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Lee SY, Kim JH, Kang S, Park KC, Cho SM, Salinas CX, Rebolledo L, Benítez HA, Mejías TC, Soutullo A, Juri E, Kim S. Detection of human enteric viral genes in a non-native winter crane fly, Trichocera maculipennis (Diptera) in the sewage treatment facilities at Antarctic stations. Parasit Vectors 2024; 17:485. [PMID: 39582010 PMCID: PMC11587659 DOI: 10.1186/s13071-024-06555-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 10/22/2024] [Indexed: 11/26/2024] Open
Abstract
BACKGROUND The Antarctic environment is susceptible to the introduction of non-native species due to its unique ecosystem, which has evolved under geographical isolation and extreme climatic conditions over an extended period. The recent introduction of the non-native winter crane fly, Trichocera maculipennis, to maritime Antarctica may pose a potential threat to the Antarctic ecosystem. In this study, we evaluated the possibility of the mechanical transmission of viruses by T. maculipennis. METHODS We assessed the potential for the mechanical transmission of viruses using next-generation sequencing (NGS), quantitative PCR (qPCR), and virus isolation methods from T. maculipennis (Tm)-related samples (Tm body-wash fluid and Tm body-ground samples) collected from habitats and sewage treatment facilities located at three research stations in Antarctica. RESULTS Virome analysis detected the genomic fragments of human adenovirus (AdV) and human endogenous retrovirus (HERV) in Tm-related samples. These viruses are commonly found in human feces. In addition, plant viruses, such as pepper mild mottle virus (PMMoV) and cucumber green mottle mosaic virus (CGMMV), both known indicators of enteric viruses, were identified in all Tm-related samples, likely originating from wastewater. However, the low quantities of AdV and HERV genomes detected in Tm-related samples through qPCR, coupled with the non-viability of AdV in virus isolation tests, indicate that T. maculipennis has limited potential for mechanical transmission under the conditions in the studies. CONCLUSIONS Our study represents the first evaluation of the potential risk of non-native species serving as vectors for viral pathogens in Antarctica. Although the viruses detected were in relatively low quantities and non-viable, this study highlights the importance of further evaluating the risks associated with non-native species, particularly as the likelihood of their introduction increases to Antarctica due to climate change and increased human activity.
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Yu J, Lee H, Cho SM, Lee Y, Kim D, Hong SG, Park SJ, Kim SG, Jin H, Lee J. Life under the snow: A year-round transcriptome analysis of Antarctic mosses in natural habitats provides insight into the molecular adaptation of plants under extreme environment. PLANT, CELL & ENVIRONMENT 2024; 47:976-991. [PMID: 38164069 DOI: 10.1111/pce.14793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 11/11/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Mosses are vital components of ecosystems, exhibiting remarkable adaptability across diverse habitats from deserts to polar ice caps. Sanionia uncinata (Hedw.) Loeske, a dominant Antarctic moss survives extreme environmental condition through perennial lifecycles involving growth and dormancy alternation. This study explores genetic controls and molecular mechanisms enabling S. uncinata to cope with seasonality of the Antarctic environment. We analysed the seasonal transcriptome dynamics of S. uncinata collected monthly from February 2015 to January 2016 in King George Island, Antarctica. Findings indicate that genes involved in plant growth were predominantly upregulated in Antarctic summer, while those associated with protein synthesis and cell cycle showed marked expression during the winter-to-summer transition. Genes implicated in cellular stress and abscisic acid signalling were highly expressed in winter. Further, validation included a comparison of the Antarctic field transcriptome data with controlled environment simulation of Antarctic summer and winter temperatures, which revealed consistent gene expression patterns in both datasets. This proposes a seasonal gene regulatory model of S. uncinate to understand moss adaptation to extreme environments. Additionally, this data set is a valuable resource for predicting genetic responses to climatic fluctuations, enhancing our knowledge of Antarctic flora's resilience to global climate change.
