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Works (22)
Updated: August 16th, 2024 13:37
2012 journal article
Structurally Conserved Nop56/58 N-terminal Domain Facilitates Archaeal Box C/D Ribonucleoprotein-guided Methyltransferase Activity
JOURNAL OF BIOLOGICAL CHEMISTRY, 287(23), 19418–19428.
MeSH headings : Archaeal Proteins / chemistry; Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Chromosomal Proteins, Non-Histone / chemistry; Chromosomal Proteins, Non-Histone / genetics; Chromosomal Proteins, Non-Histone / metabolism; Methanococcales / chemistry; Methanococcales / genetics; Methanococcales / metabolism; Methyltransferases / chemistry; Methyltransferases / genetics; Methyltransferases / metabolism; Protein Binding; Protein Structure, Tertiary; Ribonucleoproteins / chemistry; Ribonucleoproteins / genetics; Ribonucleoproteins / metabolism
TL;DR:
The archaeal Nop56/58 NTD exhibits a conserved domain structure whose exceptionally stable interaction with fibrillarin plays a role in both RNP assembly and methyltransferase activity.
(via Semantic Scholar)
open access via www.jbc.org (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2009 journal article
Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome
BMC Structural Biology, 9.
Source: NC State University Libraries
Added: August 6, 2018
2007 journal article
Conformational energy and structure in canonical and noncanonical forms of tRNA determined by temperature analysis of the rate of s(4)U8-C13 photocrosslinking
RNA, 13(11), 2000–2011.
author keywords: RNA tertiary structure; photocrosslinking rates; activation energy; conformational energy; T-1 excited state lifetimes
MeSH headings : Base Composition; Base Sequence; Buffers; Cytosine / chemistry; Molecular Sequence Data; Nucleic Acid Conformation; RNA, Bacterial; RNA, Transfer / chemistry; RNA, Transfer, Met / chemistry; RNA, Transfer, Phe / chemistry; RNA, Transfer, Val / chemistry; Temperature; Thermodynamics; Uracil / chemistry
TL;DR:
Measurements of the temperature dependence of the rate constants for photocrosslinking between the s(4)U8 and C13 have been used to investigate the tRNA conformational energy and structure in Escherichia coli tRNA(Val), tRNA (Phe), and t RNA(fMet) under different conditions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2005 journal article
Internucleotide movements during formation of 16 S rRNA-rRNA photocrosslinks and their connection to the 30 S subunit conformational dynamics
JOURNAL OF MOLECULAR BIOLOGY, 354(2), 358–374.
Contributors: W. Huggins n, S. Ghosh n , K. Nanda n & n
author keywords: 16 S rRNA tertiary structure; photocrosslinking; conformational flexibility
MeSH headings : Base Pairing; Base Sequence; Binding Sites; Cross-Linking Reagents; Escherichia coli / chemistry; Escherichia coli / genetics; Escherichia coli / radiation effects; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation / radiation effects; Nucleotides / chemistry; Nucleotides / metabolism; Nucleotides / radiation effects; Photochemistry; Protein Conformation / radiation effects; Protein Subunits; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / radiation effects; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / metabolism; RNA, Ribosomal, 16S / radiation effects; RNA, Transfer / chemistry; RNA, Transfer / genetics; RNA, Transfer / metabolism; Ribosomal Proteins / chemistry; Ribosomal Proteins / genetics; Ribosomal Proteins / metabolism; Ribosomes / chemistry; Ribosomes / metabolism; Ribosomes / radiation effects; Ultraviolet Rays
TL;DR:
Results show that photocrosslinking is an indicator for sites where there is internucleotide conformational flexibility and these sites are largely restricted to parts of the 30 S subunit associated with ribosome function.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2004 journal article
A 16S rRNA-tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome
NUCLEIC ACIDS RESEARCH, 32(22), 6548–6556.
