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3. Globin mRNA reduction for whole-blood transcriptome sequencing

Author

University of Helsinki, Research Program of Molecular Neurology, University of Helsinki, Research Programs Unit, Krjutskov, Kaarel, Koel, Mariann, Roost, Anne Mari, Katayama, Shintaro, Einarsdottir, Elisabet, Jouhilahti, Eeva-Mari, Soderhall, Cilla, Jaakma, Ulle, Plaas, Mario, Vesterlund, Liselotte, Lohi, Hannes, Salumets, Andres, Kere, Juha, University of Helsinki, Research Program of Molecular Neurology, University of Helsinki, Research Programs Unit, Krjutskov, Kaarel, Koel, Mariann, Roost, Anne Mari, Katayama, Shintaro, Einarsdottir, Elisabet, Jouhilahti, Eeva-Mari, Soderhall, Cilla, Jaakma, Ulle, Plaas, Mario, Vesterlund, Liselotte, Lohi, Hannes, Salumets, Andres, and Kere, Juha

Abstract

The transcriptome analysis of whole-blood RNA by sequencing holds promise for the identification and tracking of biomarkers; however, the high globin mRNA (gmRNA) content of erythrocytes hampers whole-blood and buffy coat analyses. We introduce a novel gmRNA locking assay (GlobinLock, GL) as a robust and simple gmRNA reduction tool to preserve RNA quality, save time and cost. GL consists of a pair of gmRNA-specific oligonucleotides in RNA initial denaturation buffer that is effective immediately after RNA denaturation and adds only ten minutes of incubation to the whole cDNA synthesis procedure when compared to non-blood RNA analysis. We show that GL is fully effective not only for human samples but also for mouse and rat, and so far incompletely studied cow, dog and zebrafish.

Published
2016

4. Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing

Author

University of Helsinki, Juha Kere / Principal Investigator, Wang, Jingwen, Vesterlund, Liselotte, Kere, Juha, Jiao, Hong, University of Helsinki, Juha Kere / Principal Investigator, Wang, Jingwen, Vesterlund, Liselotte, Kere, Juha, and Jiao, Hong

Abstract

Zebrafish (Danio rerio) has emerged as a model organism to investigate vertebrate development and human genetic diseases. However, the zebrafish genome annotation is still ongoing and incomplete, and there are still new gene transcripts to be found. With the introduction of massive parallel sequencing, whole transcriptome studies became possible. In the present study, we aimed to discover novel transcribed regions (NTRs) using developmental transcriptome data from RNA sequencing. In order to achieve this, we developed an in-house bioinformatics pipeline for NTR discovery. Using the pipeline, we detected 152 putative NTRs that at the time of discovery were not annotated in Ensembl and NCBI gene database. Four randomly selected NTRs were successfully validated using RT-PCR, and expression profiles of 10 randomly selected NTRs were evaluated using qRT-PCR. The identification of these 152 NTRs provide new information for zebrafish genome annotation as well as new candidates for studies of zebrafish gene function.

Published
2016

5. Functional Analyses of the Crohn's Disease Risk Gene LACC1

Author

Assadi, Ghazaleh, Vesterlund, Liselotte, Bonfiglio, Ferdinando, Mazzurana, Luca, Cordeddu, Lina, Schepis, Danika, Mjösberg, Jenny, Ruhrmann, Sabrina, Fabbri, Alessia, Vukojevic, Vladana, Percipalle, Piergiorgio, Salomons, Florian A., Laurencikiene, Jurga, Törkvist, Leif, Halfvarson, Jonas, D'Amato, Mauro, Assadi, Ghazaleh, Vesterlund, Liselotte, Bonfiglio, Ferdinando, Mazzurana, Luca, Cordeddu, Lina, Schepis, Danika, Mjösberg, Jenny, Ruhrmann, Sabrina, Fabbri, Alessia, Vukojevic, Vladana, Percipalle, Piergiorgio, Salomons, Florian A., Laurencikiene, Jurga, Törkvist, Leif, Halfvarson, Jonas, and D'Amato, Mauro

