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  1. Article ; Online: De Novo Assembly and Annotation of the Vaginal Metatranscriptome Associated with Bacterial Vaginosis.

    Cho, Won Kyong / Jo, Yeonhwa / Jeong, Seri

    International journal of molecular sciences

    2022  Volume 23, Issue 3

    Abstract: The vaginal microbiome plays an important role in women's health and disease. Here we reanalyzed 40 vaginal transcriptomes from a previous study of de novo assembly (metaT-Assembly) followed by functional annotation. We identified 286,293 contigs and ... ...

    Abstract The vaginal microbiome plays an important role in women's health and disease. Here we reanalyzed 40 vaginal transcriptomes from a previous study of de novo assembly (metaT-Assembly) followed by functional annotation. We identified 286,293 contigs and further assigned them to 25 phyla, 209 genera, and 339 species.
    MeSH term(s) Adult ; Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Female ; Gene Expression Profiling/methods ; Gene Expression Regulation, Bacterial ; Humans ; Metagenomics/methods ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Vagina/microbiology ; Vaginosis, Bacterial/microbiology ; Young Adult
    Chemical Substances DNA, Bacterial ; DNA, Ribosomal ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2022-01-30
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23031621
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: De Novo Assembly and Annotation of the Vaginal Metatranscriptome Associated with Bacterial Vaginosis

    Won Kyong Cho / Yeonhwa Jo / Seri Jeong

    International Journal of Molecular Sciences, Vol 23, Iss 1621, p

    2022  Volume 1621

    Abstract: The vaginal microbiome plays an important role in women’s health and disease. Here we reanalyzed 40 vaginal transcriptomes from a previous study of de novo assembly (metaT-Assembly) followed by functional annotation. We identified 286,293 contigs and ... ...

    Abstract The vaginal microbiome plays an important role in women’s health and disease. Here we reanalyzed 40 vaginal transcriptomes from a previous study of de novo assembly (metaT-Assembly) followed by functional annotation. We identified 286,293 contigs and further assigned them to 25 phyla, 209 genera, and 339 species. Lactobacillus iners and Lactobacillus crispatus dominated the microbiome of non-bacterial vaginosis (BV) samples, while a complex of microbiota was identified from BV-associated samples. The metaT-Assembly identified a higher number of bacterial species than the 16S rRNA amplicon and metaT-Kraken methods. However, metaT-Assembly and metaT-Kraken exhibited similar major bacterial composition at the species level. Binning of metatranscriptome data resulted in 176 bins from major known bacteria and several unidentified bacteria in the vagina. Functional analyses based on Clusters of Orthologous Genes (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways suggested that a higher number of transcripts were expressed by the microbiome complex in the BV-associated samples than in non-BV-associated samples. The KEGG pathway analysis with an individual bacterial genome identified specific functions of the identified bacterial genome. Taken together, we demonstrated that the metaT-Assembly approach is an efficient tool to understand the dynamic microbial communities and their functional roles associated with the human vagina.
    Keywords vagina ; transcriptome ; de novo assembly ; microbiome ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 572
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: A tryptophan-based assay method to search regulatory compounds for transcriptionally controlled tumor protein.

    Jo, Seri / Jang, Eun-Hwa / Kim, Hwa Young / Lee, Kyunglim / Kim, Mi-Sun / Shin, Dong Hae

    Biochemical and biophysical research communications

    2023  Volume 692, Page(s) 149363

    Abstract: Transcriptionally controlled tumor protein (TCTP) is a highly conserved protein performing a large number of cellular functions by binding with various partner proteins. The importance of its roles in many diseases requires an assay method to find ... ...