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Kang S, Kim S, Park KC, Petrašiūnas A, Shin HC, Jo E, Cho SM, Kim JH. Molecular evidence for multiple origins and high genetic differentiation of non-native winter crane fly, Trichocera maculipennis (Diptera: Trichoceridae), in the maritime Antarctic. ENVIRONMENTAL RESEARCH 2024; 242:117636. [PMID: 37952853 DOI: 10.1016/j.envres.2023.117636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Native biodiversity and ecosystems of Antarctica safeguarded from biological invasion face recent threats from non-native species, accelerated by increasing human activities and climate changes. Over two decades ago, the winter crane fly, Trichocera maculipennis, was first detected on King George Island. It has now successfully colonized several research stations across King George Island. To understand the origin, genetic diversity, and population structure of this Holarctic species, we conducted mitochondrial DNA cytochrome c oxidase subunit I (COI) sequence analysis across both its native and invasive ranges. In parallel, we performed microsatellite loci analysis within the invasive ranges, utilizing 12 polymorphic microsatellite markers. Furthermore, we compared body sizes among adult males and females collected from three different locations of King George Island. Our COI sequence analysis exhibited two different lineages present on King George Island. Lineage I was linked to Arctic Svalbard and Polish cave populations and Lineage II was related to Canadian Terra Nova National Park populations, implying multiple origins. Microsatellite analysis further exhibited high levels of genetic diversity and significant levels of genetic differentiation among invasive populations. Body sizes of adult T. maculipennis were significantly different among invasive populations but were not attributed to genetics. This significant genetic diversity likely facilitated the rapid colonization and establishment of T. maculipennis on King George Island, contributing to their successful invasion. Molecular analysis results revealed a substantial amount of genetic variation within invasive populations, which can serve as management units for invasive species control. Furthermore, the genetic markers we developed in the study will be invaluable tools for tracking impending invasion events and the travel routes of new individuals. Taken together, these findings illustrate the highly invasive and adaptable characteristics of T. maculipennis. Therefore, immediate action is necessary to mitigate their ongoing invasion and facilitate their eradication.
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Kim B, Do H, Kim BM, Lee JH, Kim S, Kim EJ, Lee J, Cho SM, Kim K. Freezing-enhanced oxidation of iodide by hydrogen peroxide in the presence of antifreeze proteins from the Arctic yeast Leucosporidium sp.AY30. ENVIRONMENTAL RESEARCH 2022; 212:113233. [PMID: 35390302 DOI: 10.1016/j.envres.2022.113233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 02/21/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Ice-binding proteins (IBPs), originating from Arctic or Antarctic microorganisms, have freeze-inhibiting characteristics, allowing these organisms to survive in polar regions. Despite their significance in polar environments, the mechanism through which IBPs affect the chemical reactions in ice by controlling ice crystal formation has not yet been reported. In this study, a new mechanism for iodide (I-) activation into triiodide (I3-), which is the abundant iodine species in seawater, by using hydrogen peroxide (H2O2) in a frozen solution with IBPs was developed. A significant enhancement of I- activation into I3- was observed in the presence of Arctic-yeast-originating extracellular ice-binding glycoprotein (LeIBP) isolated from Leucosporidium sp. AY30, and a further increase in the I3- concentration was observed with the introduction of H2O2 to the frozen solution (25 times higher than in the aqueous solution after 24 h of reaction). The reaction in the ice increased with an increase in LeIBP concentration. The in-situ pH measurement in ice using cresol red (CR) revealed protons accumulated in the ice grain boundaries by LeIBP. However, the presence of LeIBP did not influence the acidity of the ice. The enhanced freeze concentration effect of H2O2 by LeIBP indicated that larger ice granules were formed in the presence of LeIBP. The results suggest that LeIBP affects the formation and morphology of ice granules, which reduces the total volume of ice boundaries throughout the ice. This leads to an increased local concentration of I- and H2O2 within the ice grain boundaries. IBP-assisted production of gaseous iodine in a frozen environment provides a previously unrecognized formation mechanism of active iodine species in the polar regions.