MeSH headings : Base Sequence; Binding Sites; Escherichia coli / genetics; Kinetics; Light; Molecular Sequence Data; Nucleotides / analysis; Puromycin / pharmacology; RNA, Bacterial / chemistry; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / metabolism; RNA, Transfer, Amino Acyl / chemistry; RNA, Transfer, Amino Acyl / metabolism; RNA, Transfer, Val / chemistry; RNA, Transfer, Val / metabolism; Ribosomes / chemistry; Ribosomes / metabolism; Ribosomes / radiation effects; Transcription, Genetic
TL;DR:
Results indicate an altered interaction between the tRNA anticodon and the 30S subunit for the t RNA in the P/E hybrid state compared with its interaction in the classic P/P state.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2004 journal article
Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome
NUCLEIC ACIDS RESEARCH, 32(4), 1518–1526.
MeSH headings : Base Sequence; Escherichia coli / genetics; Lasers; Molecular Sequence Data; Photons; Purine Nucleosides / radiation effects; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / radiation effects; Ribosomes / radiation effects; Ultraviolet Rays
TL;DR:
Cross- linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than arefrequency obtained with transilluminator irradiation, probably due to intensity-dependent photoreversal.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2004 journal article
Pattern of 4-thiouridine-induced cross-linking in 16S ribosomal RNA in the Escherichia coli 30S subunit
BIOCHEMISTRY, 43(28), 8923–8934.
MeSH headings : Base Sequence; Escherichia coli / genetics; Molecular Sequence Data; Molecular Structure; Photochemistry; RNA, Ribosomal, 16S / chemistry; Ribosomes / chemistry; Sequence Analysis, RNA; Thiouridine / chemistry; Ultraviolet Rays
TL;DR:
The locations of RNA-RNA cross-links in 16S rRNA were determined after in vivo incorporation of 4-thiouridine (s(4)U) into RNA in a strain of Escherichia coli deficient in pyrimidine synthesis and irradiation at >320 nm to find RNA cross- links different from UVB-induced cross- Links that would be valuable for monitoring the 30S subunit in functional complexes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2003 journal article
Action spectra for UV-light induced RNA-RNA crosslinking in 16S ribosomal RNA in the ribosome
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 2(6), 688–693.
MeSH headings : Base Sequence; DNA / chemistry; DNA / radiation effects; Electrophoresis, Polyacrylamide Gel; Escherichia coli / chemistry; Molecular Sequence Data; Nucleic Acid Conformation; Photochemistry; RNA, Bacterial / chemistry; RNA, Bacterial / metabolism; RNA, Bacterial / radiation effects; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / metabolism; RNA, Ribosomal, 16S / radiation effects; Ribosomes / radiation effects; Spectrophotometry, Ultraviolet; Ultraviolet Rays
TL;DR:
The frequency of crosslinking for eight 16S rRNA crosslinks was determined as a function of wavelength of irradiation and the action spectra correspond to the absorption spectra of at least one of the participating nucleotides.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2003 journal article
Conformational change in the 16S rRNA in the Escherichia coli 70S ribosome induced by P/P- and P/E-site tRNA(Phe) binding
BIOCHEMISTRY, 42(49), 14386–14396.
MeSH headings : Acetylation / radiation effects; Binding Sites / radiation effects; Cytosine / chemistry; Cytosine / radiation effects; Escherichia coli / chemistry; Escherichia coli / genetics; Escherichia coli / radiation effects; Nucleic Acid Conformation / radiation effects; Peptide Chain Elongation, Translational / genetics; Peptide Chain Elongation, Translational / radiation effects; Photochemistry; Poly U / chemistry; Poly U / genetics; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / radiation effects; RNA, Messenger / chemistry; RNA, Messenger / genetics; RNA, Messenger / radiation effects; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / genetics; RNA, Ribosomal, 16S / radiation effects; RNA, Transfer, Phe / chemistry; RNA, Transfer, Phe / genetics; RNA, Transfer, Phe / radiation effects; Ribosomes / chemistry; Ribosomes / genetics; Ribosomes / radiation effects; Transcription, Genetic / radiation effects; Ultraviolet Rays
TL;DR:
Results indicate a limited structural change in the small subunit around C967 and C1400 during tRNA P-site binding sensitive to the type of mRNA that is used, and indicates an alternative arrangement in this region in empty ribosomes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2001 journal article
Arrangement of the central pseudoknot region of 16S rRNA in the 30S ribosomal subunit determined by site-directed 4-thiouridine crosslinking
RNA, 7(1), 71–84.
