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Azzalini E, Di Stefano B, Canzonieri V, Venesio T, Miglio U, Marchiò C, Sapino A, Previderè C, Fattorini P, Bonin S. Quantifying mRNA in Highly Degraded Fixed Tissues by Nanostring Technology: A Comparative Study. Methods Protoc 2024; 7:40. [PMID: 38804334 PMCID: PMC11130824 DOI: 10.3390/mps7030040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024] Open
Abstract
Archive tissues are the most available source of human tissues useful for molecular analysis in translational research. The main issues for those specimens are the modification and degradation of biomolecules, namely proteins, DNA, and RNA. In the last decade, several high-throughput analytical methods have been applied to archive tissues. Although histological tissues are fixed in neutral-buffered formalin nowadays, in the recent past, Bouin's solution was also used in tissue processing. The present study aims to investigate the feasibility of nCounter Nanostring hybridization in quantifying mRNA in highly degraded samples, such as Bouin's fixed and paraffin-embedded (BFPE) tissues, in comparison to the standard formalin-fixed and paraffin-embedded (FFPE) tissues as a source of RNA. A total of 16 paraffin-embedded tissue blocks from eight patients were analyzed (8 were FFPE and 8 were BEPE). Nanostring technology was applied to 300 ng of each RNA sample, whereas 360 ng of the same templates were retrotranscribed and submitted to qPCR and ddPCR. Our results show that the Nanostring technology outperforms the reference methods (ddPCR and qPCR) in detecting target mRNA in FFPE and BFPE samples. However, even Nanostring technology does not escape the limitation imposed by the degradation of the RNA templates, which could lead to misleading conclusions on the gene expression level.
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Affiliation(s)
- Eros Azzalini
- Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (E.A.); (B.D.S.); (V.C.); (S.B.)
| | - Barbara Di Stefano
- Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (E.A.); (B.D.S.); (V.C.); (S.B.)
| | - Vincenzo Canzonieri
- Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (E.A.); (B.D.S.); (V.C.); (S.B.)
- Pathology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano-National Cancer Institute, 33081 Pordenone, Italy
| | - Tiziana Venesio
- Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia-IRCCS, 10060 Candiolo, Italy; (T.V.); (U.M.); (C.M.); (A.S.)
| | - Umberto Miglio
- Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia-IRCCS, 10060 Candiolo, Italy; (T.V.); (U.M.); (C.M.); (A.S.)
| | - Caterina Marchiò
- Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia-IRCCS, 10060 Candiolo, Italy; (T.V.); (U.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Anna Sapino
- Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia-IRCCS, 10060 Candiolo, Italy; (T.V.); (U.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Carlo Previderè
- Laboratorio di Genetica Forense, Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, 27100 Pavia, Italy;
| | - Paolo Fattorini
- Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (E.A.); (B.D.S.); (V.C.); (S.B.)
| | - Serena Bonin
- Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (E.A.); (B.D.S.); (V.C.); (S.B.)
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Identification of Reference Genes in Chicken Intraepithelial Lymphocyte Natural Killer Cells Infected with Very-virulent Infectious Bursal Disease Virus. Sci Rep 2020; 10:8561. [PMID: 32444639 PMCID: PMC7244580 DOI: 10.1038/s41598-020-65474-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Due to the limitations in the range of antibodies recognising avian viruses, quantitative real-time PCR (RT-qPCR) is still the most widely used method to evaluate the expression of immunologically related genes in avian viruses. The objective of this study was to identify suitable reference genes for mRNA expression analysis in chicken intraepithelial lymphocyte natural killer (IEL-NK) cells after infection with very-virulent infectious bursal disease virus (vvIBDV). Fifteen potential reference genes were selected based on the references available. The coefficient of variation percentage (CV%) and average count of these 15 genes were determined by NanoString technology for control and infected samples. The M and V values for shortlisted reference genes (ACTB, GAPDH, HMBS, HPRT1, SDHA, TUBB1 and YWHAZ) were calculated using geNorm and NormFinder. GAPDH, YWHAZ and HMBS were the most stably expressed genes. The expression levels of three innate immune response related target genes, CASP8, IL22 and TLR3, agreed in the NanoString and RNA sequencing (RNA-Seq) results using one or two reference genes for normalisation (not HMBS). In conclusion, GAPDH and YWHAZ could be used as reference genes for the normalisation of chicken IEL-NK cell gene responses to infection with vvIBDV.
