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  1. Article ; Online: A short guide on blue fluorescent proteins: limits and perspectives.

    Seo, Pil-Won / Kim, Geun-Joong / Kim, Jeong-Sun

    Applied microbiology and biotechnology

    2024  Volume 108, Issue 1, Page(s) 208

    Abstract: The advent of the so-called colorful biology era is in line with the discovery of fluorescent proteins (FPs), which can be widely used to detect the intracellular locations of macromolecules or to determine the abundance of metabolites in organelles. The ...

    Abstract The advent of the so-called colorful biology era is in line with the discovery of fluorescent proteins (FPs), which can be widely used to detect the intracellular locations of macromolecules or to determine the abundance of metabolites in organelles. The application of multiple FPs that emit different spectra and colors could be implemented to precisely evaluate cellular events. FPs were initially established with the emergence of the green fluorescent protein (GFP) from jellyfish. Red fluorescent proteins (RFPs) from marine anemones and several corals adopt fluorescent chromophores that are similar to GFP. Chromophores of GFP and GFP-like FPs are formed through the oxidative rearrangement of three chromophore-forming residues, thereby limiting their application to only oxidative environments. Alternatively, some proteins can be fluorescent upon their interaction with cellular prosthetic cofactors and, thus, work in aerobic and anaerobic conditions. The modification of an NADPH-dependent blue fluorescent protein (BFP) also expanded its application to the quantization of NADPH in the cellular environment. However, cofactor-dependent BFPs have an intrinsic weakness of poor photostability with a high fluorescent background. This review explores GFP-derived and NADPH-dependent BFPs with a focus on NADPH-dependent BFPs, which might be technically feasible in the near future upon coupling with two-photon fluorescence microscopy or nucleic acid-mimickers. KEY POINTS: • Oxidation-dependent GFP-like BFPs and redox-free NADPH-dependent BFPs • GFPs of weak photostability and intensity with a high fluorescent background • Real-time imaging using mBFP under two-photon fluorescence microscopy.
    MeSH term(s) Animals ; NADP ; Green Fluorescent Proteins/genetics ; Anthozoa ; Coloring Agents ; Phenylpropionates
    Chemical Substances NADP (53-59-8) ; Green Fluorescent Proteins (147336-22-9) ; 2-benzyl-3-formylpropanoic acid (96686-58-7) ; Coloring Agents ; Phenylpropionates
    Language English
    Publishing date 2024-02-14
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-024-13012-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Biotransformation of 2-keto-4-hydroxybutyrate via aldol condensation using an efficient and thermostable carboligase from Deinococcus radiodurans.

    Jeong, Yeon-Ju / Seo, Min-Ju / Sung, Bong Hyun / Kim, Jeong-Sun / Yeom, Soo-Jin

    Bioresources and bioprocessing

    2024  Volume 11, Issue 1, Page(s) 9

    Abstract: The bioconversion of 4-hydroxy-2-keto acid derivatives via aldol condensation of formaldehyde and pyruvate has received substantial attention as potential source of chemicals for production of amino acids, hydroxy carboxylic acids, and chiral aldehydes. ... ...

    Abstract The bioconversion of 4-hydroxy-2-keto acid derivatives via aldol condensation of formaldehyde and pyruvate has received substantial attention as potential source of chemicals for production of amino acids, hydroxy carboxylic acids, and chiral aldehydes. We developed an environmentally friendly biocatalyst consisting of a novel thermostable class II pyruvate aldolase from Deinococcus radiodurans with maltose-binding protein (MBP-DrADL), which has specific activity of 46.3 µmol min
    Language English
    Publishing date 2024-01-16
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2785482-6
    ISSN 2197-4365 ; 2197-4365
    ISSN (online) 2197-4365
    ISSN 2197-4365
    DOI 10.1186/s40643-024-00727-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: One-Pot Biosynthesis of 2-Keto-4-hydroxybutyrate from Cheap C1 Compounds Using Rationally Designed Pyruvate Aldolase and Methanol Dehydrogenase.

    Jeong, Yeon-Ju / Seo, Pil-Won / Seo, Min-Ju / Ju, Su-Bin / Kim, Jeong-Sun / Yeom, Soo-Jin

    Journal of agricultural and food chemistry

    2023  Volume 71, Issue 10, Page(s) 4328–4336

    Abstract: One-carbon chemicals (C 1s) are potential building blocks as they are cheap, sustainable, and abiotic components. Methanol-derived formaldehyde can be another versatile building block for the production of 2-keto-4-hydroxyacid derivatives that can be ... ...

