, it was necessary to verify that in an artificial insect vector-free condition. Seeds were harvested from two ToLCNDV-infected zucchini squash cultivars in Naples in 2017 and 2018 to examine whether ToLCNDV can be transmitted from zucchini squash seeds to young plants. Viral DNA was amplified from these seeds and 1- to 3-week-old seedlings germinated from them with a ToLCNDV-specific primer set. According to PCR results, viral contamination was confirmed from all harvested seeds and dissemination was proven from 61.36% of tested seedling samples. Mechanical transmission from seed-borne virus-infected seedlings to healthy zucchini squash plants was also succesful, demonstrating that seedlings from ToLCNDV-infected seeds did act as inoculum. This is the first report demonstrating that ToLCNDV is a seed-transmissible virus in zucchini squash plants in Italy.
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http://dx.doi.org/10.3390/plants9050563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7284533PMC
April 2020

Synthesis and evaluation of butein derivatives for in vitro and in vivo inflammatory response suppression in lymphedema.

Eur J Med Chem 2020 Jul 6;197:112280. Epub 2020 Apr 6.

Bio-Center, Gyeonggido Business & Science Accelerator, 147 Gwanggyo-ro, Suwon, 16229, Republic of Korea. Electronic address:

Herein, we demonstrate that butein (1) can prevent swelling in a murine lymphedema model by suppressing tumor necrosis factor α (TNF-α) production. Butein derivatives were synthesized and evaluated to identify compounds with in vitro anti-inflammatory activity. Among them, 20 μM of compounds 7j, 7m, and 14a showed 50% suppression of TNF-α production in mouse peritoneal macrophages after lipopolysaccharide stimulation. Compound 14a, exhibited the strongest potency with an in vitro IC of 14.6 μM and suppressed limb volume by 70% in a murine lymphedema model. The prodrug strategy enabled a six-fold increase in kinetic solubility of compound 1 and five-fold higher levels of active metabolite in the blood for compound 14a via oral administration in the pharmacokinetics study. We suggest that the compound 14a could be developed as a potential therapeutic agent targeting anti-inflammatory activity to alleviate lymphedema progression.
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http://dx.doi.org/10.1016/j.ejmech.2020.112280DOI Listing
July 2020

The threat of seed-transmissible pepper yellow leaf curl Indonesia virus in chili pepper.

Microb Pathog 2020 Jun 10;143:104132. Epub 2020 Mar 10.

College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, South Korea. Electronic address:

Recently, chili pepper (Capsicum annuum) plants in Indonesia have been devastated by a notorious bipartite begomovirus infection named Pepper yellow leaf curl Indonesia virus (PepYLCIV), which causes a distinct decrease in chili pepper production. Pepper yellow diseases have been known since early 2000; however, the spread of this virus thus far is distressing. These diseases can reduce chili yields by 20-100% in Indonesia. As previously known, begomovirus can be transmitted through whitefly to several host plants from the families Solanaceae, Compositae, and Leguminosae. In the field, a single plant was observed with severe symptoms of pepper yellow leaf curl disease, while other plants in the same field were asymptomatic and healthy. The observation leads to the possibility that the virus can be transmitted from previously infected chili pepper plants through seeds, as begomovirus transmission through seeds has been reported before. This study was conducted using seeds from chili peppers infected with viruses from different places in Indonesia. Whole seeds, embryos, and seedlings from PepYLCIV infected seeds were investigated in this study by performing viral genome DNA extraction, uracil DNA glycosylase-PCR, and sequencing analysis. Results revealed that both DNA-A and DNA-B of PepYLCIV in seeds and embryos of infected chili pepper plants were detected. The results also showed that 25-67% of PepYLCIV DNA-A and 50-100% of DNA-B were detected from seedlings grown from infected chili pepper seed collected from different location, thus confirming PepYLCIV as a seed-transmissible virus in chili pepper plants.
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http://dx.doi.org/10.1016/j.micpath.2020.104132DOI Listing
June 2020

Life Cycle-Based Host Range Analysis for Tomato Spotted Wilt Virus in Korea.

Plant Pathol J 2020 Feb 1;36(1):67-75. Epub 2020 Feb 1.

Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342, Korea.

