Journal: Scientific Reports

Article Title: Chronic hypoxia for the adaptation of extracellular vesicle phenotype

doi: 10.1038/s41598-024-73453-1

Figure Lengend Snippet: Doubling time and morphology in hypoxic culture (A , B) . Doubling time in hours, of HepG2 (A) and PC3 (B) cells when cultured in normoxia and 5% O 2 hypoxia over a 15-day period after a period of adaptation for at least two weeks. Doubling time was calculated every three days in hypoxia and every six days in normoxia and was not significantly different between conditions (HepG2 p = 0.179, PC3 p = 0.080). (C) Brightfield micrographs of HepG2 (top) and PC3 (bottom) cells cultured in normoxia (left) and hypoxia (right). Scale bars are 200 μm. Hypoxia micrographs taken after culture in 5% O 2 for approximately one month and after cryopreservation whilst maintaining hypoxic conditions.

Article Snippet: Fig. 3 Phenotype of HepG2 and PC3 cells when cultured in chronic 5% O 2 hypoxia. (A) Heatmap of protein expression in HepG2 and PC3 cells produced using the gplots package in Rstudio.

Techniques: Cell Culture

Journal: Scientific Reports

Article Title: Chronic hypoxia for the adaptation of extracellular vesicle phenotype

doi: 10.1038/s41598-024-73453-1

Figure Lengend Snippet: Phenotype of HepG2 and PC3 cells when cultured in chronic 5% O 2 hypoxia. (A) Heatmap of protein expression in HepG2 and PC3 cells produced using the gplots package in Rstudio. Green denotes higher expression and red denotes lower expression. The dendrogram shows hierarchical clustering of samples. (B , C) Chord plots summarising the major changes in protein expression in HepG2 (B) and PC3 (C) cells produced from a list of BP GO terms produced using StringDB and the GOplot package in R. The right side displays the 10 Biological Process Gene Ontology terms most associated with the changes in protein expression. The left side shows the proteins with the greatest change in expression. A blue or red label denotes a downregulation or upregulation in conditions of hypoxia, respectively. The coloured chords denote membership of the highly changed genes within the most significant GO terms. n = 3. Abbreviations: AH = acute hypoxia, BP GO = biological process gene ontology, CH = chronic hypoxia, HG2 = HepG2, N = normoxia.

Article Snippet: Fig. 3 Phenotype of HepG2 and PC3 cells when cultured in chronic 5% O 2 hypoxia. (A) Heatmap of protein expression in HepG2 and PC3 cells produced using the gplots package in Rstudio.

Techniques: Cell Culture, Expressing, Produced

Journal: Scientific Reports

Article Title: Chronic hypoxia for the adaptation of extracellular vesicle phenotype

doi: 10.1038/s41598-024-73453-1

Figure Lengend Snippet: Summarised list of biological process (BP) gene ontology (GO) terms associated with changes in protein expression in PC3 cells cultured in chronic hypoxia.

Article Snippet: Fig. 3 Phenotype of HepG2 and PC3 cells when cultured in chronic 5% O 2 hypoxia. (A) Heatmap of protein expression in HepG2 and PC3 cells produced using the gplots package in Rstudio.

Techniques: Expressing, Cell Culture

Journal: Scientific Reports

Article Title: Chronic hypoxia for the adaptation of extracellular vesicle phenotype

doi: 10.1038/s41598-024-73453-1

Figure Lengend Snippet: Extracellular vesicle production and content in different oxygen conditions. Panels A - C show values for HepG2, panels D - F show values for PC3. (A, D) Mean number of particles produced in 72 hours in different oxygen conditions normalised to cell number. (B, E) Mean size of particles produced in 72 hours in different oxygen conditions (C, F) Mean protein content of EVs produced in 72 hours in different oxygen conditions. Normoxia refers to culture under standard tissue culture conditions with atmospheric oxygen. Acute hypoxia refers to culture of cells in 5% O 2 hypoxia for 72 hours. Chronic hypoxia also refers to culture of cells in 5% O 2 with at least two weeks additional culture in 5% O 2 hypoxia prior to experimentation. Error bars in all panels are SEM. Asterisks (*) denote significance determined by one-way ANOVA with Tukey’s HSD test, * = p ≤ 0.05, ** = p ≤ 0.01, *** = p ≤ 0.001.

Article Snippet: Fig. 3 Phenotype of HepG2 and PC3 cells when cultured in chronic 5% O 2 hypoxia. (A) Heatmap of protein expression in HepG2 and PC3 cells produced using the gplots package in Rstudio.

Techniques: Produced

Journal: Scientific Reports

Article Title: Chronic hypoxia for the adaptation of extracellular vesicle phenotype

doi: 10.1038/s41598-024-73453-1

Figure Lengend Snippet: Protein expression in HepG2 and PC3 EVs in different oxygen conditions. Panel ( A ) shows data for HepG2, panel ( B ) shows data for PC3. The global protein expression of EVs was measured with proteomics and hierarchical clustering was performed in R using the gplots package. EVs were harvested for 72 h from cells cultured in either normoxic, AH, or CH conditions. Normoxia refers to culture under standard tissue culture conditions with atmospheric oxygen. AH refers to culture of cells in 5% O 2 hypoxia for 72 h. CH refers to culture of cells in 5% O 2 with at least two weeks additional culture in 5% O 2 hypoxia prior to experimentation. n = 3, except in PC3 N where n = 2 Abbreviations: AH = acute hypoxia, CH = chronic hypoxia, N = normoxia.