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Toor A, Culibrk L, Singhera GK, Moon KM, Prudova A, Foster LJ, Moore MM, Dorscheid DR, Tebbutt SJ. Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium. PLoS One 2018; 13:e0209652. [PMID: 30589860 PMCID: PMC6307744 DOI: 10.1371/journal.pone.0209652] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022] Open
Abstract
Aspergillus fumigatus (A. fumigatus) is a wide-spread fungus that is a potent allergen in hypersensitive individuals but also an opportunistic pathogen in immunocompromised patients. It reproduces asexually by releasing airborne conidiospores (conidia). Upon inhalation, fungal conidia are capable of reaching the airway epithelial cells (AECs) in bronchial and alveolar tissues. Previous studies have predominantly used submerged monolayer cultures for studying this host-pathogen interaction; however, these cultures do not recapitulate the mucocililary differentiation phenotype of the in vivo epithelium in the respiratory tract. Thus, the aim of this study was to use well-differentiated primary human bronchial epithelial cells (HBECs) grown at the air-liquid interface (ALI) to determine their transcriptomic and proteomic responses following interaction with A. fumigatus conidia. We visualized conidial interaction with HBECs using confocal laser scanning microscopy (CLSM), and applied NanoString nCounter and shotgun proteomics to assess gene expression changes in the human cells upon interaction with A. fumigatus conidia. Western blot analysis was used to assess the expression of top three differentially expressed proteins, CALR, SET and NUCB2. CLSM showed that, unlike submerged monolayer cultures, well-differentiated ALI cultures of primary HBECs were estimated to internalize less than 1% of bound conidia. Nevertheless, transcriptomic and proteomic analyses revealed numerous differentially expressed host genes; these were enriched for pathways including apoptosis/autophagy, translation, unfolded protein response and cell cycle (up-regulated); complement and coagulation pathways, iron homeostasis, nonsense mediated decay and rRNA binding (down-regulated). CALR and SET were confirmed to be up-regulated in ALI cultures of primary HBECs upon exposure to A. fumigatus via western blot analysis. Therefore, using transcriptomics and proteomics approaches, ALI models recapitulating the bronchial epithelial barrier in the conductive zone of the respiratory tract can provide novel insights to the molecular response of bronchial epithelial cells upon exposure to A. fumigatus conidia.
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Affiliation(s)
- Amreen Toor
- Experimental Medicine, University of British Columbia, Vancouver, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Luka Culibrk
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Gurpreet K. Singhera
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Anna Prudova
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
| | - Delbert R. Dorscheid
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - Scott J. Tebbutt
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, Canada
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Rebuli ME, Pawlak EA, Walsh D, Martin EM, Jaspers I. Distinguishing Human Peripheral Blood NK Cells from CD56 dimCD16 dimCD69 +CD103 + Resident Nasal Mucosal Lavage Fluid Cells. Sci Rep 2018; 8:3394. [PMID: 29467466 PMCID: PMC5821812 DOI: 10.1038/s41598-018-21443-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 02/02/2018] [Indexed: 02/08/2023] Open
Abstract
Natural killer (NK) cells are members of the innate lymphoid cells group 1 (ILC1s), which play a critical role in innate host defense against viruses and malignancies. While many studies have examined the role of circulating peripheral blood (PB) CD56+ NK cells, little is known about the resident CD56+ cell population. Therefore, matched CD56+ cells from nasal lavage fluid (NLF) and PB of smokers and non-smokers were compared phenotypically, via flow cytometry, and functionally, via NK-cell specific gene expression. NLF and PB CD56+ cells had similar expression of CD56, but differentially expressed tissue residency (CD69 and CD103) and cytotoxicity (CD16) markers. In addition, NLF CD56dim cells expressed lower levels of cytotoxicity-associated genes, perforin (PRF1) and granzyme B (GZMB), and increased levels of cytokines and cell signaling molecules, TRAIL, IFNGR2, and IL8, as compared to PB CD56dim cells. In smokers, ITGA2 was downregulated in NLF CD56dim cells, while markers of cytotoxic function were primarily downregulated in PB CD56dim NK cells. Overall, NLF CD56dim cells are a unique cell population that likely play a role in orchestrating innate immune responses in the nasal cavity, which is distinct from their role as a non-antigen-restricted cytotoxic CD56dim lymphocytes in the PB.