    Abstract Transcriptionally controlled tumor protein (TCTP) is a highly conserved protein performing a large number of cellular functions by binding with various partner proteins. The importance of its roles in many diseases requires an assay method to find regulatory compounds. However, the molecular characteristics of TCTP made it difficult to search for chemicals interacting with it. In this study, a tryptophan-based assay method was designed and Y151W mutant TCTP was constructed to search binding chemicals. Since there is no tryptophan in the native sequence of TCTP, the incorporation of tryptophan in the Y151W mutant was very effective to establish the method. A flavonoid library was employed to the assay with the method. With the native and Y151W mutant TCTPs, three flavonoids such as morin, myricetin and isobavachalcone have been found to interact with TCTP. Combined with native gel electrophoresis, the binding region of isobavachalcone was suggested to be the flexible loop of TCTP. This approach can be easily applicable to find binding compounds of proteins with similar molecular characteristics of TCTP.
    MeSH term(s) Humans ; Tryptophan ; Biomarkers, Tumor/metabolism ; Tumor Protein, Translationally-Controlled 1 ; Neoplasm Proteins/metabolism ; Neoplasms/metabolism
    Chemical Substances isobavachalcone (20784-50-3) ; Tryptophan (8DUH1N11BX) ; Biomarkers, Tumor ; Tumor Protein, Translationally-Controlled 1 ; Neoplasm Proteins
    Language English
    Publishing date 2023-12-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2023.149363
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro.

    Jo, Seri / Kim, Hwa Young / Shin, Dong Hae / Kim, Mi-Sun

    International journal of molecular sciences

    2022  Volume 23, Issue 9

    Abstract: 3CLpro of SARS-CoV-2 is a promising target for developing anti-COVID19 agents. In order to evaluate the catalytic activity of 3CLpros according to the presence or absence of the dimerization domain, two forms had been purified and tested. Enzyme kinetic ... ...

    Abstract 3CLpro of SARS-CoV-2 is a promising target for developing anti-COVID19 agents. In order to evaluate the catalytic activity of 3CLpros according to the presence or absence of the dimerization domain, two forms had been purified and tested. Enzyme kinetic studies with a FRET method revealed that the catalytic domain alone presents enzymatic activity, despite it being approximately 8.6 times less than that in the full domain. The catalytic domain was crystallized and its X-ray crystal structure has been determined to 2.3 Å resolution. There are four protomers in the asymmetric unit. Intriguingly, they were packed as a dimer though the dimerization domain was absent. The RMSD of superimposed two catalytic domains was 0.190 for 182 Cα atoms. A part of the long hinge loop (LH-loop) from Gln189 to Asp197 was not built in the model due to its flexibility. The crystal structure indicates that the decreased proteolytic activity of the catalytic domain was due to the incomplete construction of the substrate binding part built by the LH-loop. A structural survey with other 3CLpros showed that SARS-CoV families do not have interactions between DM-loop due to the conformational difference at the last turn of helix α7 compared with others. Therefore, we can conclude that the monomeric form contains nascent enzyme activity and that its efficiency increases by dimerization. This new insight may contribute to understanding the behavior of SARS-CoV-2 3CLpro and thus be useful in developing anti-COVID-19 agents.
    MeSH term(s) COVID-19 ; Catalytic Domain ; Coronavirus 3C Proteases ; Dimerization ; Humans ; Kinetics ; SARS-CoV-2 ; X-Rays
    Chemical Substances Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2022-05-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23095268
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A study of inhibitors of d-

    Kim, Suwon / Jo, Seri / Kim, Mi-Sun / Shin, Dong Hae

    Journal of enzyme inhibition and medicinal chemistry

    2021  Volume 36, Issue 1, Page(s) 776–784

    Abstract: d- ...

    Abstract d-
    MeSH term(s) Anti-Bacterial Agents/chemical synthesis ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Burkholderia pseudomallei/drug effects ; Burkholderia pseudomallei/enzymology ; Enzyme Inhibitors/chemical synthesis ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Molecular Docking Simulation ; Nucleotidyltransferases/antagonists & inhibitors ; Nucleotidyltransferases/metabolism
    Chemical Substances Anti-Bacterial Agents ; Enzyme Inhibitors ; Nucleotidyltransferases (EC 2.7.7.-) ; glutamine-synthetase adenylyltransferase (EC 2.7.7.42)
    Language English
    Publishing date 2021-03-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2082578-X
    ISSN 1475-6374 ; 1475-6366
    ISSN (online) 1475-6374
    ISSN 1475-6366
    DOI 10.1080/14756366.2021.1900166
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online ; E-Book: Contracting for design and construction services in the public sector

    Adler, John O.

    (Cornerstones of Public Procurement Series)

    2024  

    Abstract: In this timely new book, author John Adler outlines the design and construction procurement process step-by-step. He explores the procurement approaches for design and construction from practical and public procurement best practice perspectives. ...

