Gene expression in human peripheral blood 48 hours after exposure to ionizing radiation
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE44201 | GEO | 2013/09/11
SECONDARY ACCESSION(S): PRJNA189053
REPOSITORIES: GEO
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Project description:Analysis of human peripheral blood 48 hours after irradiation ex vivo with graded doses of gamma rays. Results have been used in building and testing classifiers to predict exposure dose for use in radiological triage, and also provide insight into immune cell responses. Results were compared with those from earlier times and from patients exposed in vivo. Peripheral blood from 5 healthy donors was exposed ex vivo to 0. 0.5, 2, 5, or 8 Gy gamma-rays and gene expression was analyzed up to 48 hours after exposure.
2013-09-11 | E-GEOD-44201 | biostudies-arrayexpress
Project description:Abstract Purpose: There is a recognised need to develop new methods of high throughput, rapid and minimally invasive individual dose assessment for radiation exposure. The aim of this work is to establish a panel of highly radiation responsive genes suitable for biological dosimetry and to explore inter-individual variation in response to ionising radiation exposure.Materials and method: Analysis of gene expression in response to radiation was carried out using three independent techniques (microarray, Multiplex Quantitative RT-PCR and nCounter Analysis System) in human lymphocytes in culture and circulating blood exposed ex vivo from the same donors. Results: Variations in transcriptional response to exposure to ionising radiation analysed by microarray allowed the identification of genes which can be validated and measured accurately as biomarkers of radiation exposure using other techniques. We have identified genes which are consistently up-regulated following exposure at different time points to either 2 or 4 Gy of X-rays, for all individuals in blood and cultured lymphocytes. Most down-regulated genes including cyclins, centromeric and mitotic checkpoints proteins, particularly those associated with chromosome instability and cancer can only be detected in dividing cells. Conclusions: The data provides evidence that there are a number of genes which seem suitable for biological dosimetry, like SESN1, GADD45A, CDKN1A, CCNG1, FDXR, BBC3 and MDM2. ÊThese biomarkers could potentially be used for triage after large-scale radiological incidents. Variations in transcriptional response accurately measured by MQRT-PCRæ may allow the identification of biomarkers of radiation sensitivity and individual susceptibility and therefore being useful in radiation oncology.
2011-10-20 | E-TABM-1083 | biostudies-arrayexpress
Project description:The detonation of an improvised nuclear device would produce prompt radiation consisting of both photons (gamma-rays) and neutrons. While much effort in recent years has gone into the development of radiation biodosimetry methods suitable for mass triage, the possible effect of neutrons on the endpoints studied has remained largely uninvestigated. We have used a novel neutron irradiator with an energy spectrum based on that 1-1.5 km from the epicenter of the Hiroshima blast to begin examining the effect of neutrons on global gene expression, and the impact this may have on the development of gene expression signatures for radiation biodosimetry. We have exposed peripheral blood from healthy human donors to 0, 0.1, 0.3, 0.5, or 1 Gy of neutrons ex vivo using our neutron irradiator, and compared the transcriptomic response 24 h later to that resulting from exposure to 0.1, 0.3, 0.5, 1, 2 or 4 Gy of photons (x-rays).
2017-02-22 | GSE90909 | GEO
Project description:Barnacles are ancient arthropods that, as adults, are surrounded by a hard, mineralized, outer shell that the organism produces for protection. While extensive research has been conducted on the glue-like cement that barnacles use to adhere to surfaces, less is known about the barnacle exoskeleton, especially the process by which the barnacle exoskeleton is formed. Here, we present data exploring the changes that occur as the barnacle cyprid undergoes metamorphosis to become a sessile juvenile with a mineralized exoskeleton. Scanning electron microscope data show dramatic morphological changes in the barnacle exoskeleton following metamorphosis. Energy-dispersive X-ray spectroscopy indicates a small amount of calcium (8%) 1 h post-metamorphosis that steadily increases to 28% by 2 days following metamorphosis. Raman spectroscopy indicates calcite in the exoskeleton of a barnacle 2 days following metamorphosis and no detectable calcium carbonate in exoskeletons up to 3 h post-metamorphosis. Confocal microscopy indicates during this 2 day period, barnacle base plate area and height increases rapidly (0.001 mm2 h-1 and 0.30 µm h-1, respectively). These results provide critical information into the early life stages of the barnacle, which will be important for developing an understanding of how ocean acidification might impact the calcification process of the barnacle exoskeleton.
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Project description:Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology. These samples were analyzed with 16S rRNA gene sequencing, inferred gene function profiles, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics through the Qiita, PICRUSt, and GNPS pipelines, respectively. The human sample microbiomes clustered with the corresponding sample types in the American Gut Project (http://www.americangut.org), and the fermented food samples produced a separate cluster. The microbial communities of the household surfaces were primarily sourced from the fermented foods, and their consumption was associated with increased gut microbial diversity. Untargeted metabolomics revealed that human skin and fermented food samples had separate chemical ecologies and that stool was more similar to fermented foods than to other sample types. Metabolites from the fermented foods, including plant products such as procyanidin and pheophytin, were present in the skin and stool samples of the individuals consuming the foods. Some food metabolites were modified during digestion, and others were detected in stool intact. This study represents a first-of-its-kind analysis of multi-omics data that achieved time intervals matching those of classic microbiological culturing. IMPORTANCE Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial microbiology or other areas where complex microbial dysbioses require immediate intervention. The reason for this is the length of time required to generate and analyze omics data. Here, we describe the development and application of a pipeline for multi-omics data analysis in time frames matching those of the culture-based approaches often used for these applications. This study applied multi-omics methods effectively in clinically relevant time frames and sets a precedent toward their implementation in clinical medicine and industrial microbiology.
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Project description:An oseltamivir-resistant influenza A pandemic (H1N1) 2009 virus evolved and emerged from zero to 52% of detectable virus within 48 hours of a patient's exposure to oseltamivir. Phylogenetic analysis and data gathered by pyrosequencing and cloning directly on clinical samples suggest that the mutant emerged de novo.
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Project description:Background Vaccinations against SARS-CoV-2 have been a topic of political, social, and medical intrigue since the declaration of the COVID-19 pandemic in early 2020. The vaccine side effects have been relatively mild to date, with few observed systemic effects. Case presentation A 69-year-old previously healthy female presented with symptoms of asymmetric bilateral lower and upper extremity weakness 2 days after vaccination with the Pfizer-BioNTech mRNA vaccine. MRI of the cervical spine revealed a non-compressive myelitis extending from C3-4 to T2-3. Common known causes of transverse myelitis were ruled out by diagnostic techniques. Conclusions Transverse myelitis is a rare autoimmune disorder that has been shown to have a temporal association with vaccination in the past. With a progressively partisan societal view on vaccinations, it is important for clinicians to remain vigilant on documenting potential associations without encouraging fear of causation.
| S-EPMC8423772 | biostudies-literature
Project description:The aim of this study was to analyze the host responses to ionizing radiation by nuclear factor-κB (NF-κB) bioluminescence imaging-guided transcriptomic tool. Transgenic mice, carrying the NF-κB-driven luciferase gene, were exposed to a single dose of 8.5 Gy total-body irradiation. In vivo imaging showed that a maximal NF-κB-dependent bioluminescent intensity was observed at 3 h after irradiation and ex vivo imaging showed that liver, intestine, and brain displayed strong NF-κB activations. Microarray analysis of these organs showed that irradiation altered gene expression signatures in an organ-specific manner. Pathway analysis showed that pathways associated with metabolism and immune system were altered primarily in liver and intestine. the upregulation of fatty acid binding protein 4, serum amyloid A2, and serum amyloid A3, which are participated in both inflammation and lipid metabolism, suggesting that irradiation might affect the cross pathways of metabolism and inflammation. Moreover, The upregulation of chemokine (CC-motif) ligand 5, chemokine (CC-motif) ligand 20, and Jagged 1 genes suggested that these genes might contribute to the radiation enteropathy. Male transgenic mice (6 to 8 weeks old) were exposed to a single dose of whole-body X-rays generated at 6 MV (Clinac® 21EX medical linear accelerator, Varian, Palo Alto, CA, USA) and at a dose rate of 4 Gy/min. Mice were imaged at 0 h, 1 h, 3 h, 9 h, 24 h, 48 h, or 72 h, or on 7 d or 14 d after irradiation with 8.5 Gy. RNAs were extracted at 3 h after irradiation.
2012-01-01 | E-GEOD-25208 | biostudies-arrayexpress
Project description:Genome-wide expression analysis comparison with and without ionizing radiation in p53 mutant and wild type Drosophila larvae Genome-wide expression analysis comparison with and without ionizing radiation in p53 mutant (p53^5A-1-4) and wild type (y^1 w^1118) Drosophila third instar larvae. 4000R of X-rays used in IR-treated Drosophila. Analyzed 2hr and 18hr after exposure with age-matched larvae in non-treated controls.
2012-04-17 | E-GEOD-37404 | biostudies-arrayexpress
Project description:BackgroundDisease severity may change in the first week after acute respiratory distress syndrome (ARDS) onset. The aim of this study was to evaluate whether the reclassification of disease severity after 48 h (i.e. day 3) of ARDS onset could help in predicting mortality and determine factors associated with ARDS persistence and mortality.MethodsWe performed a secondary analysis of a 3-year prospective, observational cohort study of ARDS in a tertiary care referral center. Disease severity was reclassified after 48 h of enrollment, and cases that still fulfilled the Berlin criteria were regarded as nonresolving ARDS.ResultsA total of 1034 ARDS patients were analyzed. Overall hospital mortality was 57.7% (56.7%, 57.5%, and 58.6% for patients with initial mild, moderate, and severe ARDS, respectively, p = 0.189). On day 3 reclassification, the hospital mortality rates were as follows: resolved (42.1%), mild (47.9%), moderate (62.4%), and severe ARDS (76.1%) (p < 0.001). Patients with improving severity on day 3 had lower mortality (48.8%), whereas patients with the same or worsening severity on day 3 had higher mortality (62.7% and 76.3%, respectively). Patients who were older, had lower PaO2/FiO2, or higher positive end-expiratory pressure on day 1 were significantly associated with nonresolving ARDS on day 3. A Cox regression model with ARDS severity as a time-dependent covariate and competing risk analysis demonstrated that ARDS severity was independently associated with hospital mortality, and nonresolving ARDS had significantly increased hazard of death than resolved ARDS (p < 0.0001). Cumulative mortality curve for ARDS severity comparisons demonstrated significantly different (overall comparison, p < 0.001).ConclusionsReclassification of disease severity after 48 h of ARDS onset could help to divide patients into subgroups with greater separation in terms of mortality. The reviews of this paper are available via the supplemental material section.
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