author keywords: 16S rRNA three-dimensional structure; intramolecular RNA-RNA crosslinks; mRNA decoding region
MeSH headings : Base Sequence; Cross-Linking Reagents; DNA Ligases / metabolism; DNA, Single-Stranded / chemistry; Escherichia coli / genetics; Escherichia coli / virology; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Oligoribonucleotides / chemical synthesis; Oligoribonucleotides / chemistry; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / drug effects; Reverse Transcriptase Polymerase Chain Reaction; Ribosomes / chemistry; Ribosomes / drug effects; Ribosomes / ultrastructure; Thiouridine / pharmacology; Transcription, Genetic
TL;DR:
Results indicate that part of the central pseudoknot is in close contact with the decoding region, with helix 27 in the 885-912 interval and with part of domain III RNA.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2001 journal article
Construction and analysis of base-paired regions of the 16S rRNA in the 30S ribosomal subunit determined by constraint satisfaction molecular modelling
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 19(6), 495–513.
author keywords: molecular modelling; RNA structure; ribosomal RNA; comparative sequence analysis
MeSH headings : Base Pairing; Base Sequence; Computer Simulation; Escherichia coli / genetics; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; RNA; RNA, Bacterial / chemistry; RNA, Ribosomal, 16S / chemistry; Ribosomes
TL;DR:
These molecular models provide insight into the connection between patterns of H-bonding, the presence of unpaired nucleotides, and the overall geometry of each element.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2001 journal article
Short-range RNA-RNA crosslinking methods to determine rRNA structure and interactions
METHODS, 25(3), 333–343.
MeSH headings : Cross-Linking Reagents / pharmacology; DNA Ligases / chemistry; DNA Ligases / isolation & purification; DNA, Complementary / chemistry; Electrophoresis, Polyacrylamide Gel; Models, Molecular; Nucleic Acid Conformation; RNA / chemistry; RNA / ultrastructure; RNA, Messenger / chemistry; RNA, Ribosomal / chemistry; RNA, Ribosomal, 16S / chemistry; RNA, Transfer / chemistry; Ultraviolet Rays
TL;DR:
Details of procedures to analyze RNA-RNA crosslinks made by far-UV irradiation (< 300 nm) or made by irradiation with near-UV light on RNA containing photosensitive nucleotides, in the present case containing 4-thiouridine are described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2000 journal article
Initiation factor 3-induced structural changes in the 30 S ribosomal subunit and in complexes containing tRNA(f)(Met) and mRNA
JOURNAL OF MOLECULAR BIOLOGY, 299(3), 615–628.
author keywords: initiation factor 3; UV-induced crosslinking; 16 S rRNA coformational change; molecular model; 16 S rRNA-tRNA interaction
MeSH headings : Alkalies / metabolism; Anticodon / genetics; Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Base Sequence; Binding Sites / radiation effects; Escherichia coli / chemistry; Escherichia coli / genetics; Hydrolysis; Models, Molecular; Nucleic Acid Conformation; Peptide Initiation Factors / chemistry; Peptide Initiation Factors / metabolism; Prokaryotic Initiation Factor-3; Protein Binding / radiation effects; Protein Structure, Tertiary; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; RNA, Messenger / genetics; RNA, Messenger / metabolism; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / genetics; RNA, Ribosomal, 16S / metabolism; RNA, Transfer, Met / genetics; RNA, Transfer, Met / metabolism; RNA-Binding Proteins / chemistry; RNA-Binding Proteins / metabolism; Ribosomal Proteins / chemistry; Ribosomal Proteins / metabolism; Ribosomes / chemistry; Ribosomes / genetics; Ribosomes / metabolism; Transcription, Genetic / genetics; Ultraviolet Rays
TL;DR:
Initiation factor 3 (IF3) acts to switch the decoding preference of the small ribosomal subunit from elongator to initiator tRNA, indicating they are not mediated through tRNA(f)(Met) or mRNA.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2000 journal article
Organization of the 16S rRNA around its 5 ' terminus determined by photochemical crosslinking in the 30S ribosomal subunit
RNA, 6(1), 26–40.