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Hwang J, Kim B, Lee MJ, Kim EJ, Cho SM, Lee SG, Han SJ, Kim K, Lee JH, Do H. Importance of rigidity of ice-binding protein (FfIBP) for hyperthermal hysteresis activity and microbial survival. Int J Biol Macromol 2022; 204:485-499. [PMID: 35149098 DOI: 10.1016/j.ijbiomac.2022.02.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 01/18/2023]
Abstract
Ice-binding proteins (IBPs) are well-characterized proteins responsible for the cold-adaptation mechanisms. Despite extensive structural and biological investigation of IBPs and antifreeze proteins, only a few studies have considered the relationship between protein stabilization and thermal hysteresis (TH) activity as well as the implication of hyperactivity. Here, we investigated the important role of the head capping region in stabilization and the hyper-TH activity of FfIBP using molecular dynamics simulation. Data comparison revealed that residues on the ice-binding site of the hyperactive FfIBP are immobilized, which could be correlated with TH activity. Further comparison analysis indicated the disulfide bond in the head region is mainly involved in protein stabilization and is crucial for hyper-TH activity. This finding could also be generalized to known hyperactive IBPs. Furthermore, in mimicking the physiological conditions, bacteria with membrane-anchored FfIBP formed brine pockets in a TH activity-dependent manner. Cells with a higher number of TH-active IBPs showed an increased number of brine pockets, which may be beneficial for short- and long-term survival in cold environments by reducing the salt concentration. The newly identified conditions for hyper-TH activity and their implications on bacterial survival provide insights into novel mechanistic aspects of cold adaptation in polar microorganisms.
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Kim EJ, Chae H, Yu J, Kim H, Cho SM, Shin SC, Choi HG, Kim S, Han SJ. Mitochondrial genome of the Antarctic microalga Micractinium simplicissimum KSF0127 (Chlorellaceae, Trebouxiophyceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:878-879. [PMID: 33796665 PMCID: PMC7971331 DOI: 10.1080/23802359.2021.1886010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report the first mitochondrial genome of the Antarctic microalga Micractinium simplicissimum KSF0127. The circular mitochondrial genome was 67,923 bp in length and contained 45 protein-coding genes, one ribosomal RNA gene, and 60 transfer RNA genes. The phylogenetic tree was constructed with eight previously reported mitogenome sequences and showed the phylogenetic position of M. simplicissimum KSF0127 within the Chlorellaceae family.
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Cho SM, Lee H, Hong SG, Lee J. Study of Ecophysiological Responses of the Antarctic Fruticose Lichen Cladonia borealis Using the PAM Fluorescence System under Natural and Laboratory Conditions. PLANTS (BASEL, SWITZERLAND) 2020; 9:E85. [PMID: 31936612 PMCID: PMC7020452 DOI: 10.3390/plants9010085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/20/2019] [Accepted: 01/07/2020] [Indexed: 11/16/2022]
Abstract
Antarctic lichens have been used as indicators of climate change for decades, but only a few species have been studied. We assessed the photosynthetic performance of the fruticose lichen Cladonia borealis under natural and laboratory conditions using the PAM fluorescence system. Compared to that of sun-adapted Usnea sp., the photosynthetic performance of C. borealis exhibits shade-adapted lichen features, and its chlorophyll fluorescence does not occur during dry days without rain. To understand its desiccation-rehydration responses, we measured changes in the PSII photochemistry in C. borealis under the average light intensity of dawn light and daylight and the desiccating conditions of its natural microclimate. Interestingly, samples under daylight and rapid-desiccation conditions showed a delayed reduction in Fv'/Fm' and rETRmax, and an increase in Y(II) and Y(NPQ) levels. These results suggest that the photoprotective mechanism of C. borealis depends on sunlight and becomes more efficient with improved desiccation tolerance. Amplicon sequencing revealed that the major photobiont of C. borealis was Asterochloris irregularis, which has not been reported in Antarctica before. Collectively, these results from both field and laboratory could provide a better understanding of specific ecophysiological responses of shade-adapted lichens in the Antarctic region.
