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Jørgensen KM, Færgestad Mosleth E, Hovde Liland K, Hopf NB, Holdhus R, Stavrum AK, Gjertsen BT, Kirkeleit J. Global Gene Expression Response in Peripheral Blood Cells of Petroleum Workers Exposed to Sub-Ppm Benzene Levels. Int J Environ Res Public Health 2018; 15:ijerph15112385. [PMID: 30373255 PMCID: PMC6266895 DOI: 10.3390/ijerph15112385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/21/2018] [Accepted: 10/24/2018] [Indexed: 01/14/2023]
Abstract
Altered gene expression in pathways relevant to leukaemogenesis, as well as reduced levels of circulating lymphocytes, have been reported in workers that were exposed to benzene concentrations below 1 ppm. In this study, we analysed whole blood global gene expression patterns in a worker cohort with altered levels of T cells and immunoglobulins IgM and IgA at three time points; pre-shift, post-shift (after three days), and post-recovery (12 hours later). Eight benzene exposed tank workers performing maintenance work in crude oil cargo tanks with a mean benzene exposure of 0.3 ppm (range 0.1–0.5 ppm) and five referents considered to be unexposed were examined by gene expression arrays. By using our data as independent validation, we reanalysed selected genes that were reported to be altered from previous studies of workers being exposed to sub-ppm benzene levels Four out of six genes previously proposed as marker genes in chronically exposed workers separated benzene exposed workers from unexposed referents (CLEC5, ACSL1, PRG2, IFNB1). Even better separation of benzene exposed workers and referents was observed for short-term exposure for genes in the Jak-STAT pathway, particularly elevated expression of IL6 and reduced expression of IL19.
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Affiliation(s)
- Katarina M Jørgensen
- Department of Clinical Science, University of Bergen, P.O. Box 7804, N-5020 Bergen, Norway.
- Institute of Marine Research, P.O. Box 1870 Nordnes, N-5817 Bergen, Norway.
| | | | - Kristian Hovde Liland
- Nofima AS, Osloveien 1, N-1430 Ås, Norway.
- Faculty of Science and Technology, Norwegian University of Life Sciences, NO-1430 Ås, Norway.
| | - Nancy B Hopf
- Institute for Work and Health (IST), Universities of Lausanne and Geneva, CH-1066 Lausanne-Epalinges, Switzerland.
| | - Rita Holdhus
- Department of Clinical Science, University of Bergen, P.O. Box 7804, N-5020 Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, P.O. Box 1400, N-5021 Bergen, Norway.
| | - Anne-Kristin Stavrum
- Department of Clinical Science, University of Bergen, P.O. Box 7804, N-5020 Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, P.O. Box 1400, N-5021 Bergen, Norway.
| | - Bjørn Tore Gjertsen
- Center for Cancer Biomarkers (CCBIO), Department of Clinical Science, Precision Oncology Research Group, University of Bergen, P.O. Box 7804, N-5020 Bergen, Norway.
| | - Jorunn Kirkeleit
- Department of Clinical Science, University of Bergen, P.O. Box 7804, N-5020 Bergen, Norway.
- Department of Global Public Health and Primary Care, University of Bergen, P.O. Box 7804, N-5020 Bergen, Norway.
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Jørgensen KM, Wennevik V, Eide Sørvik AG, Unneland L, Prusov S, Ayllon F, Glover KA. Investigating the frequency of triploid Atlantic salmon in wild Norwegian and Russian populations. BMC Genet 2018; 19:90. [PMID: 30285613 PMCID: PMC6171226 DOI: 10.1186/s12863-018-0676-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/19/2018] [Indexed: 12/18/2022] Open
Abstract
Background Fish may display variations in ploidy, including three sets of chromosomes, known as triploidy. A recent study revealed a frequency of ~ 2% spontaneous (i.e., non-intentional) triploidy in domesticated Atlantic salmon produced in Norwegian aquaculture in the period 2007–2014. In contrast, the frequency of triploidy in wild salmon populations has not been studied thus far, and in wild populations of other organisms, it has been very rarely studied. In population genetic data sets, individuals that potentially display chromosome abnormalities, such as triploids with three alleles, are typically excluded on the premise that they may reflect polluted or otherwise compromised samples. Here, we critically re-investigated the microsatellite genetic profile of ~ 6000 wild Atlantic salmon sampled from 80 rivers in Norway and Russia, to investigate the frequency of triploid individuals in wild salmon populations for the first time. Results We detected a single triploid salmon, and five individuals displaying three alleles at one of the loci, thus regarded as putatively trisomic. This gave an overall frequency of triploid and putatively trisomic individuals in the data set of 0.017 and 0.083% respectively. The triploid salmon was an adult female, and had spent 2 years in freshwater and 2 years in the sea. Conclusions We conclude that the frequency of naturally-occurring triploid Atlantic salmon in wild Norwegian and Russian populations is very low, and many-fold lower than the frequency of spontaneous triploids observed in aquaculture. Our results suggest that aquaculture rearing conditions substantially increase the probability of triploidy to develop, and/or permits greater survival of triploid individuals, in comparison to the wild. Electronic supplementary material The online version of this article (10.1186/s12863-018-0676-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Vidar Wennevik
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | | | - Laila Unneland
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO), Murmansk, 183038, Russia
| | - Fernando Ayllon
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway.,Sea lice Research Centre, Department of Biology, University of Bergen, N-5020, Bergen, Norway
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Arendrup MC, Meletiadis J, Zaragoza O, Jørgensen KM, Marcos-Zambrano LJ, Kanioura L, Cuenca-Estrella M, Mouton JW, Guinea J. Multicentre determination of rezafungin (CD101) susceptibility of Candida species by the EUCAST method. Clin Microbiol Infect 2018; 24:1200-1204. [PMID: 29505881 DOI: 10.1016/j.cmi.2018.02.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/30/2018] [Accepted: 02/14/2018] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Rezafungin (CD101) is a new long-acting echinocandin allowing weekly dosing, currently undergoing phase-II clinical trials for invasive candidiasis. The aim of this study was to assess rezafungin's in vitro activity against the most frequent Candida species following the EUCAST methodology. METHODS The susceptibility of 2018 clinical Candida isolates was determined at four European laboratories. In parallel, six control strains were repeatedly tested. Wild-type upper limits (WT-ULs), defined as the MIC value where the wild-type distribution ends, were determined following the principles for EUCAST ECOFF-setting. RESULTS The lowest rezafungin MICs (geometric MIC (GM-MIC), MIC range (mg/L)) were observed for C. albicans (0.016, 0.002-0.125) and the highest for C. parapsilosis (1.657, 0.063->4). MICs for the remaining species were in between these values (GM-MICs 0.048-0.055). Visual and statistical WT-ULs were identical for C. glabrata (0.125), C. krusei (0.125), C. parapsilosis (4), and C. tropicalis (0.25). If adopting these WT-ULs for classification into WT and non-WT populations, 1/413 C. glabrata, 1/402 C. krusei, 1/398 C. parapsilosis, and 1/402 C. tropicalis isolates were categorized as non-WT, all of which derived from Laboratory 1. For C. albicans unexplained laboratory variation was observed (WT-UL: 0.063-0.125 in Laboratories 1 and 2 versus 0.016 in Laboratories 3 and 4). A similar systematic difference was observed comparing the MICs for the three C. albicans QC strains, specifically, obtained in Laboratories 1and 2 with those in Laboratories 3 and 4. DISCUSSION Rezafungin displayed species-specific activity similar to other echinocandins. Interlaboratory variation was observed for the most susceptible species C. albicans clinical and QC strains, an observation that warrants further investigation.
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Affiliation(s)
- M C Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark; Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - J Meletiadis
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands; Clinical Microbiology Laboratory, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - O Zaragoza
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - K M Jørgensen
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
| | - L J Marcos-Zambrano
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - L Kanioura
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M Cuenca-Estrella
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - J W Mouton
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - J Guinea
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
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Jørgensen KM, Egeberg A, Gislason GH, Skov L, Thyssen JP. Anxiety, depression and suicide in patients with prurigo nodularis. J Eur Acad Dermatol Venereol 2016; 31:e106-e107. [PMID: 27505149 DOI: 10.1111/jdv.13827] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K M Jørgensen
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - A Egeberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - G H Gislason
- Department of Cardiology, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark.,The Danish Heart Foundation, Copenhagen, Denmark.,The National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - L Skov
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - J P Thyssen
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
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Øye OK, Jørgensen KM, Hjelle SM, Sulen A, Ulvang DM, Gjertsen BT. Gel2DE - a software tool for correlation analysis of 2D gel electrophoresis data. BMC Bioinformatics 2013; 14:215. [PMID: 23829206 PMCID: PMC3710208 DOI: 10.1186/1471-2105-14-215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/01/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Two-dimensional gel electrophoresis (2DE) is a powerful technique for studying protein isoforms and their modifications. Existing commercial 2D image analysis tools rely on spot detection that limits analysis of complex protein profiles, e.g. spot appearance/disappearance or overlapping spots. Pixel-by-pixel correlation analysis, an analysis technique for identifying relations between protein patterns in gel images and external variables, can overcome such limitations in spot analysis. RESULTS We have implemented the first publically available pixel-by-pixel correlation analysis tool, the software Gel2DE. 2D immunoblot time course analysis of p53 protein stabilization in response to ionizing irradiation shows that pixel-by-pixel analysis can yield an overall activation biosignature for p53, despite changing spots shape, size and position. CONCLUSIONS Pixel-by-pixel correlation of aligned 2D images permits analysis of complex protein patterns. We anticipate that the Gel2DE correlation software will be a useful tool for future bioinformatics discoveries through 2D gel electrophoresis.
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Jørgensen KM, Haddow PC. Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes. J Bioinform Comput Biol 2011; 9:579-95. [PMID: 21776610 DOI: 10.1142/s0219720011005410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 02/18/2011] [Accepted: 02/19/2011] [Indexed: 11/18/2022]
Abstract
Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.
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Affiliation(s)
- Katarina M Jørgensen
- Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
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Skavland J, Jørgensen KM, Hadziavdic K, Hovland R, Jonassen I, Bruserud O, Gjertsen BT. Specific cellular signal-transduction responses to in vivo combination therapy with ATRA, valproic acid and theophylline in acute myeloid leukemia. Blood Cancer J 2011; 1:e4. [PMID: 22829110 PMCID: PMC3255270 DOI: 10.1038/bcj.2011.2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 12/14/2010] [Accepted: 01/03/2011] [Indexed: 12/25/2022] Open
Abstract
Acute myeloid leukemia (AML) frequently comprises mutations in genes that cause perturbation in intracellular signaling pathways, thereby altering normal responses to growth factors and cytokines. Such oncogenic cellular signal transduction may be therapeutic if targeted directly or through epigenetic regulation. We treated 24 selected elderly AML patients with all-trans retinoic acid for 2 days before adding theophylline and the histone deacetylase inhibitor valproic acid (ClinicalTrials.gov NCT00175812; EudraCT no. 2004-001663-22), and sampled 11 patients for peripheral blood at day 0, 2 and 7 for single-cell analysis of basal level and signal-transduction responses to relevant myeloid growth factors (granulocyte-colony-stimulating factor, granulocyte/macrophage-colony-stimulating factor, interleukin-3, Flt3L, stem cell factor, erythropoietin, CXCL-12) on 10 signaling molecules (CREB, STAT1/3/5, p38, Erk1/2, Akt, c-Cbl, ZAP70/Syk and rpS6). Pretreatment analysis by unsupervised clustering and principal component analysis divided the patients into three distinguishable signaling clusters (non-potentiated, potentiated basal and potentiated signaling). Signal-transduction pathways were modulated during therapy and patients moved between the clusters. Patients with multiple leukemic clones demonstrated distinct stimulation responses and therapy-induced modulation. Individual signaling profiles together with clinical and hematological information may be used to early identify AML patients in whom epigenetic and signal-transduction targeted therapy is beneficial.
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Jørgensen KM, Hjelle SM, Øye OK, Puntervoll P, Reikvam H, Skavland J, Anderssen E, Bruserud Ø, Gjertsen BT. Untangling the intracellular signalling network in cancer--a strategy for data integration in acute myeloid leukaemia. J Proteomics 2010; 74:269-81. [PMID: 21075225 DOI: 10.1016/j.jprot.2010.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 08/31/2010] [Accepted: 11/03/2010] [Indexed: 01/10/2023]
Abstract
Protein and gene networks centred on the regulatory tumour suppressor proteins may be of crucial importance both in carcinogenesis and in the response to chemotherapy. Tumour suppressor protein p53 integrates intracellular data in stress responses, receiving signals and translating these into differential gene expression. Interpretation of the data integrated on p53 may therefore reveal the response to therapy in cancer. Proteomics offers more specific data - closer to "the real action" - than the hitherto more frequently used gene expression profiling. Integrated data analysis may reveal pathways disrupted at several regulatory levels. Ultimately, integrated data analysis may also contribute to finding key underlying cancer genes. We here proposes a Partial Least Squares Regression (PLSR)-based data integration strategy, which allows simultaneous analysis of proteomic data, gene expression data and classical clinical parameters. PLSR collapses multidimensional data into fewer relevant dimensions for data interpretation. PLSR can also aid identification of functionally important modules by also performing comparison to databases on known biological interactions. Further, PLSR allows meaningful visualization of complex datasets, aiding interpretation of the underlying biology. Extracting the true biological causal mechanisms from heterogeneous patient populations is the key to discovery of new therapeutic options in cancer.
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Jørgensen KM. [Hospital admission interview in nursing anno 1996]. Klin Sygepleje 1997; 11:44-51. [PMID: 9414500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Jørgensen KM, Hansen AO. [Cutbacks. A paltry 21 million could close down deaconess hospital]. Sygeplejersken 1990; 90:10-2. [PMID: 2089694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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