    Author's details John O. Adler
    Series title Cornerstones of Public Procurement Series
    Abstract In this timely new book, author John Adler outlines the design and construction procurement process step-by-step. He explores the procurement approaches for design and construction from practical and public procurement best practice perspectives.
    Keywords Public works/Planning ; Government purchasing ; Construction projects/Planning ; Construction industry
    Subject code 363.60973
    Language English
    Size 1 online resource (283 pages)
    Publisher Routledge
    Publishing place New York, NY
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 1-000-90244-7 ; 1-003-27697-0 ; 1-00-327697-0 ; 9781032233765 ; 978-1-000-90244-0 ; 978-1-003-27697-5 ; 978-1-00-327697-5 ; 1032233761
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  7. Article ; Online: Amentoflavone, a potent natural matrix metalloproteinase 2 inhibitor.

    Jo, Seri / Kim, Mi-Sun / Kim, Hwa-Young / Kim, Suwon / Kam, Heejin / Choi, Haein / Shin, Dong Hae

    Natural product research

    2023  , Page(s) 1–8

    Abstract: Gelatinase A (MMP-2) has been studied and proven to play a vital role in the intrusion and metastasis of cancer. Flavonoids influence on molecular and cellular functions of MMP-2 and thus a systematic investigation of flavonoids against the ... ...

    Abstract Gelatinase A (MMP-2) has been studied and proven to play a vital role in the intrusion and metastasis of cancer. Flavonoids influence on molecular and cellular functions of MMP-2 and thus a systematic investigation of flavonoids against the metalloproteolytic activity of MMP-2 has been performed in this study. A fluorescence resonance energy transfer method was used to investigate the inhibitory activities of various flavonoids. Flavone, flavonol and isobavachalcone derivatives showed their inhibitory activity against MMP-2. Surprisingly, the most effective inhibitor was Amentoflavone and its blocking function was superior to other flavonoids. Its IC50 value was 0.689 μM. An induced-fit docking study was carried out to survey its extraordinary activity. The binding mode of Amentoflavone is quite similar to that of (2 ∼ {S})-2-[2-[4-(4-methoxyphenyl) phenyl] sulfanylphenyl] pentanedioic acid complexed with MMP-9. Amentoflavone interacts with the functional zinc and catalytic residue, Glu202. Therefore, the docking study reasonably confirmed the strong inhibitory activity of Amentoflavone.
    Language English
    Publishing date 2023-12-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2185747-7
    ISSN 1478-6427 ; 1478-6419
    ISSN (online) 1478-6427
    ISSN 1478-6419
    DOI 10.1080/14786419.2023.2294108
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A triple-targeting inhibitory activity of Rose Bengal on polysaccharide biosynthesis of Burkholderia pseudomallei.

    Kim, Suwon / Jo, Seri / Kim, Mi-Sun / Shin, Dong H

    Archiv der Pharmazie

    2021  Volume 354, Issue 6, Page(s) e2000360

    Abstract: Sugar nucleotidyltransferases (SNTs) participate in various biosynthesis pathways constructing polysaccharides in Gram-negative bacteria. In this study, a triple-targeting inhibitory activity of Rose Bengal against SNTs such as d-glycero-α-d-manno- ... ...

    Abstract Sugar nucleotidyltransferases (SNTs) participate in various biosynthesis pathways constructing polysaccharides in Gram-negative bacteria. In this study, a triple-targeting inhibitory activity of Rose Bengal against SNTs such as d-glycero-α-d-manno-heptose-1-phosphate guanylyltransferase (HddC), d-glycero-β-d-manno-heptose-1-phosphate adenylyltransferase (HldC), and 3-deoxy-d-manno-oct-2-ulosonic acid cytidylyltransferase (KdsB) from Burkholderia pseudomallei is provided. Rose Bengal effectively suppresses the nucleotidyltransferase activity of the three SNTs, and its IC
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Burkholderia pseudomallei/drug effects ; Burkholderia pseudomallei/enzymology ; Drug Design ; Enzyme Inhibitors/pharmacology ; Humans ; Inhibitory Concentration 50 ; Melioidosis/drug therapy ; Melioidosis/microbiology ; Nucleotidyltransferases/antagonists & inhibitors ; Polysaccharides, Bacterial/biosynthesis ; Rose Bengal/pharmacology
    Chemical Substances Anti-Bacterial Agents ; Enzyme Inhibitors ; Polysaccharides, Bacterial ; Rose Bengal (1ZPG1ELY14) ; Nucleotidyltransferases (EC 2.7.7.-) ; guanylyltransferase (EC 2.7.7.-) ; glutamine-synthetase adenylyltransferase (EC 2.7.7.42)
    Language English
    Publishing date 2021-02-08
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 6381-2
    ISSN 1521-4184 ; 0365-6233 ; 1437-1014
    ISSN (online) 1521-4184
    ISSN 0365-6233 ; 1437-1014
    DOI 10.1002/ardp.202000360
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online ; E-Book: Physiology of marine mammals