Abstract

Background Genetic variation in the Laccase (multicopper oxidoreductase) domain-containing 1 (LACC1) gene has been shown to affect the risk of Crohn's disease, leprosy and, more recently, ulcerative colitis and juvenile idiopathic arthritis. LACC1 function appears to promote fatty-acid oxidation, with concomitant inflammasome activation, reactive oxygen species production, and anti-bacterial responses in macrophages. We sought to contribute to elucidating LACC1 biological function by extensive characterization of its expression in human tissues and cells, and through preliminary analyses of the regulatory mechanisms driving such expression. Methods We implemented Western blot, quantitative real-time PCR, immunofluorescence microscopy, and flow cytometry analyses to investigate fatty acid metabolism-immune nexus (FAMIN; the LACC1 encoded protein) expression in subcellular compartments, cell lines and relevant human tissues. Gene-set enrichment analyses were performed to initially investigate modulatory mechanisms of LACC1 expression. A small-interference RNA knockdown in vitro model system was used to study the effect of FAMIN depletion on peroxisome function. Results FAMIN expression was detected in macrophage-differentiated THP-1 cells and several human tissues, being highest in neutrophils, monocytes/macrophages, myeloid and plasmacytoid dendritic cells among peripheral blood cells. Subcellular co-localization was exclusively confined to peroxisomes, with some additional positivity for organelle endomembrane structures. LACC1 co-expression signatures were enriched for genes involved in peroxisome proliferator-activated receptors (PPAR) signaling pathways, and PPAR ligands downregulated FAMIN expression in in vitro model systems. Conclusion FAMIN is a peroxisome-associated protein with primary role(s) in macrophages and other immune cells, where its metabolic functions may be modulated by PPAR signaling events. However, the precise molecular mechanisms through whic

Published
2016
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6. Functional Analyses of the Crohn’s Disease Risk Gene LACC1

Author

Assadi, Ghazaleh, primary, Vesterlund, Liselotte, additional, Bonfiglio, Ferdinando, additional, Mazzurana, Luca, additional, Cordeddu, Lina, additional, Schepis, Danika, additional, Mjösberg, Jenny, additional, Ruhrmann, Sabrina, additional, Fabbri, Alessia, additional, Vukojevic, Vladana, additional, Percipalle, Piergiorgio, additional, Salomons, Florian A., additional, Laurencikiene, Jurga, additional, Törkvist, Leif, additional, Halfvarson, Jonas, additional, and D’Amato, Mauro, additional

Published
2016
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7. Correction: Corrigendum: Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos

Author

Madissoon, Elo, primary, Jouhilahti, Eeva-Mari, additional, Vesterlund, Liselotte, additional, Töhönen, Virpi, additional, Krjutškov, Kaarel, additional, Petropoulos, Sophie, additional, Einarsdottir, Elisabet, additional, Linnarsson, Sten, additional, Lanner, Fredrik, additional, Månsson, Robert, additional, Hovatta, Outi, additional, Bürglin, Thomas R., additional, Katayama, Shintaro, additional, and Kere, Juha, additional

Published
2016
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8. Globin mRNA reduction for whole-blood transcriptome sequencing

Author

Krjutškov, Kaarel, primary, Koel, Mariann, additional, Roost, Anne Mari, additional, Katayama, Shintaro, additional, Einarsdottir, Elisabet, additional, Jouhilahti, Eeva-Mari, additional, Söderhäll, Cilla, additional, Jaakma, Ülle, additional, Plaas, Mario, additional, Vesterlund, Liselotte, additional, Lohi, Hannes, additional, Salumets, Andres, additional, and Kere, Juha, additional

Published
2016
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10. Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos

Author

Madissoon, Elo, primary, Jouhilahti, Eeva-Mari, additional, Vesterlund, Liselotte, additional, Töhönen, Virpi, additional, Krjutškov, Kaarel, additional, Petropoulos, Sophie, additional, Einarsdottir, Elisabet, additional, Linnarsson, Sten, additional, Lanner, Fredrik, additional, Månsson, Robert, additional, Hovatta, Outi, additional, Bürglin, Thomas R., additional, Katayama, Shintaro, additional, and Kere, Juha, additional

Published
2016
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12. The human PRD-like homeobox gene LEUTX has a central role in embryo genome activation

Author

Jouhilahti, Eeva-Mari, primary, Madissoon, Elo, additional, Vesterlund, Liselotte, additional, Töhönen, Virpi, additional, Krjutŝkov, Kaarel, additional, Reyes, Alvaro Plaza, additional, Petropoulos, Sophie, additional, Månsson, Robert, additional, Linnarsson, Sten, additional, Bürglin, Thomas, additional, Lanner, Fredrik, additional, Hovatta, Outi, additional, Katayama, Shintaro, additional, and Kere, Juha, additional

Published
2016
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13. Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development

Author

Töhönen, Virpi, primary, Katayama, Shintaro, additional, Vesterlund, Liselotte, additional, Jouhilahti, Eeva-Mari, additional, Sheikhi, Mona, additional, Madissoon, Elo, additional, Filippini-Cattaneo, Giuditta, additional, Jaconi, Marisa, additional, Johnsson, Anna, additional, Bürglin, Thomas R., additional, Linnarsson, Sten, additional, Hovatta, Outi, additional, and Kere, Juha, additional

Published
2015
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14. Aberrant splicing of genes involved in haemoglobin synthesis and impaired terminal erythroid maturation inSF 3B1mutated refractory anaemia with ring sideroblasts