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Affiliation(s)
- Meghan E Rebuli
- Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica A Pawlak
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dana Walsh
- Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth M Martin
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ilona Jaspers
- Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Ee Uli J, Yong CSY, Yeap SK, Rovie-Ryan JJ, Mat Isa N, Tan SG, Alitheen NB. RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque ( Macaca fascicularis). PeerJ 2017; 5:e3566. [PMID: 28828235 PMCID: PMC5563440 DOI: 10.7717/peerj.3566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/21/2017] [Indexed: 12/25/2022] Open
Abstract
The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology. A total of 174,208,078 paired end 70 base pair sequencing reads were obtained from the Illumina Hi-Seq 2500 sequencer. The overall mapping percentage of the sequencing reads to the M. fascicularis reference genome ranged from 53–63%. Categorisation of expressed genes to Gene Ontology (GO) and KEGG pathway categories revealed that GO terms with the highest number of associated expressed genes include Cellular process, Catalytic activity, and Cell part, while for pathway categorisation, the majority of expressed genes in lymph node, spleen, and thymus fall under the Global overview and maps pathway category, while 266, 221, and 138 genes from lymph node, spleen, and thymus were respectively enriched in the Immune system category. Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production. Differential gene expression analysis among the three tissues revealed 574 differentially expressed genes (DEG) between lymph and spleen, 5402 DEGs between lymph and thymus, and 7008 DEGs between spleen and thymus. Venn diagram analysis of expressed genes revealed a total of 2,630, 253, and 279 tissue-specific genes respectively for lymph node, spleen, and thymus tissues. This is the first time the lymph node, spleen, and thymus transcriptome of the Peninsular Malaysian cynomolgus macaque have been sequenced via RNA-Seq. Novel transcriptomic data will further enrich the present M. fascicularis genomic database and provide future research potentials, including novel transcript discovery, comparative studies, and molecular markers development.
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Affiliation(s)
- Joey Ee Uli
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Christina Seok Yien Yong
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University, Sepang, Selangor, Malaysia
| | - Jeffrine J Rovie-Ryan
- Department of Wildlife and National Parks (DWNP), Ex-Situ Conservation Division, Department of Wildlife and National Parks, Kuala Lumpur, Malaysia
| | - Nurulfiza Mat Isa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Soon Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Radke L, Sandig G, Lubitz A, Schließer U, von Horsten HH, Blanchard V, Keil K, Sandig V, Giese C, Hummel M, Hinderlich S, Frohme M. In Vitro Evaluation of Glycoengineered RSV-F in the Human Artificial Lymph Node Reactor. Bioengineering (Basel) 2017; 4:bioengineering4030070. [PMID: 28952549 PMCID: PMC5615316 DOI: 10.3390/bioengineering4030070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/27/2017] [Accepted: 08/03/2017] [Indexed: 11/16/2022] Open
Abstract
Subunit vaccines often require adjuvants to elicit sustained immune activity. Here, a method is described to evaluate the efficacy of single vaccine candidates in the preclinical stage based on cytokine and gene expression analysis. As a model, the recombinant human respiratory syncytial virus (RSV) fusion protein (RSV-F) was produced in CHO cells. For comparison, wild-type and glycoengineered, afucosylated RSV-F were established. Both glycoprotein vaccines were tested in a commercial Human Artificial Lymph Node in vitro model (HuALN®). The analysis of six key cytokines in cell culture supernatants showed well-balanced immune responses for the afucosylated RSV-F, while immune response of wild-type RSV-F was more Th1 accentuated. In particular, stronger and specific secretion of interleukin-4 after each round of re-stimulation underlined higher potency and efficacy of the afucosylated vaccine candidate. Comprehensive gene expression analysis by nCounter gene expression assay confirmed the stronger onset of the immunologic reaction in stimulation experiments with the afucosylated vaccine in comparison to wild-type RSV-F and particularly revealed prominent activation of Th17 related genes, innate immunity, and comprehensive activation of humoral immunity. We, therefore, show that our method is suited to distinguish the potency of two vaccine candidates with minor structural differences.