    Castellini, Michael / Mellish, Jo-Ann

    adaptations to the ocean

    (CRC marine biology series)

    2024  

    Abstract: This unique undergraduate textbook considers what makes a marine mammal different from terrestrial mammals, focusing on the physiological and biochemical characteristics that have allowed this group of mammals to effectively exploit the hostile marine ... ...

    Author's details edited by Michael Castellini and Jo-Ann Mellish
    Series title CRC marine biology series
    Abstract "This unique undergraduate textbook considers what makes a marine mammal different from terrestrial mammals, focusing on the physiological and biochemical characteristics that have allowed this group of mammals to effectively exploit the hostile marine environment. The contents are organised around common student questions such as " How do mammals stay warm in a cold ocean?" while each chapter provides a set of PowerPoint slides for instructors to use in teaching. Study Questions and Future Implications points conclude each chapter, while full-colour images and comprehensive, accessible content make this the definitive textbook for marine mammal physiology"--
    Keywords Marine animals/Physiology ; Marine animals/Adaptation
    Subject code 591.77
    Language English
    Dates of publication 2024-2024
    Size 1 online resource (369 pages) :, illustrations.
    Edition First edition.
    Publisher CRC Press
    Publishing place Boca Raton, FL
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 1-00-329746-3 ; 1-000-87310-2 ; 978-1-00-329746-8 ; 9781032285702 ; 978-1-000-87310-8 ; 1032285702
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  10. Article ; Online: Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro

    Seri Jo / Hwa Young Kim / Dong Hae Shin / Mi-Sun Kim

    International Journal of Molecular Sciences, Vol 23, Iss 5268, p

    2022  Volume 5268

    Abstract: 3CLpro of SARS-CoV-2 is a promising target for developing anti-COVID19 agents. In order to evaluate the catalytic activity of 3CLpros according to the presence or absence of the dimerization domain, two forms had been purified and tested. Enzyme kinetic ... ...

    Abstract 3CLpro of SARS-CoV-2 is a promising target for developing anti-COVID19 agents. In order to evaluate the catalytic activity of 3CLpros according to the presence or absence of the dimerization domain, two forms had been purified and tested. Enzyme kinetic studies with a FRET method revealed that the catalytic domain alone presents enzymatic activity, despite it being approximately 8.6 times less than that in the full domain. The catalytic domain was crystallized and its X-ray crystal structure has been determined to 2.3 Å resolution. There are four protomers in the asymmetric unit. Intriguingly, they were packed as a dimer though the dimerization domain was absent. The RMSD of superimposed two catalytic domains was 0.190 for 182 Cα atoms. A part of the long hinge loop (LH-loop) from Gln189 to Asp197 was not built in the model due to its flexibility. The crystal structure indicates that the decreased proteolytic activity of the catalytic domain was due to the incomplete construction of the substrate binding part built by the LH-loop. A structural survey with other 3CLpros showed that SARS-CoV families do not have interactions between DM-loop due to the conformational difference at the last turn of helix α7 compared with others. Therefore, we can conclude that the monomeric form contains nascent enzyme activity and that its efficiency increases by dimerization. This new insight may contribute to understanding the behavior of SARS-CoV-2 3CLpro and thus be useful in developing anti-COVID-19 agents.
    Keywords SARS-CoV-2 3CL protease ; catalytic domain ; X-ray crystallography ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 500
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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