(TSWV) is one of the plant viruses transmitted by thrips and causes severe economic damage to various crops. From 2008 to 2011, to identify natural host species of TSWV in South Korea, weeds and crops were collected from 5 regions (Seosan, Yesan, Yeonggwang, Naju, and Suncheon) where TSWV occurred and were identified as 1,104 samples that belong to 144 species from 40 families. According to reverse transcription-polymerase chain reaction, TSWV was detected from 73 samples from 23 crop species, 5 of which belonged to family Solanaceae. Additionally, 42 weed species were confirmed as natural hosts of TSWV with three different life cycles, indicating that these weed species could play an important role as virus reservoirs during no cultivation periods of crops. This study provides up-to-date comprehensive information for TSWV natural hosts in South Korea.
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http://dx.doi.org/10.5423/PPJ.FT.12.2019.0290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012576PMC
February 2020

Identification of begomoviruses from different cryptic species of Bemisia tabaci in Bangladesh.

Microb Pathog 2020 Feb 13;142:104069. Epub 2020 Feb 13.

Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Institute of Plant Medicine, Kyungpook National University, Daegu, Republic of Korea; Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, Republic of Korea. Electronic address:

Bemisia tabaci is a global species complex consisting of at least 40 cryptic species. It is also a vector for at least 100 species of begomovirus, many of which cause severe crop damage. The relationship between begomoviruses and cryptic species of the B. tabaci species complex, however, remains unclear. Our previous study [13] was identified four cryptic species (Asia I, Asia II 1, Asia II 5, and Asia II 10) of B. tabaci from Bangladesh. Using those 110 whitefly samples, vector-based PCR analysis identified 8 different begomovirus species: BYVMV, BGYVV, OELCV, SLCCV, SLCV, TbCSV, ToLCBV, and ToLCNDV. The overall rate of virus infection was 26.4%, and BYVMV and ToLCNDV were the most frequently detected in the B. tabaci vector. Virus infection rates for Asia I, Asia II 1, Asia II 5, and Asia II 10 were 22.4% (15/67), 35% (7/20), 27.3% (6/22), and 100% (1/1), respectively. Each cryptic species infected multiple virus species, but SLCCV, TbCSV, and BGYVV were each only detected in, Asia I, Asia II 1, and Asia II 5, respectively. This study demonstrates the geographic distribution of various begomoviruses in Bangladesh and their relationships with cryptic species of B. tabaci.
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http://dx.doi.org/10.1016/j.micpath.2020.104069DOI Listing
February 2020

Enhanced Anticancer Effect of Adding Magnesium to Vitamin C Therapy: Inhibition of Hormetic Response by SVCT-2 Activation.

Transl Oncol 2020 Feb 31;13(2):401-409. Epub 2019 Dec 31.

Yeom Chang-Hwan Hospital, Seoul, 06605, Republic of Korea. Electronic address:

l-Ascorbic acid (vitamin C, AA) is known as an antioxidant, but at high concentrations, AA can kill cancer cells through a prooxidant property. Sodium-dependent vitamin C transporter family-2 (SVCT-2) determines the cellular uptake of AA, and the activity of SVCT-2 is directly related to the anticancer activity of AA. Cancer cells that showed high SVCT-2 expression levels were more sensitive to AA treatment than cancer cells with low SVCT-2 expression levels. Cells with low SVCT-2 expression showed a hormetic response to a low dose of AA. Magnesium ions, which are known to activate SVCT-2, could increase the V value of SVCT-2, so we investigated whether providing magnesium supplements to cancer cells with low SVCT-2 expression that had shown a hormetic response to AA would elevate the V value of SVCT-2, allowing more AA to accumulate. To evaluate the effects of magnesium on cancer cells, MgSO and MgCl were screened as magnesium supplements; both forms showed synergistic anticancer effects with AA. Taken together, the results of this study suggest that magnesium supplementation enhanced the anticancer effect of AA by inhibiting the hormetic response at a low dose. This study has also demonstrated that AA treatment with magnesium supplementation provided more effective anticancer therapy than AA treatment alone.
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http://dx.doi.org/10.1016/j.tranon.2019.10.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6940627PMC
February 2020

Avian influenza virus transmission is suppressed in chickens fed expressing the 3D8 single-chain variable fragment protein.

Acta Vet Hung 2019 12;67(4):610-618

Animal Biotechnology Division, National Institute of Animal Science, RDA, 1500 Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.

The 3D8 single-chain variable fragment (scFv) is a mini-antibody sequence with independent nuclease activity that shows antiviral effects against all types of viruses in chickens and mice. In this study, chickens were treated daily with an oral dose of 10 CFU expressing either a secreted or anchored 3D8 scFv for three weeks. After administration, the chickens were challenged with avian influenza virus (AIV). From each experimental group, three chickens were directly infected with 100 µL of 10 EID/mL H9N2 AIV and seven chickens were indirectly challenged through contact transmission. oropharyngeal and cloacal swab samples were collected at 3, 5, 7, and 9 days post-inoculation (dpi) from AIV-challenged chickens, AIV Shedding titres were measured by quantitative real-time PCR. Contact transmission in the chickens that were fed 3D8 scFv-secreting showed a significant reduction in viral shedding when compared with other groups. These results suggest that secreting 3D8 provides a basis for the development of ingestible antiviral probiotics with activity against AIV.
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http://dx.doi.org/10.1556/004.2019.060DOI Listing
December 2019

Oral administration of expressing a 3D8 single-chain variable fragment (scFv) enhances chicken growth and conserves immune homeostasis.

3 Biotech 2019 Jul 24;9(7):282. Epub 2019 Jun 24.

1Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, 1500, Wanju-gun, 441-706 Republic of Korea.

The present study was aimed to investigate the effects of 3D8 scFv-secreting Probiotic () on growth performance, inflammatory responses, and intestinal microbial flora in chickens. To this end, a total of 14 healthy wild-type chickens were divided into two experimental groups. Each group was orally administrated with a daily dose of 10 colony-forming units (CFU) of 3D8 scFv-producing or wild-type (WT) for 35 days. Administration of /3D8 scFv significantly improved the body weight of chickens when compared to /WT group. The bacterial taxonomic composition of the fecal microbiota was determined by pyrosequencing of 16S rRNA gene amplicons. , and were dominant phyla in two experimental groups. However, in 3D8 treatment groups at genus level, the was highly abundant, being represented by 18.12%. In addition, serum levels of primary cytokines such as IL-6, IL-8, TNF-α, IFN-γ, IL-4, and IGF1 were markedly reduced in the probiotic 3D8 group. In summary, our results indicate that the administration of expressing 3D8 scFv has a modulatory effect on inflammatory responses, improves weight gain while not affecting the common microbial composition of the chicken intestine.
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http://dx.doi.org/10.1007/s13205-019-1811-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591341PMC
July 2019

Yeast (1 → 3)-(1 → 6)-β-d-glucan alleviates immunosuppression in gemcitabine-treated mice.

Int J Biol Macromol 2019 Sep 3;136:1169-1175. Epub 2019 Jun 3.

Department of Family Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea. Electronic address:

Gemcitabine (2'-deoxy-2',2'-difluorocytidine, dFdC) is one of the most effective chemotherapy drugs commonly used for treatment of various tumors. Despite its significant anticancer effects, some adverse effects create obstacles to treatment. The main toxicity of gemcitabine is myelosuppression, which not only reduces patient quality of life, but also hinders further anticancer treatment. In this respect, immunotherapy can address these drawbacks because of its ability to enhance the patient's immune system. To improve immune system function, yeast-derived β-glucans, which are well-known biologic response modifiers, were administered to gemcitabine-treated mice. The in vivo experiment revealed that orally administered yeast (1 → 3)-(1 → 6)-β-d-glucan effectively alleviated myelosuppression associated with gemcitabine-induced pancytopenia. Moreover, analysis of myelopoiesis-related cytokine expression through real-time PCR demonstrated that β-glucan treatment significantly upregulated hematopoietic responses in gemcitabine-treated mice. Furthermore, orally administered β-glucan significantly induced the expression of IFN-γ and IL-2 in splenocytes of gemcitabine-treated mice. It also restored the cytotoxicity of splenocytes against YAC-1 in gemcitabine-treated mice and displayed a positive effect on gemcitabine-damaged bone marrow tissue. In conclusion, yeast β-glucans have the potential to be used as adjuvants for alleviating chemotherapy-induced immunosuppression in patients.
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http://dx.doi.org/10.1016/j.ijbiomac.2019.06.009DOI Listing
September 2019

Neural circuits underlying a psychotherapeutic regimen for fear disorders.