author keywords: 16S rRNA three-dimensional structure; intramolecular RNA-RNA cross-links; reverse transcription arrest assay
MeSH headings : Azides; Base Sequence; Cross-Linking Reagents; Molecular Sequence Data; Nucleic Acid Conformation; RNA, Ribosomal, 16S / chemistry; RNA, Transfer / chemistry; RNA, Transfer / radiation effects; Ultraviolet Rays
TL;DR:
Differences in the pattern and efficiency of crosslinking for the different constructs allow distance estimates for the crosslinked sites from nucleotide G9 to provide constraints for the arrangement of the RNA elements in the 30S subunit.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2000 chapter
Structure determination by directed photo-cross-linking in large RNA molecules with site-specific psoralen
In R.W. Skaggs & J. Schilfgaarde (Eds.), RNA-ligland interactions: Part B (Vol. 318, pp. 104–118).
Ed(s): . R.W. Skaggs & J. Schilfgaarde
MeSH headings : Azides / pharmacology; Chromatography, High Pressure Liquid; Cross-Linking Reagents / pharmacology; Cystamine / chemistry; DNA / chemistry; DNA / metabolism; Electrophoresis, Polyacrylamide Gel; Ficusin / pharmacology; Furocoumarins; Genetic Techniques; Models, Chemical; Phosphorylation; Photoaffinity Labels / pharmacology; Photosensitizing Agents / pharmacology; RNA / chemistry; RNA / drug effects; RNA / metabolism; RNA / radiation effects; RNA, Ribosomal, 16S / metabolism; Time Factors; Transcription, Genetic; Ultraviolet Rays
Source: NC State University Libraries
Added: August 6, 2018
2000 journal article
UV-induced crosslinks in the 16S rRNAs of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implications for ribosome structure and photochemistry
NUCLEIC ACIDS RESEARCH, 28(19), 3785–3792.
MeSH headings : Bacillus subtilis / cytology; Bacillus subtilis / genetics; Bacillus subtilis / radiation effects; Base Composition; Base Sequence; Binding Sites; Conserved Sequence / genetics; Conserved Sequence / radiation effects; Escherichia coli / cytology; Escherichia coli / genetics; Escherichia coli / radiation effects; Hot Temperature; Lasers; Molecular Sequence Data; Nucleic Acid Conformation / radiation effects; Nucleotides / chemistry; Nucleotides / genetics; Nucleotides / metabolism; Nucleotides / radiation effects; Photochemistry; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; RNA, Bacterial / radiation effects; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / genetics; RNA, Ribosomal, 16S / metabolism; RNA, Ribosomal, 16S / radiation effects; Ribosomes / chemistry; Ribosomes / genetics; Ribosomes / radiation effects; Thermus / cytology; Thermus / genetics; Thermus / radiation effects; Transcription, Genetic; Ultraviolet Rays
TL;DR:
The overall similarity of crosslink positions in the three organisms suggests that the crosslinks arise from tertiary interactions that are highly conserved but with differences in detail in some regions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1999 journal article
Effects of tetracycline and spectinomycin on the tertiary structure of ribosomal RNA in the Escherichia coli 30 S ribosomal subunit
JOURNAL OF BIOLOGICAL CHEMISTRY, 274(23), 16576–16581.