Article Snippet: Fig. 3 Phenotype of HepG2 and PC3 cells when cultured in chronic 5% O 2 hypoxia. (A) Heatmap of protein expression in HepG2 and PC3 cells produced using the gplots package in Rstudio.

Techniques: Expressing, Cell Culture

Journal: Scientific Reports

Article Title: Chronic hypoxia for the adaptation of extracellular vesicle phenotype

doi: 10.1038/s41598-024-73453-1

Figure Lengend Snippet: Summarised list of BP GO terms associated with changes in protein expression in PC3 EVs from cell cultured in different oxygen conditions.

Article Snippet: Fig. 3 Phenotype of HepG2 and PC3 cells when cultured in chronic 5% O 2 hypoxia. (A) Heatmap of protein expression in HepG2 and PC3 cells produced using the gplots package in Rstudio.

Techniques: Expressing, Cell Culture, Gene Expression, Clinical Proteomics, Membrane

Journal: Nature Communications

Article Title: SARS-CoV-2 infection results in immune responses in the respiratory tract and peripheral blood that suggest mechanisms of disease severity

doi: 10.1038/s41467-022-30088-y

Figure Lengend Snippet: a ELISA titration curves against the SARS-CoV-2 receptor-binding domain (RBD) for IgM, IgG, and IgA in COVID-19 respiratory and paired plasma samples and non-COVID-19 respiratory samples as negative controls. Dotted lines within each graph indicates the cut-off used to determine end-point titres. b End-point titres of SARS-CoV-2 RBD antibodies between top left panel: respiratory samples of COVID-19 and non-COVID-19 patients, top right panel: respiratory and paired plasma samples of COVID-19 patients, and bottom panel: endotracheal tube aspirate (ETA), sputum, or bronchoalveolar lavage (BAL) and paired plasma samples of COVID-19 patients. Top left panel: Bars indicate median with interquartile range. Dotted line indicates the detection level. n ETA = 15, n Sputum = 20, n BAL = 6, n Non-COVID-19 ETA = 5, n Non-COVID-19 sputum = 1. Top right panel: Dotted lines connect the most closely matched plasma and respiratory samples from each patient. Bottom panel: Bars indicate the median. Statistical significance was determined with a two-sided Mann-Whitney test. n ETA = 15, n ETA matched plasma = 14, n Sputum = 20, n Sputum matched plasma = 19, n BAL = 6, n BAL matched plasma = 3. c Heatmap of percentage (%) inhibition tested by surrogate virus neutralization test (sVNT), anti-RBD ELISA titres and days post disease onset. d Correlation between anti-RBD antibody titres and (%) sVNT inhibition. Correlation was determined with a two-tailed Spearman’s correlation. e Number of samples and patients with seroconverted anti-RBD IgM, IgG, IgA and positive % sVNT inhibition. Red curved lines surrounding the donut graphs indicate the samples/patients with seroconverted IgM and IgG. Earliest samples were used for each patient when determining seroconversion which was defined as average titre + 2×SD of non-COVID-19 respiratory samples. Positive % sVNT inhibition was defined as % sVNT inhibition ≥ 20%. f Correlation of anti-RBD ELISA titres and % sVNT inhibition between respiratory samples (ETA, sputum, and BAL) and paired plasma samples collected at the closest timepoint for each patient. Correlation was determined with a two-tailed Spearman’s correlation. n ETA = 15, n ETA matched plasma = 14, n Sputum = 20, n Sputum matched plasma = 19, n BAL = 6, n BAL matched plasma = 3. Source data are provided as a Source Data file.

Article Snippet: Correlations were assessed using two-tailed Spearman’s correlation coefficient ( r s ) and visualized in R v3.6.2 as heatmaps using the corrplot package or using the online Morpheus heatmap software ( https://software.broadinstitute.org/morpheus ; the Broad Institute, MA, USA) and p-values of correlations were corrected for multiple comparisons by FDR in R v3.6.2.

Techniques: Enzyme-linked Immunosorbent Assay, Titration, Binding Assay, Clinical Proteomics, MANN-WHITNEY, Inhibition, Virus, Neutralization, Two Tailed Test

Journal: Heliyon

Article Title: Effect of illite pretreatment on germinated Brown rice with Special Reference to amino acids, antioxidants, texture, and mineral elements

doi: 10.1016/j.heliyon.2024.e28843

Figure Lengend Snippet: Profiling of mineral elements detected in the germinated brown rice treated with different doses of Illite. The heatmap was created using the heatmap function in RStudio. Quantitative data represents the means±SD.

Article Snippet: The heatmap was created using the heatmap function in RStudio.

Techniques:

Journal: Heliyon

Article Title: Effect of illite pretreatment on germinated Brown rice with Special Reference to amino acids, antioxidants, texture, and mineral elements

doi: 10.1016/j.heliyon.2024.e28843

Figure Lengend Snippet: Heatmap indicating the level of amino acids in germinated brown rice when treated with Illite. The heatmap was created using the heatmap function in RStudio. The quantitative value represent the average of at least two replicates.

Article Snippet: The heatmap was created using the heatmap function in RStudio.

Techniques: