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45 results for “Guanine”
Data from: Selectivity of Guanine Nucleotide Exchange Factor-mediated Cdc42 activation in primary human endothelial cells
<p>Data that was reported in "Selectivity of Guanine Nucleotide Exchange Factor-mediated Cdc42 activation in primary human endothelial cells" by </p> <p>Nathalie R. Reinhard<sup>1</sup>, Sanne van der Niet<sup>1</sup>, Anna Chertkova<sup>1</sup>, Marten Postma<sup>1</sup>, Theodorus W.J. Gadella Jr.<sup>1</sup>, Peter L. Hordijk<sup>1,2</sup>, and Joachim Goedhart<sup>1*</sup><br> </p> <p><strong>Affiliations:</strong></p> <p><sup>1 </sup>University of Amsterdam, Molecular Cytology, Swammerdam Institute for Life Sciences, van Leeuwenhoek Centre for Advanced Microscopy, Amsterdam, the Netherlands</p> <p><sup>2 </sup>Department of Physiology, Free University Medical Center, Amsterdam, The Netherlands</p> <p> </p> <p>*Correspondence to: j.goedhart@uva.nl</p>
Characterization of photorecruitable Guanine Exchange Factors for the study of Rho GTPases in endothelial cells
<p>Time lapses of respective figures belonging to the report titled "<strong>Characterization of photorecruitable Guanine Exchange Factors for the study of Rho GTPases in endothelial cells"</strong>. This report was written as part of the Msc programe in Biomedical Science of the University of Amsterdam. </p>
Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth
<p>Modified nucleosides in tRNAs are critical for protein translation. N<sup>1</sup>-methylguanosine-37 and N<sup>1</sup>-methylinosine-37 in tRNAs, both located at the 3’-adjacent to the anticodon, are formed by Trm5. Here we describe <em>Arabidopsis thaliana AtTRM5</em> (At3g56120) as a Trm5 ortholog. <em>Attrm5</em> mutant plants have overall slower growth as observed by slower leaf initiation rate, delayed flowering and reduced primary root length. In <em>Attrm5</em> mutants, mRNAs of flowering time genes are less abundant and correlated with delayed flowering. We show that <em>AtTRM5</em> complements the yeast <em>trm5</em> mutant, and <em>in vitro</em> methylates tRNA guanosine-37 to produce N<sup>1</sup>-methylguanosine (m<sup>1</sup>G). We also show <em>in vitro</em> that AtTRM5 methylates tRNA inosine-37 to produce N<sup>1</sup>-methylinosine (m<sup>1</sup>I) and in <em>Attrm5</em> mutant plants, we show a reduction of both N<sup>1</sup>-methylguanosine and N<sup>1</sup>-methylinosine. We also show that AtTRM5 is localized to the nucleus in plant cells. Proteomics data showed that photosynthetic protein abundance is affected in <em>Attrm5</em> mutant plants. Finally, we show tRNA-Ala aminoacylation is not affected in <em>Attrm5</em> mutants. However the abundance of tRNA-Ala and tRNA-Asp 5’ half cleavage products are deduced. Our findings highlight the bifunctionality of AtTRM5 and the importance of the post-transcriptional tRNA modifications m<sup>1</sup>G and m<sup>1</sup>I at tRNA position 37 in general plant growth and development.</p>
Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation
<p>Please refer to the publication Shin et al. (2021): "Shin CR, Choi EH, Kim G. et al. (2021). Characterization of metapopulation of <em>Ellobium chinense</em> through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation. Scientific Reports 11: 12239.</p> <p><span>The land snail <i>Ellobium chinense</i> (Pulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of <i>E. chinense</i> has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific <i>E. chinense </i>based on <i>COI</i> and 10 microsatellite markers. The analyses of 140 <i>COI </i>data from South Korea and Japan and 54 microsatellite data from South Korea revealed that <i>E. chinense</i> has high haplotype and low nucleotide diversity without showing any genetic structures that reflect geographical isolations. It strongly implies that the subfamily Ellobiinae may have first appeared around the Eocene Optimum immediately after the Paleocene–Eocene Thermal Maximum (PETM; ca. 55 mya) and the examined <i>E. chinense</i> populations in Northwestern Pacific may have been maintained in a metapopulation under the influence of the Kuroshio warm currents through the Late-Middle Pleistocene (0.350−0.126 mya) and Late Pleistocene (0.126−0.012 mya). We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in <i>COI</i> (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four <i>COI</i> hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure. </span></p>
ISOLDE model and validation statistics to support: Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies
<p>These files provide the pdb atom coordinates and structural validation of the ISOLDE structural model (Fig. 6) contained in the manuscript "Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies" </p>
Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation
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Data from: Tissue-specific mutagenesis from endogenous guanine damage is suppressed by PolK and DNA repair
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Data from: The twenty amino acids are identified by unique numbers assigned to the uracil, cytosine, adenine, and guanine found in the three base positions of the sixty-four messenger RNA genetic codons
<p>A codon's three bases consist of any combination of uracil, cytosine, adenine, or guanine and these encode the twenty amino acids. When the codon's first two bases are given specific values, and those values are multiplied, then the third base of the codon is used during translation only when the product is greater than three. Here we show that those values plus more variables within the ribosomal decoding site results in specific flow values for each of the twenty amino acid groups. These results are demonstrated in a flow chart showing the unidirectional flow which is expected during the translation process. All twenty amino acids can be represented by numbers that describe their relationship to each other and to the decoding site. We anticipate our findings will increase discussion about using a number system to better understand the translation process.</p>
Supporting materials for the article "Neutral atomic hydrogen as an efficient catalyst for interstellar formation of adenine and guanine"
<p>The data files contain the computed atomic coordinate data of all optimized molecular structures in the standard XYZ chemical file format. </p> <p>The PDF file contains 1) the potential diagrams of reaction paths for producing adenine and guanine from H-catalyzed reactions between h-pyrimidine-2-one and (cyanamide or carbodiimide), and 2) the IR and electronic adsorption spectra of intermediates, as well as 3) a detailed description to the aformentioned data files.</p>
Supporting materials for the article "Neutral atomic hydrogen as an efficient catalyst for interstellar formation of adenine and guanine"
<p>The data files contain the computed atomic coordinate data of all optimized molecular structures in the standard XYZ chemical file format. </p> <p>The PDF file contains 1) the potential diagrams of reaction paths for producing adenine and guanine from H-catalyzed reactions between h-pyrimidine-2-one and (cyanamide or carbodiimide), and 2) the IR and electronic adsorption spectra of intermediates, as well as 3) a detailed description to the aformentioned data files.</p>
SASDM95 – Candida albicans Ras-like protein 1 in complex with the guanine nucleotide exchange factor region of cell division control protein 25
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SASDM85 – GTP-binding domain of Candida albicans Ras-like protein 1 in complex with the guanine nucleotide exchange factor region of cell division control protein 25
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SASDM75 – Ras-like protein 1 guanine nucleotide exchange factor region of Candida albicans cell division control protein 25
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Archive of biochemical data sets contained in: Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies
<p>This archive contains all the biochemical data for the study "Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies". Further data supporting the structural data in this study is found in pdb and EMD accession numbers PDB ID 8TDV and EMD-41174 (RNA complex SAMHD1-T*<sub>cl</sub>) and PDB ID 8TDW and EMD-41175 (RNA complex SAMHD1-T*<sub>op</sub>). Further proteomics data is found in the Protein Exchange Database (PXD043587). </p>
A Phase III Study to Evaluate the Safety and Efficacy of Ganciclovir (Dihydroxypropoxymethyl Guanine [DHPG]) Treatment of Symptomatic Central Nervous System (CNS) Congenital Cytomegalovirus (CMV) Infe
ClinicalTrials.gov study NCT00001100. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: The twenty amino acids are identified by unique numbers assigned to the uracil, cytosine, adenine, and guanine found in the three base positions of the sixty-four messenger RNA genetic codons
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Data from: Amyloid precursor protein translation is regulated by a 3'UTR guanine quadruplex
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Identification of Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation in glioblastoma
GEO Series GSE162783. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Click-chemistry-aided quantitation and sequencing of oxidized guanines and apurinic sites uncovers their transcription-linked strand bias in human cells
GEO Series GSE272366. Homo sapiens. 8 samples. Type: Other.
Alteration of target cleavage patterns and off-target reduction of antisense oligonucleotides incorporating 2-N-carbamoyl- or (2-pyridyl)guanine
GEO Series GSE228747. Homo sapiens. 24 samples. Type: Expression profiling by array.
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