MeSH headings : Anti-Bacterial Agents / pharmacology; Base Sequence; Electrophoresis, Polyacrylamide Gel; Escherichia coli / drug effects; Escherichia coli / genetics; Escherichia coli / radiation effects; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; RNA, Bacterial / drug effects; RNA, Bacterial / metabolism; RNA, Bacterial / radiation effects; RNA, Ribosomal, 16S / drug effects; RNA, Ribosomal, 16S / radiation effects; RNA, Ribosomal, 16S / ultrastructure; Ribosomes / radiation effects; Ribosomes / ultrastructure; Spectinomycin / pharmacology; Tetracycline / pharmacology; Ultraviolet Rays
TL;DR:
Structural analysis of the 16 S rRNA in the 30 S subunit and 70 S Ribosome in the presence of ribosome-specific antibiotics was performed to determine whether they produced rRNA structural changes that might provide further insight to their action.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1999 journal article
Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling
RNA, 5(11), 1430–1439.
author keywords: 16S rRNA; base triple; comparative sequence analysis; molecular modeling
MeSH headings : Base Pairing; Base Sequence; Escherichia coli / genetics; Hydrogen Bonding; Models, Molecular; Nucleic Acid Conformation; RNA, Bacterial / chemistry; RNA, Ribosomal, 16S / chemistry; Ribosomes / genetics; Sequence Homology, Nucleic Acid
TL;DR:
Molecular modeling shows that U121 interacts with C124 in the U121 (C124:G237) base triple, which maintains isomorphic structures for the three most frequent sequence motifs, is consistent with chemical reactivity of U121 in E. coli ribosomes, and is geometrically favorable.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1998 journal article
Dependence of the 16S rRNA decoding region structure on Mg2+, subunit association, and temperature
BIOCHEMISTRY, 37(44), 15442–15448.
MeSH headings : Base Sequence; Escherichia coli; Genetic Code; Magnesium / chemistry; Magnesium / metabolism; Molecular Sequence Data; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / metabolism; Ribosomal Proteins / chemistry; Ribosomal Proteins / metabolism; Ribosomes / chemistry; Ribosomes / metabolism; Structure-Activity Relationship; Temperature; Ultraviolet Rays
TL;DR:
Cross-link frequency differences indicate that the arrangement of the decoding region of the 16S rRNA, but not in the rest of the subunit, is readily altered by Mg2+ ions and subunit association.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1998 journal article
Neighborhood of 16S rRNA nucleotides U788/U789 in the 30S ribosomal subunit determined by site-directed crosslinking
RNA, 4(11), 1373–1385.
author keywords: 16S rRNA three-dimensional structure; chemical probing; intramolecular RNA-RNA crosslinks; molecular modeling; reverse transcription arrest assay
MeSH headings : Aldehydes / metabolism; Base Sequence; Binding Sites; Butanones; Catalytic Domain; Chromatography, High Pressure Liquid; Codon / metabolism; Cross-Linking Reagents / metabolism; Electrophoresis, Polyacrylamide Gel; Escherichia coli / metabolism; Ficusin / metabolism; Guanine / analysis; Molecular Sequence Data; Nucleic Acid Conformation; Photosensitizing Agents / metabolism; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / isolation & purification; RNA, Ribosomal, 16S / metabolism; RNA, Transfer, Amino Acid-Specific / metabolism; Ribosomes / chemistry; Ribosomes / metabolism; Transcription, Genetic; Uridine / metabolism
TL;DR:
Site-specific photo crosslinking has been used to investigate the RNA neighborhood of 16S rRNA positions U788/ U789 in Escherichia coli 30S subunits and data indicate a central location close to the decoding region and central pseudoknot for nucleotides U 788/U789 in the activated 30SSubunit.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1997 journal article
Exact determination of UV-induced crosslinks in 16S ribosomal RNA in 30s ribosomal subunits
RNA, 3(6), 602–612.
Source: NC State University Libraries
Added: August 6, 2018
1997 journal article
Exact determination of UV-induced crosslinks in 16S ribosomal RNA in 30s ribosomal subunits: Erratum
RNA, 3(8), 945.
Source: NC State University Libraries
Added: August 6, 2018
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