    Abstract One-carbon chemicals (C 1s) are potential building blocks as they are cheap, sustainable, and abiotic components. Methanol-derived formaldehyde can be another versatile building block for the production of 2-keto-4-hydroxyacid derivatives that can be used for amino acids, hydroxy carboxylic acids, and chiral aldehydes. To produce 2-keto-4-hydroxybutyrate from C 1s in an environment-friendly way, we characterized an aldolase from
    MeSH term(s) Fructose-Bisphosphate Aldolase/metabolism ; Pyruvic Acid/metabolism ; Methanol/metabolism ; Aldehyde-Lyases/chemistry ; Formaldehyde
    Chemical Substances Fructose-Bisphosphate Aldolase (EC 4.1.2.13) ; Pyruvic Acid (8558G7RUTR) ; 2-keto-4-hydroxybutyrate ; alcohol dehydrogenase (acceptor) (EC 1.1.2.8) ; Methanol (Y4S76JWI15) ; Aldehyde-Lyases (EC 4.1.2.-) ; Formaldehyde (1HG84L3525)
    Language English
    Publishing date 2023-03-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 241619-0
    ISSN 1520-5118 ; 0021-8561
    ISSN (online) 1520-5118
    ISSN 0021-8561
    DOI 10.1021/acs.jafc.2c09108
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations in mismatch repair genes in methotrexate-resistant HT-29 cells.

    Kim, Ahreum / Shin, Jong-Yeon / Seo, Jeong-Sun

    Experimental & molecular medicine

    2021  Volume 53, Issue 9, Page(s) 1344–1355

    Abstract: DHFR gene amplification is commonly present in methotrexate (MTX)-resistant colon cancer cells and acute lymphoblastic leukemia. In this study, we proposed an integrative framework to characterize the amplified region by using a combination of single- ... ...

    Abstract DHFR gene amplification is commonly present in methotrexate (MTX)-resistant colon cancer cells and acute lymphoblastic leukemia. In this study, we proposed an integrative framework to characterize the amplified region by using a combination of single-molecule real-time sequencing, next-generation optical mapping, and chromosome conformation capture (Hi-C). We identified an amplification unit spanning 11 genes, from the DHFR gene to the ATP6AP1L gene position, with high adjusted interaction frequencies on chromosome 5 (~2.2 Mbp) and a twenty-fold tandemly amplified region, and novel inversions at the start and end positions of the amplified region as well as frameshift insertions in most of the MSH and MLH genes were detected. These mutations might stimulate chromosomal breakage and cause the dysregulation of mismatch repair. Characterizing the tandem gene-amplified unit may be critical for identifying the mechanisms that trigger genomic rearrangements. These findings may provide new insight into the mechanisms underlying the amplification process and the evolution of drug resistance.
    MeSH term(s) Alternative Splicing ; Biomarkers, Tumor ; Chromosome Mapping ; DNA Mismatch Repair ; Drug Resistance, Neoplasm/genetics ; Gene Amplification ; Gene Expression Regulation, Neoplastic ; Genomics/methods ; HT29 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Methotrexate/pharmacology ; Mutation ; Tandem Repeat Sequences ; Transcriptome
    Chemical Substances Biomarkers, Tumor ; Methotrexate (YL5FZ2Y5U1)
    Language English
    Publishing date 2021-09-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1328915-9
    ISSN 2092-6413 ; 1226-3613 ; 0378-8512
    ISSN (online) 2092-6413
    ISSN 1226-3613 ; 0378-8512
    DOI 10.1038/s12276-021-00668-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Integrative Genomic and Transcriptomic Analyses of Tumor Suppressor Genes and Their Role on Tumor Microenvironment and Immunity in Lung Squamous Cell Carcinoma.

    Kim, Ahreum / Lim, Sun Min / Kim, Joo-Hang / Seo, Jeong-Sun

    Frontiers in immunology

    2021  Volume 12, Page(s) 598671

    Abstract: Non-small-cell lung cancers (NSCLCs) are largely classified into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), which have different therapeutic options according to its molecular profiles and immune checkpoint expression, especially ...