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Cho SM, Kim S, Cho H, Lee H, Lee JH, Lee H, Park H, Kang S, Choi HG, Lee J. Type II Ice-Binding Proteins Isolated from an Arctic Microalga Are Similar to Adhesin-Like Proteins and Increase Freezing Tolerance in Transgenic Plants. PLANT & CELL PHYSIOLOGY 2019; 60:2744-2757. [PMID: 31418793 DOI: 10.1093/pcp/pcz162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
Microalgal ice-binding proteins (IBPs) in the polar region are poorly understood at the genome-wide level, although they are important for cold adaptation. Through the transcriptome study with the Arctic green alga Chloromonas sp. KNF0032, we identified six Chloromonas IBP genes (CmIBPs), homologous with the previously reported IBPs from Antarctic snow alga CCMP681 and Antarctic Chloromonas sp. They were organized with multiple exon/intron structures and low-temperature-responsive cis-elements in their promoters and abundantly expressed at low temperature. The biological functions of three representative CmIBPs (CmIBP1, CmIBP2 and CmIBP3) were tested using in vitro analysis and transgenic plant system. CmIBP1 had the most effective ice recrystallization inhibition (IRI) activities in both in vitro and transgenic plants, and CmIBP2 and CmIBP3 had followed. All transgenic plants grown under nonacclimated condition were freezing tolerant, and especially 35S::CmIBP1 plants were most effective. After cold acclimation, only 35S::CmIBP2 plants showed slightly increased freezing tolerance. Structurally, the CmIBPs were predicted to have β-solenoid forms with parallel β-sheets and repeated TXT motifs. The repeated TXT structure of CmIBPs appears similar to the AidA domain-containing adhesin-like proteins from methanogens. We have shown that the AidA domain has IRI activity as CmIBPs and phylogenetic analysis also supported that the AidA domains are monophyletic with ice-binding domain of CmIBPs, and these results suggest that CmIBPs are a type of modified adhesins.
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Cho SM, Song J, Chang J. Differences between caregiver-perceived and dentist-assessed oral health status of patients among intellectual disabilities. COMMUNITY DENTAL HEALTH 2019; 36:255-261. [PMID: 31664796 DOI: 10.1922/cdh_4583cho07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
OBJECTIVE This study compared the caregiver-perceived and dentist-determined oral health status of patients with intellectual disabilities to determine factors that affect caregiver-perception of patients' oral health. MATERIALS AND METHODS 297 patients [mean (SD) age = 51.9 (12.5) years] and 56 professional caregivers [42.1 (8.2) years] from three institutional facilities took part. Data were acquired via self-administered questionnaires by caregivers and oral examination by dentists. Oral hygiene condition, numbers of decayed and missing teeth, and periodontal disease reported by caregivers and dentists were compared using paired t-test and Pearson correlation. Demographic and dental factors of the patients and caregivers were analyzed using chi square and Fisher's exact tests. RESULTS Caregivers underestimated decayed and missing teeth compared to dentists (p⟨0.05). Oral hygiene condition and periodontal disease were similarly rated by the two groups. Tooth brushing, diet type, sex, and overall oral health status of the patients were associated with caregiver perception (p⟨0.05). Career length and time since caregivers last received dental care were also related factors (p⟨0.05). CONCLUSION Professional caregivers of adult patients with intellectual disabilities had different perceptions of oral health status based on patient and caregiver circumstances.
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Kang P, Cho SM, Lee J, Yim JH, Lee JH, Lee H. The complete mitogenome of the Arctic moss Aulacomnium turgidum (Wahlenb.) Schwaegr. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3446-3447. [PMID: 33366032 PMCID: PMC7707293 DOI: 10.1080/23802359.2019.1674204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Arctic moss Aulacomnium turgidum (Wahlenb.) Schwaegr. is distributed widely above the Arctic Circle and can regenerate successfully after 400 years of ice entombment. Here, we report the complete mitogenome sequence of A. turgidum (103,937 bp). The genome contains 3 ribosomal RNAs, 24 transfer RNAs, and 40 protein-encoding genes. In a phylogenetic tree generated using the combined amino acid sequences of 32 mitochondrial genes from A. turgidum, 25 Bryophyta, and three Marchantiophyta, the phylogenetic position of A. turgidum (Rhizogoniales) is close to that of the Hypnales and Ptychomniales, forming a monophyletic clade with perfect supporting values.
