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38 results for “Transferrin”
Supplements for "Understanding the interaction between a human transferrin receptor aptamer-short double stranded RNA conjugate and its cell membrane target by in silico methods"
<p>Supplements for "Understanding the interaction between a human transferrin receptor aptamer-short double stranded RNA conjugate and its cell membrane target by in silico methods". </p> <p>This supplement includes the following files:</p> <p> </p> <p>1. Structures of the most stable Protein-Aptamer complexes predicted from HADDOCK</p> <p>Haddock_Cluster1.pdb <br> Haddock_Cluster2.pdb <br> Haddock_Cluster3.pdb </p> <p>2. Structure of the most stable conformation aligned with Protein-transferring complex PDB</p> <p>cluster1_aligned.pdb <br> transferrin_aligned.pdb </p> <p>3. MM-GBSA decomposition analysis of the three replicas for Protein-Aptamer</p> <p>aptamer_new_rep01_Decomp.dat <br> aptamer_new_rep02_Decomp.dat <br> aptamer_new_rep03_Decomp.dat </p> <p>4. MM-GBSA decomposition analysis of the three replicas for Protein-Aptamer-Conjugate<br> conjugate_new_rep01_Decomp.dat <br> conjugate_new_rep02_Decomp.dat <br> conjugate_new_rep03_Decomp.dat <br> </p> <p><br> <br> </p>
Macrophage phagocytosis assay of Acinetobacter baumannii AB074, passaged 15 days in antibiotics or transferrin.
<p>Macrophage phagocytosis assay of Acinetobacter baumannii AB074, passaged 15 days in antibiotics or transferrin. Experiment #1, replica #1-2, from March 7th, 2017 and Experiment #2, replica #1-2 from March 16th, 2017</p> <p>MICs for AB074: transferrin = 4 mcg/ml; ciprofloxacin = 1 mcg/ml; meropenem = 0,5 mcg/ml</p> <p>6 groups of treatment:</p> <p>1. No drug</p> <p>2. Transferrin only, last passage dose = 16 mcg/ml </p> <p>3. Ciprofloxacin only, last passage dose = 5 mcg/ml </p> <p>4. Ciprofloxacin + transferrin, last passage dose = 0,5 mcg/ml of cipro + 16 mcg/ml of transferrin</p> <p>5. Meropenem only, last passage dose = 2,5 mcg/ml </p> <p>6. Meropenem + transferrin, last passage dose = 2,5 mcg/ml + 16 mcg/ml of transferrin</p> <p>The file name structure: group_picture#_strain_timeOfPassage_ experiment#_replica#</p>
Rapid increase in transferrin receptor recycling promotes adhesion during T cell activation
<p>This Dataset contains primary data used for the publication "Rapid increase in transferrin receptor recycling promotes adhesion during T cell activation" accepted for publication in BMC Biology on 15. July 2022</p> <p><strong>Abstract:</strong></p> <p>Background<br> T cell activation leads to increased expression of the receptor for the iron transporter transferrin (TfR) to provide iron required for the cell differentiation and clonal expansion that takes place during the days after encounter with a cognate antigen. However, T cells mobilise TfR to their surface within minutes after activation, although the reason and mechanism driving this process remain unclear.</p> <p>Results<br> Here we show that T cells transiently increase endocytic uptake and recycling of TfR upon activation, thereby boosting their capacity to import iron. We demonstrate that increased TfR recycling is powered by a fast endocytic sorting pathway relying on the membrane proteins flotillins, Rab5 and Rab11a-positive endosomes. Our data further reveal that iron import is required for a non-canonical signalling pathway involving the kinases Zap70 and PAK, which controls adhesion of the integrin LFA-1 and eventually leads to conjugation with antigen-presenting cells.</p> <p>Conclusions<br> Altogether, our data suggest that T cells boost their iron importing capacity immediately upon activation to promote adhesion to antigen-presenting cells.</p> <p> </p> <p>Data are organised in compressed (.zip) folders entitled as the corresponding Figures in the publication.</p> <p>Programs we recommend to view the files are:<br> .fcs files: FlowJo software v10 (Tree Star, Ashland, OR, USA)<br> .lsm and .czi files: ZEN 2012 SP1 and higher (Carl Zeiss, Jena, Germany)<br> .lif files: LAS X v3 (Leica Microsystems, Wetzlar, Germany)<br> .pzfx files: Prism v7 software (GraphPad, San Diego, CA, USA)</p>