    Abstract Non-small-cell lung cancers (NSCLCs) are largely classified into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), which have different therapeutic options according to its molecular profiles and immune checkpoint expression, especially PD-L1, which is a suppressive factor in the tumor microenvironment. The tumor microenvironment can be altered by the genomic mutations on specific innate immune genes as well as tumor suppressor genes, so it is essential to comprehend the association between tumor microenvironment and tumor suppressor genes to discover the promising immunotherapeutic strategy to overcome the resistance of immune check point blockade. In this study, we aimed to analyze how the somatic mutations in tumor suppressor genes affect the tumor immune microenvironment through a comprehensive analysis of mutational profiling on the representative tumor suppressor genes (
    MeSH term(s) Biomarkers, Tumor ; Carcinoma, Squamous Cell/etiology ; Carcinoma, Squamous Cell/metabolism ; Carcinoma, Squamous Cell/pathology ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Genes, Tumor Suppressor ; Genomics/methods ; Humans ; Lung Neoplasms/etiology ; Lung Neoplasms/metabolism ; Lung Neoplasms/pathology ; Lymphocytes, Tumor-Infiltrating/immunology ; Lymphocytes, Tumor-Infiltrating/metabolism ; Mutation ; Proportional Hazards Models ; Transcriptome ; Tumor Microenvironment/genetics ; Tumor Microenvironment/immunology
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2021-02-25
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2021.598671
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: ClinPharmSeq

    Seung-Been Lee / Jong-Yeon Shin / Nak-Jung Kwon / Changhoon Kim / Jeong-Sun Seo

    PLoS ONE, Vol 17, Iss 7, p e

    A targeted sequencing panel for clinical pharmacogenetics implementation.

    2022  Volume 0272129

    Abstract: The accurate identification of genetic variants contributing to therapeutic drug response or adverse effects is the first step in implementation of precision drug therapy. Targeted sequencing has recently become a common methodology for large-scale ... ...

    Abstract The accurate identification of genetic variants contributing to therapeutic drug response or adverse effects is the first step in implementation of precision drug therapy. Targeted sequencing has recently become a common methodology for large-scale studies of genetic variation thanks to its favorable balance between low cost, high throughput, and deep coverage. Here, we present ClinPharmSeq, a targeted sequencing panel of 59 genes with associations to pharmacogenetic (PGx) phenotypes, as a platform to explore the relationship between drug response and genetic variation, both common and rare. For validation, we sequenced DNA from 64 ethnically diverse Coriell samples with ClinPharmSeq to call star alleles (haplotype patterns) in 27 genes using the bioinformatics tool PyPGx. These reference samples were extensively characterized by multiple laboratories using PGx testing assays and, more recently, whole genome sequencing. We found that ClinPharmSeq can consistently generate deep-coverage data (mean = 274x) with high uniformity (30x or above = 94.8%). Our genotype analysis identified a total of 185 unique star alleles from sequencing data, and showed that diplotype calls from ClinPharmSeq are highly concordant with that from previous publications (97.6%) and whole genome sequencing (97.9%). Notably, all 19 star alleles with complex structural variation including gene deletions, duplications, and hybrids were recalled with 100% accuracy. Altogether, these results demonstrate that the ClinPharmSeq platform offers a feasible path for broad implementation of PGx testing and optimization of individual drug treatments.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Efficient regeneration of protoplasts from

    Jeong, Yeong Yeop / Noh, Yoo-Sun / Kim, Suk Weon / Seo, Pil Joon

    Biology methods & protocols

    2024  Volume 9, Issue 1, Page(s) bpae008

    Abstract: Protoplast regeneration has become a key platform for genetic and genome engineering. However, we lack reliable and reproducible methods for efficient protoplast regeneration for tomato ( ...

    Abstract Protoplast regeneration has become a key platform for genetic and genome engineering. However, we lack reliable and reproducible methods for efficient protoplast regeneration for tomato (
    Language English
    Publishing date 2024-02-06
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2396-8923
    ISSN (online) 2396-8923
    DOI 10.1093/biomethods/bpae008
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  8. Article ; Online: ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation.

    Lee, Seung-Been / Shin, Jong-Yeon / Kwon, Nak-Jung / Kim, Changhoon / Seo, Jeong-Sun

    PloS one

    2022  Volume 17, Issue 7, Page(s) e0272129

    Abstract: The accurate identification of genetic variants contributing to therapeutic drug response or adverse effects is the first step in implementation of precision drug therapy. Targeted sequencing has recently become a common methodology for large-scale ... ...

    Abstract The accurate identification of genetic variants contributing to therapeutic drug response or adverse effects is the first step in implementation of precision drug therapy. Targeted sequencing has recently become a common methodology for large-scale studies of genetic variation thanks to its favorable balance between low cost, high throughput, and deep coverage. Here, we present ClinPharmSeq, a targeted sequencing panel of 59 genes with associations to pharmacogenetic (PGx) phenotypes, as a platform to explore the relationship between drug response and genetic variation, both common and rare. For validation, we sequenced DNA from 64 ethnically diverse Coriell samples with ClinPharmSeq to call star alleles (haplotype patterns) in 27 genes using the bioinformatics tool PyPGx. These reference samples were extensively characterized by multiple laboratories using PGx testing assays and, more recently, whole genome sequencing. We found that ClinPharmSeq can consistently generate deep-coverage data (mean = 274x) with high uniformity (30x or above = 94.8%). Our genotype analysis identified a total of 185 unique star alleles from sequencing data, and showed that diplotype calls from ClinPharmSeq are highly concordant with that from previous publications (97.6%) and whole genome sequencing (97.9%). Notably, all 19 star alleles with complex structural variation including gene deletions, duplications, and hybrids were recalled with 100% accuracy. Altogether, these results demonstrate that the ClinPharmSeq platform offers a feasible path for broad implementation of PGx testing and optimization of individual drug treatments.
    MeSH term(s) Alleles ; Genotype ; Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Pharmacogenetics/methods ; Whole Genome Sequencing/methods
    Language English
    Publishing date 2022-07-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0272129
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  9. Article ; Online: Structural characterization of the type I-B CRISPR Cas7 from Thermobaculum terrenum.