Nature 2019 02 13;566(7744):339-343. Epub 2019 Feb 13.

Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea.

A psychotherapeutic regimen that uses alternating bilateral sensory stimulation (ABS) has been used to treat post-traumatic stress disorder. However, the neural basis that underlies the long-lasting effect of this treatment-described as eye movement desensitization and reprocessing-has not been identified. Here we describe a neuronal pathway driven by the superior colliculus (SC) that mediates persistent attenuation of fear. We successfully induced a lasting reduction in fear in mice by pairing visual ABS with conditioned stimuli during fear extinction. Among the types of visual stimulation tested, ABS provided the strongest fear-reducing effect and yielded sustained increases in the activities of the SC and mediodorsal thalamus (MD). Optogenetic manipulation revealed that the SC-MD circuit was necessary and sufficient to prevent the return of fear. ABS suppressed the activity of fear-encoding cells and stabilized inhibitory neurotransmission in the basolateral amygdala through a feedforward inhibitory circuit from the MD. Together, these results reveal the neural circuit that underlies an effective strategy for sustainably attenuating traumatic memories.
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http://dx.doi.org/10.1038/s41586-019-0931-yDOI Listing
February 2019

Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with .

PeerJ 2019 28;7:e6286. Epub 2019 Jan 28.

Department of Physics, Sungkyunkwan University, Suwon, South Korea.

Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.
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http://dx.doi.org/10.7717/peerj.6286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354667PMC
January 2019

RNA Binding Protein HuR Promotes Autophagosome Formation by Regulating Expression of Autophagy-Related Proteins 5, 12, and 16 in Human Hepatocellular Carcinoma Cells.

Mol Cell Biol 2019 03 1;39(6). Epub 2019 Mar 1.

Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, South Korea

Autophagy is a process of lysosomal self-degradation of cellular components by forming autophagosomes. Autophagosome formation is an essential process in autophagy and is fine-tuned by various autophagy-related gene (ATG) products, including ATG5, ATG12, and ATG16. Although several reports have shown that numerous factors affect multiple levels of gene regulation to orchestrate cellular autophagy, the detailed mechanism of autophagosome formation still needs further investigation. In this study, we demonstrate that the RNA binding protein HuR (human antigen R) performs an essential function in autophagosome formation. We observe that HuR silencing leads to inhibition of autophagosome formation and autophagic flux in liver cells. Ribonucleoprotein immunoprecipitation (RIP) assay allows the identification of , , and mRNAs as the direct targets of HuR. We further show that HuR mediates the translation of , , and mRNAs by binding to their 3' untranslated regions (UTRs). In addition, we show that HuR expression positively correlates with the levels of ATG5 and ATG12 in hepatocellular carcinoma (HCC) cells. Collectively, our results suggest that HuR functions as a pivotal regulator of autophagosome formation by enhancing the translation of , , and mRNAs and that augmented expression of HuR and ATGs may participate in the malfunction of autophagy in HCC cells.
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http://dx.doi.org/10.1128/MCB.00508-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6399664PMC
March 2019

Transcriptome profiles of tomato plants after neutron irradiation and infection with TYLCV.

Physiol Plant 2019 Feb;165(2):427-441

Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea.

Ionizing radiation is ubiquitous in the environment and can cause mutagenesis in living organisms. In this study, we examined the effects of neutron irradiation on tomato plants. Neutron irradiation decreased tomato germination rates, but most irradiated tomato plants did not show any significant phenotype. However, tomato mutants infected by Tomato yellow leaf curl virus (TYLCV) displayed resistance against TYLCV compared to the wild type (WT), which showed disease symptoms. RNA-Seq data demonstrated that the expression profiles of eight tomato mutants were significantly different from that of the WT. The transcriptomes obtained from presoaked seeds were highly altered compared to those of dry seeds. Increased irradiation time resulted in severe changes in the tomato transcriptome; however, different neutron irradiation intensities affected the expressions of different sets of genes. A high number of single-nucleotide polymorphisms in tomato transcriptomes suggest that neutron irradiation strongly impacts plant transcriptomes. The transition/transversion values among mutants were almost constant and were lower than that of the non-irradiated sample (WT), suggesting that neutron irradiation caused an effect. Taken together, this is the first report showing the effects of neutron irradiation on tomato plants by transcriptome analyses.
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http://dx.doi.org/10.1111/ppl.12913DOI Listing
February 2019

Differential responses between a vector species Bemisia tabaci and a nonvector species Trialeurodes vaporariorum following ingestion of tomato yellow leaf curl virus.

Arch Insect Biochem Physiol 2019 Feb 20;100(2):e21503. Epub 2018 Dec 20.

Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea.

In transmitting plant viruses, insect vectors undergo physiological and behavioral alterations. The whitefly Bemisia tabaci is a vector of tomato yellow leaf curl virus (TYLCV), causing severe damages to various horticultural crop plants. To determine whether whitefly alteration is specific to vector species, the responses to TYLCV ingestion were compared between B. tabaci and Trialeurodes vaporariorum, a nonvector for TYLCV. The two species were reared on TYLCV-infected and noninfected tomato, a host of TYLCV, and their longevity and fecundity were determined while rearing in either tomato or eggplant, a nonhost of TYLCV. TYLCV-ingested B. tabaci increased their developmental rates but reduced fecundity when they were reared in either tomato or eggplant compared with those of TYLCV-free ones. In contrast, TYLCV-ingested T. vaporariorum did not show any of the aforementioned changes when reared on both plant species. In addition, TYLCV-ingested B. tabaci increased their levels of three heat shock protein genes ( hsp20, hsp70, and hsp90) against thermal stress, whereas TYLCV-ingested T. vaporariorum did not. The presence of TYLCV virions was identified in two colonies of both species via polymerase chain reaction analysis. TYLCV was detected in the whole body, saliva, and eggs of B. tabaci, while TYLCV was detected only in the whole body but not in the saliva and eggs of T. vaporariorum. The present results strongly indicated that TYLCV specifically manipulate physiological processes of the vector species, B. tabaci.
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http://dx.doi.org/10.1002/arch.21517DOI Listing
February 2019

Complete Genome Sequence of Lactobacillus reuteri SKKU-OGDONS-01, Isolated from a Chicken's Small Intestine.

Microbiol Resour Announc 2018 Nov 21;7(20). Epub 2018 Nov 21.

Department of Genetic Engineering, Sungkyunkwan University, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea.

Lactobacillus reuteri SKKU-OGDONS-01 is a potentially indigenous probiotic strain isolated from the small intestine of a 27-week-old chicken. The complete genome of L. reuteri SKKU-OGDONS-01 comprises a single circular chromosome. Its length is 2,259,968 bp, with a G+C content of 38.9%.
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http://dx.doi.org/10.1128/MRA.01251-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256620PMC
November 2018

Complete Genome Sequence of Lactobacillus reuteri Byun-re-01, Isolated from Mouse Small Intestine.

Microbiol Resour Announc 2018 Nov 1;7(17). Epub 2018 Nov 1.

Department of Genetic Engineering, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea.

Lactic acid bacteria (LAB) are generally recognized as safe (GRAS) and serve as probiotic bacteria when consumed in adequate amounts. Here, we report the complete genome sequence of Lactobacillus reuteri Byun-re-01, isolated from mouse small intestine.
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http://dx.doi.org/10.1128/MRA.00984-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256494PMC
November 2018

Complete Genome Sequence of Lactobacillus johnsonii Strain Byun-jo-01, Isolated from the Murine Gastrointestinal Tract.

Microbiol Resour Announc 2018 Oct 18;7(15). Epub 2018 Oct 18.

Department of Genetic Engineering, Sungkyunkwan University, Suwon, Republic of Korea.

We report here the complete genome sequence of Lactobacillus johnsonii strain Byun-jo-01, which was isolated from the murine gastrointestinal tract. The genome was determined using both PacBio and Illumina sequencing. L. johnsonii strain Byun-jo-01 contains a single circular chromosome of 1,959,519 bp, and its GC content is 34.7%.
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http://dx.doi.org/10.1128/MRA.00985-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256439PMC
October 2018

Whole-Genome Sequence of Lactobacillus salivarius DJ-sa-01, Isolated from Chicken Small Intestine.

Microbiol Resour Announc 2018 Oct 11;7(14). Epub 2018 Oct 11.

Department of Genetic Engineering, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea.