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Choi S, Lemberger‐Truelove ME, Cho SM. The Influence of Disruption of Core Beliefs, Social Support, and Rumination on Posttraumatic Growth for Korean Undergraduate Students. THE JOURNAL OF HUMANISTIC COUNSELING 2019. [DOI: 10.1002/johc.12121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Byun MY, Cho SM, Lee J, Park H, Lee H. The complete mitochondrial genome of an Antarctic moss Chorisodontium aciphyllum (Hook. f. & Wilson) Broth. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1605856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Cho SM, Byun MY, Lee H, Park H, Lee J. The complete mitogenome of the Antarctic moss Bartramia patens Brid. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1610096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Cho SM, Lee H, Jo H, Lee H, Kang Y, Park H, Lee J. Comparative transcriptome analysis of field- and chamber-grown samples of Colobanthus quitensis (Kunth) Bartl, an Antarctic flowering plant. Sci Rep 2018; 8:11049. [PMID: 30038328 PMCID: PMC6056519 DOI: 10.1038/s41598-018-29335-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 07/09/2018] [Indexed: 11/09/2022] Open
Abstract
Colobanthus quitensis is one of the two vascular plants inhabiting the Antarctic. In natural habitats, it grows in the form of a cushion or mats, commonly observed in high latitudes or alpine vegetation. Although this species has been investigated over many years to study its geographical distribution and physiological adaptations to climate change, very limited genetic information is available. The high-throughput sequencing with a de novo assembly analysis yielded 47,070 contigs with blast-hits. Through the functional classification and enrichment analysis, we identified that photosynthesis and phenylpropanoid pathway genes show differential expression depending on the habitat environment. We found that the known 'plant core environmental stress response (PCESR)' genes were abundantly expressed in Antarctic samples, and confirmed that their expression is mainly induced by low-temperature. In addition, we suggest that differential expression of thermomorphogenesis-related genes may contribute to phenotypic plasticity of the plant, for instance, displaying a cushion-like phenotype to adapt to harsh environments.
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Kupriyanova EV, Cho SM, Park YI, Pronina NA, Los DA. The complete genome of a cyanobacterium from a soda lake reveals the presence of the components of CO 2-concentrating mechanism. PHOTOSYNTHESIS RESEARCH 2016; 130:151-165. [PMID: 26908147 DOI: 10.1007/s11120-016-0235-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
At present geological epoch, the carbon concentrating mechanism (CCM) of cyanobacteria represents the obligatory tool for adaptation to low content of CO2 in the atmosphere and for the maintenance of sufficient photosynthetic activity. Functional CCM was found in modern cyanobacteria from different ecological niches. However, the presence of such mechanism in species that inhabit soda lakes is not obvious due to high content of inorganic carbon (C i) in the environment. Here we analyze CCM components that have been identified by sequencing of the whole genome of the alkaliphilic cyanobacterium Microcoleus sp. IPPAS B-353. The composition of the CCM components of Microcoleus is similar to that of 'model' β-cyanobacteria, freshwater and marine Synechococcus or Synechocystis spp. However, CahB1 protein of Microcoleus, which is the homolog of CcaA, the carboxysomal β-type carbonic anhydrase (CA) of β-cyanobacteria, appeared to be the only active CA located in cell envelopes. The conservative regions of CcmM, CahG (a homolog of archeal γ-CAs, Cam/CamH), and ChpX of Microcoleus possess single amino acid substitutions that may cause a lack of CA activities. Unlike model cyanobacteria, Microcoleus induces only one BicA-type bicarbonate transporter in response to C i limitation. The differences in the appearance of CCM components and in their characteristics between alkaliphilic Microcoleus and freshwater or marine cyanobacteria are described. The possible reasons for the maintenance of CCM components in cyanobacteria, which permanently live at high concentrations of C i in soda lakes, are discussed.