    Seo, Pil-Won / Gu, Do-Heon / Kim, Ji-Won / Kim, Jun-Hong / Park, Suk-Youl / Kim, Jeong-Sun

    Biochimica et biophysica acta. Proteins and proteomics

    2023  Volume 1871, Issue 3, Page(s) 140900

    Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) in many prokaryotes functions as an adaptive immune system against mobile genetic elements. A heterologous ribonucleoprotein silencing complex composed of CRISPR-associated (Cas) proteins ...

    Abstract Clustered regularly interspaced short palindromic repeats (CRISPR) in many prokaryotes functions as an adaptive immune system against mobile genetic elements. A heterologous ribonucleoprotein silencing complex composed of CRISPR-associated (Cas) proteins and a CRISPR RNA (crRNA) neutralizes the incoming mobile genetic elements. The type I and III silencing complexes commonly include a protein-helical backbone of several copies of identical subunits, for example, Cas7 in the type I silencing complex. In this study, we structurally characterized type I-B Cas7 (Csh2 from Thermobaculum terrenum; TterCsh2). The revealed crystal structure of TterCsh2 shows a typical glove-like architecture of Cas7, which consists of a palm, a thumb, and a finger domain. Csh2 proteins have 5 conserved sequence motifs that are arranged to form a presumable crRNA-binding site in the TterCsh2 structure. This crRNA binding site of TterCsh2 is structurally and potentially comparable to those observed in helix-forming Cas7 structures in other sub-types. Analysis of the reported Cas7 structures and their sequences suggests that Cas7s can be divided into at least two sub-classes. These data will broaden our understanding on the Cascade complex of CRISPR/Cas systems.
    MeSH term(s) Bacteria ; RNA ; Binding Sites
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2023-01-20
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2918798-9
    ISSN 1878-1454 ; 1570-9639
    ISSN (online) 1878-1454
    ISSN 1570-9639
    DOI 10.1016/j.bbapap.2023.140900
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  10. Article ; Online: The tumor immune microenvironmental analysis of 2,033 transcriptomes across 7 cancer types

    Sungjae Kim / Ahreum Kim / Jong-Yeon Shin / Jeong-Sun Seo

    Scientific Reports, Vol 10, Iss 1, Pp 1-

    2020  Volume 10

    Abstract: Abstract Understanding the tumor microenvironment is important to efficiently identify appropriate patients for immunotherapies in a variety of cancers. Here, we presented the tumor microenvironmental analysis of 2,033 cancer samples across 7 cancer ... ...

    Abstract Abstract Understanding the tumor microenvironment is important to efficiently identify appropriate patients for immunotherapies in a variety of cancers. Here, we presented the tumor microenvironmental analysis of 2,033 cancer samples across 7 cancer types: colon adenocarcinoma, skin cutaneous melanoma, kidney renal papillary cell carcinoma, sarcoma, pancreatic adenocarcinoma, glioblastoma multiforme, and pheochromocytoma / paraganglioma from The Cancer Genome Atlas cohort. Unsupervised hierarchical clustering based on the gene expression profiles separated the cancer samples into two distinct clusters, and characterized those into immune-competent and immune-deficient subtypes using the estimated abundances of infiltrated immune and stromal cells. We demonstrated differential tumor microenvironmental characteristics of immune-competent subtypes across 7 cancer types, particularly immunosuppressive tumor microenvironment features in kidney renal papillary cell carcinoma with significant poorer survival rates and immune-supportive features in sarcoma and skin cutaneous melanoma. Additionally, differential genomic instability patterns between the subtypes were found across the cancer types, and discovered that immune-competent subtypes in most of cancer types had significantly higher immune checkpoint gene expressions. Overall, this study suggests that our subtyping approach based on transcriptomic data could contribute to precise prediction of immune checkpoint inhibitor responses in a wide range of cancer types.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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