Protein sialylation affects the pH-dependent binding of ferric ion to human serum transferrin - experimental data
<p>Experimental data for a paper entitled <em>Protein sialylation affects the pH-dependent binding of ferric ion to human serum transferrin</em> (<a href="https://doi.org/10.1039/D4DT01311E">https://doi.org/10.1039/D4DT01311E</a>).</p> <p> </p> <p>Separate files are provided with the following information:</p> <p> </p> <p>1. Experimental data:</p> <p>a) "Fluorescence + IFE corrections" worksheet contains the fluorescence data used for the subsequent calculations.</p> <p>Fluorescence values were measured in triplicate the Tecan Spark M10 multimode microplate reader using multiple <em>z</em>-positions (distance from the lens to the bottom of the microplate well) and baseline correction. </p> <p>Fluorescence was corrected for the inner filter effect and normalized as described in the Supplementary Information (citation data will be updated pending publication).</p> <p>Additional information on the <em>z</em>-position inner filter effect correction method (ZINFE) can be found here: <a title="DOI URL" href="https://doi.org/10.1021/acs.analchem.2c01031" target="_blank" rel="noopener">https://doi.org/10.1021/acs.analchem.2c01031</a>.</p> <p>b) "Absorbance spectra" worksheet contains the averaged absorbance spectra and absorbance spectra of each replicated measurement.</p> <p> </p> <p>2. Titrations</p> <p>The dependence of the measured fluorescence on the concentration of added FeNTA was modelled according to the binding polynomial for two iron binding sites (<a href="https://doi.org/10.1016/S0076-6879(08)04205-5" target="_blank" rel="noopener">https://doi.org/10.1016/S0076-6879(08)04205-5</a>).</p> <p>The results for all titrations are provided as separate files with 4 worksheets each: titration data, calculation of the free iron according to the binding polynomial (<a href="https://doi.org/10.1039/d3ay01261a" target="_blank" rel="noopener">https://doi.org/10.1039/d3ay01261a</a>), the least squares calculation of the fluorescence according to the binding polynomial for each data point using the solver routine in Excel, and the “jackknife” procedure for estimating the uncertainties of the titration parameters (<a href="https://doi.org/10.1021/ed075p119" target="_blank" rel="noopener">https://doi.org/10.1021/ed075p119</a>). </p> <p>Separate files are provided for the determination of the active protein fraction and the fluorescence signal corresponding to the complete saturation of the binding sites.</p> <p> </p> <p>3. Results and sensitivity analyses:</p> <p>Local sensitivity analysis was performed to assess the impact of concentration fluctuations on the uncertainties associated with the results.</p> <p>Concentrations were adjusted to both higher (H) and lower (L) estimates, based on adding or subtracting one standard deviation from the average concentrations, creating four scenarios: LL, LH, HL, HH.</p> <p>The results for all titrations are provided as separate files with 5 worksheets each: the results obtained directly from titration data and the results obtained by all 4 scenarios.</p> <p>Standard deviations of the obtained titration parameters were adjusted using this expanded set.</p> <p> </p> <p>4. All data used for tables and plots in the manuscript, including statistical analyses and miscellaneous data:</p> <p>a) "Tables" worksheet contains all tables in the manuscript and the Supplementary Information (citation data will be updated pending publication),</p> <p>b) "fsp" worksheet contains the data on the pH-dependence of the site preference factor, <em>f</em>sp (<a href="https://doi.org/10.1042/bj1930717" target="_blank" rel="noopener">https://doi.org/10.1042/bj1930717</a>),</p> <p>c) "ΔΔrG" worksheet contains all ΔΔr<em>G</em> values reported in the manuscript,</p> <p>d) "Error propagation" contains the error propagation calculations for all values reported in the manuscript.</p> <p> </p>