We have identified the whole-genome sequence of Lactobacillus salivarius DJ-sa-01, a potential probiotic strain for poultry, isolated from a chicken small intestine. We used the PacBio and Illumina platforms to obtain the sequence of the entire single circular chromosome.
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http://dx.doi.org/10.1128/MRA.00987-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256648PMC
October 2018

High diversity and potential translocation of DNA viruses in ballast water.

Mar Pollut Bull 2018 Dec 27;137:449-455. Epub 2018 Oct 27.

South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea. Electronic address:

Ballast water is a common vector for the transport of invasive species to new marine and aquatic environments. We used a metagenomics approach to examine the composition and diversity of viral communities in ballast water from ships originating in Mexico, Saudi Arabia, New York, and Panama, and in water from the port of their destination in Busan, Korea. Myoviridae was the most abundant virus family in ballast water, followed Podoviridae and Siphoviridae. We also identified viruses that infect invertebrates, amoebas, and algae in ballast water and in the Busan port water. Interestingly, there were several viruses that infect humans or other animals (Swinepox virus, Raccoonpox virus, Suid herpesvirus, and Human endogenous retrovirus) in the samples from New York and Panama. In addition, there were giant viruses in all the ballast water samples, especially, identified Megavirus chilensis in New York and Panama, and Pandoravirus salinus in Mexico and Saudi Arabia. These results provide detailed descriptions of the characteristics of the viruses present in ballast water, document significant viral diversity, and indicate the potential translocation of viruses via ballast water.
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http://dx.doi.org/10.1016/j.marpolbul.2018.10.053DOI Listing
December 2018

The Possible Role of Neurobeachin in Extinction of Contextual Fear Memory.

Sci Rep 2018 09 13;8(1):13752. Epub 2018 Sep 13.

Center for Cognition and Sociality, Institute for Basic Science, Daejeon, 34047, Republic of Korea.

Established fear memory becomes vulnerable to disruption after memory retrieval and extinction; this labile state is critical for inhibiting the return of fear memory. However, the labile state has a very narrow time window after retrieval, and underlying molecular mechanisms are not well known. To that end, we isolated the hippocampus immediately after fear memory retrieval and performed proteomics. We identified Neurobeachin (NBEA), an autism-related regulator of synaptic protein trafficking, to be upregulated after contextual fear memory retrieval. NBEA protein expression was rapid and transient after fear memory retrieval at the synapse. Nbea mRNA was enriched at the synapses, and the rapid induction of NBEA expression was blocked by inhibition of the mammalian target of rapamycin (mTOR)-dependent signaling pathway. Mice with cornu ammonis 1 (CA1)-specific Nbea shRNA knockdown showed normal fear acquisition and contextual fear memory but impaired extinction, suggesting an important role of Nbea in fear memory extinction processes. Consistently, Nbea heterozygotes showed normal fear acquisition and fear memory recall but showed impairment in extinction. Our data suggest that NBEA is necessary either for induction of memory lability or for the physiological process of memory extinction.
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http://dx.doi.org/10.1038/s41598-018-30589-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137154PMC
September 2018

Sulfuretin Prevents Obesity and Metabolic Diseases in Diet Induced Obese Mice.

Biomol Ther (Seoul) 2019 01;27(1):107-116

Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea.

The global obesity epidemic and associated metabolic diseases require alternative biological targets for new therapeutic strategies. In this study, we show that a phytochemical sulfuretin suppressed adipocyte differentiation of preadipocytes and administration of sulfuretin to high fat diet-fed obese mice prevented obesity and increased insulin sensitivity. These effects were associated with a suppressed expression of inflammatory markers, induced expression of adiponectin, and increased levels of phosphorylated ERK and AKT. To elucidate the molecular mechanism of sulfuretin in adipocytes, we performed microarray analysis and identified activating transcription factor 3 (Atf3) as a sulfuretin-responsive gene. Sulfuretin elevated Atf3 mRNA and protein levels in white adipose tissue and adipocytes. Consistently, deficiency of Atf3 promoted lipid accumulation and the expression of adipocyte markers. Sulfuretin's but not resveratrol's anti-adipogenic effects were diminished in deficient cells, indicating that is an essential factor in the effects of sulfuretin. These results highlight the usefulness of sulfuretin as a new anti-obesity intervention for the prevention of obesity and its associated metabolic diseases.
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http://dx.doi.org/10.4062/biomolther.2018.090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6319556PMC
January 2019
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