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Affiliation(s)
- Lars Radke
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, Wildau 15745, Germany.
- Institute of Pathology, Charitè-University Medicine Berlin, Augustenburger Platz 1, Berlin 13353, Germany.
| | - Grit Sandig
- Laboratory of Biochemistry, Department of Life Sciences and Technology, Beuth University of Applied Sciences, Seestraße 64, Berlin 13347, Germany.
| | - Annika Lubitz
- ProBioGen AG, Goethestraße 54, Berlin 13086, Germany.
| | | | - Hans Henning von Horsten
- Department of Life Science Engineering, HTW Berlin University of Applied Sciences, Wilhelminenhofstraße 75a, Berlin 12459, Germany.
| | - Veronique Blanchard
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité Medical University Berlin, Augustenburger Platz 1, Berlin 13353, Germany.
| | - Karolin Keil
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, Wildau 15745, Germany.
| | - Volker Sandig
- ProBioGen AG, Goethestraße 54, Berlin 13086, Germany.
| | | | - Michael Hummel
- Institute of Pathology, Charitè-University Medicine Berlin, Augustenburger Platz 1, Berlin 13353, Germany.
| | - Stephan Hinderlich
- Laboratory of Biochemistry, Department of Life Sciences and Technology, Beuth University of Applied Sciences, Seestraße 64, Berlin 13347, Germany.
| | - Marcus Frohme
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, Wildau 15745, Germany.
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Sandig G, von Horsten HH, Radke L, Blanchard V, Frohme M, Giese C, Sandig V, Hinderlich S. Engineering of CHO Cells for the Production of Recombinant Glycoprotein Vaccines with Xylosylated N-glycans. Bioengineering (Basel) 2017; 4:bioengineering4020038. [PMID: 28952517 PMCID: PMC5590453 DOI: 10.3390/bioengineering4020038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/22/2017] [Accepted: 04/24/2017] [Indexed: 11/25/2022] Open
Abstract
Xylose is a general component of O-glycans in mammals. Core-xylosylation of N-glycans is only found in plants and helminth. Consequently, xylosylated N-glycans cause immunological response in humans. We have used the F-protein of the human respiratory syncytial virus (RSV), one of the main causes of respiratory tract infection in infants and elderly, as a model protein for vaccination. The RSV-F protein was expressed in CHO-DG44 cells, which were further modified by co-expression of β1,2-xylosyltransferase from Nicotiana tabacum. Xylosylation of RSV-F N-glycans was shown by monosaccharide analysis and MALDI-TOF mass spectrometry. In immunogenic studies with a human artificial lymph node model, the engineered RSV-F protein revealed improved vaccination efficacy.
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Affiliation(s)
- Grit Sandig
- Laboratory of Biochemistry, Department of Life Sciences and Technology, Beuth University of Applied Sciences Berlin, Seestrasse 64, 13347 Berlin, Germany.
| | - Hans Henning von Horsten
- Department of Life Science Engineering, HTW Berlin University of Applied Sciences, Wilhelminenhofstraße 75a, 12459 Berlin, Germany.
| | - Lars Radke
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
| | - Véronique Blanchard
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité Medical University Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
| | - Marcus Frohme
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
| | | | - Volker Sandig
- ProBioGen AG, Goethestrasse 54, 13086 Berlin, Germany.
| | - Stephan Hinderlich
- Laboratory of Biochemistry, Department of Life Sciences and Technology, Beuth University of Applied Sciences Berlin, Seestrasse 64, 13347 Berlin, Germany.
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Bentley-Hewitt KL, Hedderley DI, Monro J, Martell S, Smith H, Mishra S. Comparison of quantitative real-time polymerase chain reaction with NanoString® methodology using adipose and liver tissues from rats fed seaweed. N Biotechnol 2016; 33:380-6. [DOI: 10.1016/j.nbt.2016.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 12/17/2015] [Accepted: 01/07/2016] [Indexed: 12/19/2022]
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Amna T, Hassan MS, Al-Deyab SS, Khil MS, Hwang I. Impact on gene expression in response to silver-decorated titania nanomatrix using an in vitro satellite cell culture model. Polym Bull (Berl) 2015. [DOI: 10.1007/s00289-015-1581-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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