Transferrin gene ChIP-seq data
<p>ChIP-seq Peak-calling data to support the supplementary information to:</p> <p><strong>In severe alcoholic hepatitis, serum transferrin constitutes an independent mortality predictor indicating an impaired HNF4</strong><strong>αsignaling. </strong>Stephen R. Atkinson, MD<sup>*</sup>; Karim Hamesch, MD<sup>*</sup>; Igor Spivak, MD; Nurdan Guldiken, PhD; Joaquín Cabezas, PhD<sup>3</sup>; Josepmaria Argemi, PhD; Igor Theurl, MD, Heinz Zoller, MD; Sheng Cao, MD; Philippe Mathurin, MD; Vijay H. Shah, MD; Christian Trautwein, MD; Ramon Bataller, MD; Mark R. Thursz, MD<sup>+</sup>; Pavel Strnad, MD<sup>+</sup></p>
Isothermal titration calorimetric study on the binding of iron to human serum transferrin - experimental data
<p>Experimental data for a paper entitled <em>Glycoproteomics meets thermodynamics: a calorimetric study of the effect of sialylation and synergistic anion on the binding of iron to human serum transferrin</em> (<a href="https://doi.org/10.1016/j.jinorgbio.2023.112207">https://doi.org/10.1016/j.jinorgbio.2023.112207</a>).<br> <br> Separate files are provided with the following information:<br> <br> 1. ITC titrations of native (Tf+s) and desialylated (Tf-s) apo-transferrin with FeNTA in the presence of carbonate and oxalate.<br> <br> a) Raw data with corresponding fit results are available in .apj file format: <a href="https://zenodo.org/api/files/188f4399-e839-4710-8a28-996af05961aa/Borko et al. ITC - Malvern Microcal format.zip?versionId=e1a08c09-9401-42fa-a626-683a2fcc1be5">Borko et al. ITC - Malvern Microcal format.zip </a><br> <br> The files can be accessed using MicroCal PEAQ-ITC Analysis software, which can be downloaded here:<br> <br> <a href="https://www.malvernpanalytical.com/en/support/product-support/microcal-range/microcal-itc-range/microcal-peaq-itc#software">https://www.malvernpanalytical.com/en/support/product-support/microcal-range/microcal-itc-range/microcal-peaq-itc#software</a><br> <br> b) The raw data including control experiments are also available in ASCII (.csv) format: <a href="https://zenodo.org/api/files/188f4399-e839-4710-8a28-996af05961aa/Borko et al. ITC - ASCII format.zip?versionId=20ecf17b-54d9-4b33-8de9-a6f256211cc6">Borko et al. ITC - ASCII format.zip</a></p> <p>2. Overview of titration results, including error propagation and inputs for statistical analysis: <a href="https://zenodo.org/api/files/188f4399-e839-4710-8a28-996af05961aa/Borko%20et%20al.%20-%20Results.xlsx">Borko et al. - Results.xlsx</a><br> <br> 3. Graph of the overall effect of desialylation and synergistic anion on the thermodynamic parameters for the reaction of native (Tf+s) and desialylated (Tf-s) apotransferrin with FeNTA, based on the values of ∆<sub>r</sub><em>H</em>° and -<em>T</em>∆<sub>r</sub><em>S</em>°: <a href="https://zenodo.org/api/files/188f4399-e839-4710-8a28-996af05961aa/Borko%20et%20al.%20-%20dH%20vs.%20-TdS%20plot.xlsx">Borko et al. - dH vs. -TdS plot.xlsx</a></p> <p>4. Complete statistical analysis of results: <a href="https://zenodo.org/api/files/188f4399-e839-4710-8a28-996af05961aa/Borko%20et%20al.%20-%20Statistics.xlsx">Borko et al. - Statistics.xlsx </a><br> <br> a) Shapiro-Wilk test for normality of data.<br> b) Brown-Forsythe test for homogeneity of variances.<br> c) One-way and two-way ANOVA for all parameters, including Welch-James one-way ANOVA with approximate degrees of freedom and an overview of the obtained results.<br> d) Hedges' d values for effect size.