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Cho SM, Jeoung SC, Song JY, Kupriyanova EV, Pronina NA, Lee BW, Jo SW, Park BS, Choi SB, Song JJ, Park YI. Genomic Survey and Biochemical Analysis of Recombinant Candidate Cyanobacteriochromes Reveals Enrichment for Near UV/Violet Sensors in the Halotolerant and Alkaliphilic Cyanobacterium Microcoleus IPPAS B353. J Biol Chem 2015; 290:28502-28514. [PMID: 26405033 DOI: 10.1074/jbc.m115.669150] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteriochromes (CBCRs), which are exclusive to and widespread among cyanobacteria, are photoproteins that sense the entire range of near-UV and visible light. CBCRs are related to the red/far-red phytochromes that utilize linear tetrapyrrole (bilin) chromophores. Best characterized from the unicellular cyanobacterium Synechocystis sp. PCC 6803 and the multicellular heterocyst forming filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Anabaena sp. PCC 7120, CBCRs have been poorly investigated in mat-forming, nonheterocystous cyanobacteria. In this study, we sequenced the genome of one of such species, Microcoleus IPPAS B353 (Microcoleus B353), and identified two phytochromes and seven CBCRs with one or more bilin-binding cGMP-specific phosphodiesterase, adenylyl cyclase and FhlA (GAF) domains. Biochemical and spectroscopic measurements of 23 purified GAF proteins from phycocyanobilin (PCB) producing recombinant Escherichia coli indicated that 13 of these proteins formed near-UV and visible light-absorbing covalent adducts: 10 GAFs contained PCB chromophores, whereas three contained the PCB isomer, phycoviolobilin (PVB). Furthermore, the complement of Microcoleus B353 CBCRs is enriched in near-UV and violet sensors, but lacks red/green and green/red CBCRs that are widely distributed in other cyanobacteria. We hypothesize that enrichment in short wavelength-absorbing CBCRs is critical for acclimation to high-light environments where this organism is found.
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Kupriyanova EV, Sinetova MA, Cho SM, Park YI, Los DA, Pronina NA. CO2-concentrating mechanism in cyanobacterial photosynthesis: organization, physiological role, and evolutionary origin. PHOTOSYNTHESIS RESEARCH 2013; 117:133-146. [PMID: 23733616 DOI: 10.1007/s11120-013-9860-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/25/2013] [Indexed: 06/02/2023]
Abstract
The cellular and molecular organization of the CO2-concentrating mechanism (CCM) of cyanobacteria is reviewed. The primary processes of uptake, translocation, and accumulation of inorganic carbon (Ci) near the active site of carbon assimilation by the enzyme ribulose-1,5-bisphosphate carboxylase in the C3 cycle in cyanobacteria are described as one of the specialized forms of CO2 concentration which occurs in some photoautotrophic cells. The existence of this form of CO2 concentration expands our understanding of photosynthetic Ci assimilation. The means of supplying Ci to the C3 cycle in cyanobacteria is not by simple diffusion into the cell, but it is the result of coordinated functions of high-affinity systems for the uptake of CO2 and bicarbonate, as well as intracellular CO2/HCO3 (-) interconversions by carbonic anhydrases. These biochemical events are under genetic control, and they serve to maintain cellular homeostasis and adaptation to CO2 limitation. Here we describe the organization of the CCM in cyanobacteria with a special focus on the CCM of relict halo- and alkaliphilic cyanobacteria of soda lakes. We also assess the role of the CCM at the levels of the organism, the biosphere, and evolution.