Author

Conte, Simona, primary, Katayama, Shintaro, additional, Vesterlund, Liselotte, additional, Karimi, Mohsen, additional, Dimitriou, Marios, additional, Jansson, Monika, additional, Mortera‐Blanco, Teresa, additional, Unneberg, Per, additional, Papaemmanuil, Elli, additional, Sander, Birgitta, additional, Skoog, Tiina, additional, Campbell, Peter, additional, Walfridsson, Julian, additional, Kere, Juha, additional, and Hellström‐Lindberg, Eva, additional

Published
2015
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15. Signal regulatory protein alpha is present in several neutrophil granule populations and is rapidly mobilized to the cell surface to negatively fine-tune neutrophil accumulation in inflammation

Author

Stenberg, Åsa, Karlsson, Anna, Feuk-Lagerstedt, Elisabeth, Christenson, Karin, Bylund, Johan, Oldenborg, Anna, Vesterlund, Liselotte, Matozaki, Takashi, Sehlin, Janove, Oldenborg, Per-Arne, Stenberg, Åsa, Karlsson, Anna, Feuk-Lagerstedt, Elisabeth, Christenson, Karin, Bylund, Johan, Oldenborg, Anna, Vesterlund, Liselotte, Matozaki, Takashi, Sehlin, Janove, and Oldenborg, Per-Arne

Abstract

Signal regulatory protein alpha (SIRPα) is a cell surface glycoprotein with inhibitory functions, which may regulate neutrophil transmigration. SIRPα is mobilized to the neutrophil surface from specific granules, gelatinase granules, and secretory vesicles following inflammatory activation in vitro and in vivo. The lack of SIRPα signaling and the ability to upregulate SIRPα to the cell surface promote neutrophil accumulation during inflammation in vivo.

Published
2014
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18. Signal Regulatory Protein Alpha Is Present in Several Neutrophil Granule Populations and Is Rapidly Mobilized to the Cell Surface to Negatively Fine-Tune Neutrophil Accumulation in Inflammation

Author

Stenberg, Åsa, primary, Karlsson, Anna, additional, Feuk-Lagerstedt, Elisabeth, additional, Christenson, Karin, additional, Bylund, Johan, additional, Oldenborg, Anna, additional, Vesterlund, Liselotte, additional, Matozaki, Takashi, additional, Sehlin, Janove, additional, and Oldenborg, Per-Arne, additional

Published
2014
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19. Erythropoiesis In SF3B1 Mutated RARS Is Disrupted During Terminal Erythroid Maturation

Author

Conte, Simona, primary, Vesterlund, Liselotte, additional, Katayama, Shintaro, additional, Karimi, Mohsen, additional, Papaemmanuil, Elli, additional, Jansson, Monika, additional, Mortera-Blanco, Teresa, additional, Dimitriou, Marios, additional, Sander, Birgitta, additional, Skoog, Tiina, additional, Campbell, Peter J., additional, Kere, Juha, additional, Unneberg, Per, additional, and Hellström-Lindberg, Eva, additional

Published
2013
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24. The Zebrafish Orthologue of the Dyslexia Candidate Gene DYX1C1 Is Essential for Cilia Growth and Function

Author

Chandrasekar, Gayathri, Vesterlund, Liselotte, Hultenby, Kjell, Tapia-Páez, Isabel, and Kere, Juha

Subjects
*DYSLEXIA, *DISEASE susceptibility, *ZEBRA danio, *PEPTIDES, *LABORATORY rodents, *NEURONS, *DEVELOPMENTAL biology, *EMBRYOLOGY
Abstract

DYX1C1, a susceptibility gene for dyslexia, encodes a tetratricopeptide repeat domain containing protein that has been implicated in neuronal migration in rodent models. The developmental role of this gene remains unexplored. To understand the biological function(s) of zebrafish dyx1c1 during embryonic development, we cloned the zebrafish dyx1c1 and used morpholino-based knockdown strategy. Quantitative real-time PCR analysis revealed the presence of dyx1c1 transcripts in embryos, early larval stages and in a wide range of adult tissues. Using mRNA in situ hybridization, we show here that dyx1c1 is expressed in many ciliated tissues in zebrafish. Inhibition of dyx1c1 produced pleiotropic phenotypes characteristically associated with cilia defects such as body curvature, hydrocephalus, situs inversus and kidney cysts. We also demonstrate that in dyx1c1 morphants, cilia length is reduced in several organs including Kupffer’s vesicle, pronephros, spinal canal and olfactory placode. Furthermore, electron microscopic analysis of cilia in dyx1c1 morphants revealed loss of both outer (ODA) and inner dynein arms (IDA) that have been shown to be required for cilia motility. Considering all these results, we propose an essential role for dyx1c1 in cilia growth and function. [ABSTRACT FROM AUTHOR]

Published
2013
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