<br> <br> All calculations were performed using the built-in functions in Excel 365 or the Real Statistics Resource Pack, which can be downloaded here:<br> <br> <a href="https://www.real-statistics.com/free-download/real-statistics-resource-pack/">https://www.real-statistics.com/free-download/real-statistics-resource-pack/</a><br> <br> After installation, it may be necessary to change the source of the XRealStats add-in to automatically update the calculations using the Edit Links dialogue. The location of the installed XRealStats.xlam file may need to be added to the Trusted Locations in the Excel Trust Center settings.<br> <br> 5. Welch-James Two-way ANOVA with approximate degrees of freedom performed with Rstudio (version 2022.01.1 build554) using the welchADF package for R (version 4.2.1): <a href="https://zenodo.org/api/files/188f4399-e839-4710-8a28-996af05961aa/Borko%20et%20al.%20-%20WelchADF%202-way%20ANOVA%20%28Rstudio%29.zip">Borko et al. - WelchADF 2-way ANOVA (Rstudio).zip</a><br> <br> More details about the welchADF package can be found here: <a href="https://doi.org/10.32614/RJ-2017-049">https://doi.org/10.32614/RJ-2017-049</a><br> <br> 6. UHPLC chromatograms used to assign the structures and content of N-glycans in native and desialylated apo-transferrin, including the Python script for peak integration: <a href="https://zenodo.org/api/files/188f4399-e839-4710-8a28-996af05961aa/Borko%20et%20al.%20-%20UHPLC%20chromatograms.zip">Borko et al. - UHPLC chromatograms.zip</a></p> <p>For additional details and background, please visit: <a href="https://glymech.pharma.hr//GlyMech.html">https://glymech.pharma.hr//GlyMech.html</a>.</p> <p> </p>
Effect of Red Meat Intake on Occurrence of Serum Non-transferrin Bound Iron (NTBI)
ClinicalTrials.gov study NCT03019393. IPD Sharing: NO. Countries: 1. Publications: 5.
Comparing Reticulocyte Hemoglobin and Transferrin Saturation to Guide Iron Treatment in People on Dialysis
ClinicalTrials.gov study NCT06906835. IPD Sharing: YES. Countries: 1. Publications: 4.
Effect of Iron Status on Occurrence of Non-transferrin-bound Iron (NTBI) in Serum in Response to an Oral Iron Load
ClinicalTrials.gov study NCT02831712. IPD Sharing: Not stated. Countries: 1. Publications: 12.
Iron Interventions and Non-transferrin-bound Iron (NTBI) in Women
ClinicalTrials.gov study NCT01404533. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Benefit of Carbohydrate Deficient Transferrin to Detect Chronic Alcohol Abuse in the Elderly
ClinicalTrials.gov study NCT02822911. IPD Sharing: NO. Countries: 1. Publications: 0.
The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis [single cell RNA-Seq]
GEO Series GSE157743. Homo sapiens. 102 samples. Type: Expression profiling by high throughput sequencing.
The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis [TF KD RNA-Seq]
GEO Series GSE157744. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Liver sinusoidal endothelial cells induce BMP6 expression in response to non-transferrin bound iron
GEO Series GSE215324. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis [isogenic CTC lines RNA-Seq]
GEO Series GSE157742. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
Transferrin Receptor contributes to PANoptosis in thyroid cancer
GEO Series GSE280138. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Efficacy and Safety Study of Iron Sucrose and Oral Iron Acetyl-transferrin Hydroglycerin
ClinicalTrials.gov study NCT00802139. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Impact of Transferrin Saturation Guided Maintenance Treatment on Quality of Life in HFE Haemochromatosis
ClinicalTrials.gov study NCT04779593. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Iron Supplementation During Pregnancy and Non-Transferrin-Bound Iron (NTBI)
ClinicalTrials.gov study NCT01264042. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Transferrin Saturation and Asthenia in Hemochromatosis
ClinicalTrials.gov study NCT03356548. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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