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Yang EC, Boo GH, Kim HJ, Cho SM, Boo SM, Andersen RA, Yoon HS. Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles. Protist 2011; 163:217-31. [PMID: 22001261 DOI: 10.1016/j.protis.2011.08.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 08/07/2011] [Indexed: 11/24/2022]
Abstract
Molecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlier studies did not include representatives from all taxonomic classes. We used a five-gene (nuclear encoded SSU rRNA; plastid encoded rbcL, psaA, psbA, psbC) analysis with a subset of 89 taxa representing all 16 heterokont classes to infer a phylogenetic tree. There were three major clades. The Aurearenophyceae, Chrysomerophyceae, Phaeophyceae, Phaeothamniophyceae, Raphidophyceae, Schizocladiophyceae and Xanthophyceae formed the SI clade. The Chrysophyceae, Eustigmatophyceae, Pinguiophyceae, Synchromophyceae and Synurophyceae formed the SII clade. The Bacillariophyceae, Bolidophyceae, Dictyochophyceae and Pelagophyceae formed the SIII clade. These three clades were also found in a ten-gene analysis. The approximately unbiased test rejected alternative hypotheses that forced each class into either of the other two clades. Morphological and biochemical data were not available for all 89 taxa, however, existing data were consistent with the molecular phylogenetic tree, especially for the SIII clade.
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Ronchi CBB, Ronchi CF, Correa CR, Cho SM, Park KM, Rasmussen H, Saltzman E, Yeum K. Modification of Antioxidant Status by Ingesting Angelica keiskei (Ak) and/or Glycine max (Gm) in Subjects with Metabolic syndrome (MS). FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.106.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Boo SM, Kim HS, Shin W, Boo GH, Cho SM, Jo BY, Kim JH, Kim JH, Yang EC, Siver PA, Wolfe AP, Bhattacharya D, Andersen RA, Yoon HS. Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes. Mol Ecol 2010; 19:4328-38. [PMID: 25241409 DOI: 10.1111/j.1365-294x.2010.04813.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multigene data set, we study the phylogeography of the freshwater heterokont alga Synura petersenii sensu lato. Our results suggest that this Synura morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co-occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein-coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus Synura is considerably older than currently proposed. The availability of tectonically relevant geological time (10⁷-10⁸ years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explains global patterns of microbial eukaryote distribution and that processes of dispersal remain poorly understood.
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Heo DH, Cho YJ, Sheen SH, Hong MS, Cho SM, Park SH. 3D reconstructions of spinal segmental arteries using CT angiography: applications in minimally invasive spinal procedures. AJNR Am J Neuroradiol 2010; 31:1635-9. [PMID: 20507934 DOI: 10.3174/ajnr.a2137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Injury to spinal segmental arteries may potentially occur during spinal surgery, particularly during anterior or minimally invasive approaches. Use of a noninvasive radiologic tool to evaluate these arteries before surgery may reduce this risk. MATERIAL AND METHODS We performed spinal CT angiography and reconstructed 3D images of segmental arteries in 41 patients. We classified the pathways and locations of the segmental arteries into 4 zones (A, B, C, and D) according to pedicle and vertebral endplates. We designated segmental arteries from T8 to L1 as "high-level segmental arteries" and those from L2 to L4, as "low-level segmental arteries." We compared the distribution of segmental arteries between these 2 groups. We also investigated anatomic variations of segmental arteries and the rate of occurrence of the artery of Adamkiewicz. RESULTS In all patients, 3D reconstruction images from spinal CT angiography clearly showed the pathways of segmental arteries on the vertebral bodies. Most of the segmental arteries passed the middle portion of the vertebral body (zones B and C). However, 51 of 738 segmental arteries (6.9%) had uncommon pathways (zones A and D), and segmental arteries from L2 to L4 had a higher incidence of uncommon pathways than higher level vertebrae (P < .05). We also observed 2 types of segmental artery anatomic variation, agenesis and dual supply. CONCLUSIONS We suggest that spinal CT angiography can help to precisely visualize the spinal segmental arteries and surrounding bony structures and can aid clinicians in deciding on optimal approaches for spinal surgery.
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Aldini G, Regazzoni L, Scevaroli M, Carini M, Chun HK, Cho SM, Park KM, Yeum K. An integrated high resolution mass spectrometric and bioinformatic approach for the rapid identification of flavonoids in plant extract. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.921.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kam HJ, Shin YM, Cho SM, Kim SY, Kim KW, Park RW. Development of a Decision Support Model for Screening Attention-deficit Hyperactivity Disorder with Actigraph-based Measurements of Classroom Activity. Appl Clin Inform 2010; 1:377-93. [PMID: 23616848 DOI: 10.4338/aci-2010-05-ra-0033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 10/10/2010] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Questionnaire-based ADHD screening tests may not always be objective or accurate, owing to both subjectivity and prejudice. Despite attempts to develop objective measures to characterize ADHD, no widely applicable index currently exists. The principal aim of this study was to develop a decision support model for ADHD screening by monitoring children's school activities using a 3-axial actigraph. METHODS Actigraphs were placed on the non-dominant wrists of 153 children for 3 hours, while they were at school. Children who scored high on the questionnaires were clinically examined by child psychiatrists, who then confirmed ADHD. Mean, variance, and ratios of low-level (0.5-1.0G) and high-level (1.6-3.2G) activity were extracted as activity features from 142 children (10 ADHD, 132 non-ADHD). Two decision-tree models were constructed using the C5.0 algorithm: [A] from whole hours (class + playtime) and [B] during classes. Accuracy, sensitivity, and specificity were evaluated. PPV, NPV, likelihood ratio, and AUC were also calculated for evaluation. RESULTS [Model A] One child without ADHD was misclassified, resulting in an accuracy score of 99.30%. Sensitivity and NPV were 1.0000. Specificity and PPV were 0.992 and 0.803-0.909, respectively. [Model B] Two children without ADHD were misclassified, resulting in an accuracy score of 98.59%. Specificity and PPV were scored at 0.985 and 0.671-0.832, respectively. CONCLUSION The selected features were consistent with the findings of previous studies. Objective screening of latent patients with ADHD can be accomplished with a simple watch-like sensor, which is worn for just a few hours while the child attends school. The model proposed herein can be applied to a great many children without heavy cost in time and manpower cost, and would generate valuable results from a public health perspective.
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Nissapatorn V, Noor Azmi MA, Cho SM, Fong MY, Init I, Rohela M, Khairul Anuar A, Quek KF, Latt HM. Toxoplasmosis: prevalence and risk factors. J OBSTET GYNAECOL 2009; 23:618-24. [PMID: 14617462 DOI: 10.1080/01443610310001604376] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A total of 200 pregnant women were recruited in this cross-sectional study. The overall seroprevalence of toxoplasmosis in pregnant women was found to be 49%, in which 39%, 4% and 6% for anti-Toxoplasma IgG, IgM and both anti-Toxoplasma IgG and IgM antibodies, respectively. We found the differences in Toxoplasma seroprevalence rates among the races were significant: the highest rate was in the Malays (55.7%), followed by the Indian (55.3%) and the Chinese (19.4%) (P<0.05) populations. An increase in Toxoplasma seroprevalence with increasing parity was detected (P<0.05). Women with no children had a prevalence of 39.7%, while women with one or more than two children had a prevalence of 44.2% and 62.9%, respectively. In this study, there was no significant association between Toxoplasma seroprevalence and various possible risk factors in pregnant women (P>0.05). When multivariate analysis was performed, no significant association between Toxoplasma seroprevalence and history of contact with cats, consumption of undercooked meat and blood transfusion was found (P>0.05). We did not find any newly diagnosed cases of acute acquired toxoplasmosis in pregnancy during the study period.
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Al-Khafaji A, Alousi M, Cho SM. A response to 'Autotriggering of pressure support ventilation during general anaesthesia'. Anaesthesia 2006; 61:619. [PMID: 16704626 DOI: 10.1111/j.1365-2044.2006.04680.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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