| 1. |
|
|
| 2. |
- Strömberg, Sara, et al.
(författare)
-
A high-throughput strategy for protein profiling in cell microarrays using automated image analysis
- 2007
-
Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 7:13, s. 2142-2150
-
Tidskriftsartikel (refereegranskat)abstract
- Advances in antibody production render a growing supply of affinity reagents for immunohistochemistry (IHC), and tissue microarray (TMA) technologies facilitate simultaneous analysis of protein expression in a multitude of tissues. However, collecting validated IHC data remains a bottleneck problem, as the standard method is manual microscopical analysis. Here we present a high-throughput strategy combining IHC on a recently developed cell microarray with a novel, automated image-analysis application (TMAx). The software was evaluated on 200 digital images of IHC-stained cell spots, by comparing TMAx annotation with manual annotation performed by seven human experts. A high concordance between automated and manual annotation of staining intensity and fraction of IHC-positive cells was found. in a limited study, we also investigated the possibility to assess the correlation between mRNA and protein levels, by using TMAx output results for relative protein quantification and quantitative real-time PCR for the quantification of corresponding transcript levels. In conclusion, automated analysis of immunohistochemically stained in vitro-cultured cells in a microarray format can be used for high-throughput protein profiling, and extraction of RNA from the same cell lines provides a basis for comparing transcription and protein expression on a global scale.
|
|
| 3. |
- Uhlén, Mathias, et al.
(författare)
-
A human protein atlas for normal and cancer tissues based on antibody proteomics
- 2005
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 4:12, s. 1920-1932
-
Tidskriftsartikel (refereegranskat)abstract
- Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, similar to 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.
|
|
| 4. |
- Andersson, Sandra, et al.
(författare)
-
The Transcriptomic and Proteomic Landscapes of Bone Marrow and Secondary Lymphoid Tissues
- 2014
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:12, s. e115911-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The sequencing of the human genome has opened doors for global gene expression profiling, and the immense amount of data will lay an important ground for future studies of normal and diseased tissues. The Human Protein Atlas project aims to systematically map the human gene and protein expression landscape in a multitude of normal healthy tissues as well as cancers, enabling the characterization of both housekeeping genes and genes that display a tissue-specific expression pattern. This article focuses on identifying and describing genes with an elevated expression in four lymphohematopoietic tissue types (bone marrow, lymph node, spleen and appendix), based on the Human Protein Atlas-strategy that combines high throughput transcriptomics with affinity-based proteomics. Results: An enriched or enhanced expression in one or more of the lymphohematopoietic tissues, compared to other tissue-types, was seen for 693 out of 20,050 genes, and the highest levels of expression were found in bone marrow for neutrophilic and erythrocytic genes. A majority of these genes were found to constitute well-characterized genes with known functions in lymphatic or hematopoietic cells, while others are not previously studied, as exemplified by C19ORF59. Conclusions: In this paper we present a strategy of combining next generation RNA-sequencing with in situ affinity-based proteomics in order to identify and describe new gene targets for further research on lymphatic or hematopoietic cells and tissues. The results constitute lists of genes with enriched or enhanced expression in the four lymphohematopoietic tissues, exemplified also on protein level with immunohistochemical images.
|
|
| 5. |
- Andersson, Sandra, 1978-
(författare)
-
Validation of antibodies for tissue based immunoassays
- 2015
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In situ protein detection in human tissues using antibodies reveals the cellular protein localization, and affinity-based proteomic studies can help to discover proteins involved in the development of diseases. However, antibodies often suffer from cross-reactivity, and the lack of positive and negative tissue controls for uncharacterized proteins complicates the mapping of the proteome. The aim of this thesis is thus to improve the methodology for validating antibodies used for immunostaining on formalin-fixed paraffin-embedded tissues.Two of the papers include comparisons between mRNA-expression and immunostaining of corresponding protein. In paper I, ISH and IHC staining patterns were compared on consecutive TMA-slides. The study of well-characterized genes showed that ISH could be used for validation of antibodies. ISH was further used for antibody evaluation, and could validate four out of nine antibodies showing potentially interesting staining patterns. In paper III, transcriptomic data generated by RNA-sequencing were used to identify tissue specific expression in lymphohematopoietic tissues. An increased expression in one or more of these tissues compared to other tissue types was seen for 693 genes, and these were further compared to the staining patterns of corresponding proteins in tissues.Antibody labeling is necessary for many immunoassays. In paper II, two techniques for antibody-biotinylation were compared, aiming to find a stringent labeling method for antibodies used for immunostaining on TMAs. The ZBPA-method, binding specifically to Fc-part of antibodies, was found to be superior to the Lightning Link-biotinylation kit targeting amine groups, since labeling of amine groups on stabilizing proteins in the antibody buffer causes unspecific staining.The localization of the estrogen receptor beta (ERβ) in human normal and cancer tissues was studied in paper IV. Thorough evaluation of 13 antibodies using positive and negative control cell lines showed that only one antibody, PPZ0506, is specific for ERβ in all three immunoassays used. Contradictory to previously published data, tissue profiling using PPZ0506 showed that ERβ is expressed in a limited number of normal and cancer tissues.In conclusion, the present investigations present tools for validation of antibodies used for large-scale studies of protein expression in tissues.
|
|
| 6. |
|
|
| 7. |
|
|
| 8. |
- Asplund, Kenneth, et al.
(författare)
-
Caregivers' Reactions to the Physical Appearance of a Person in the Final Stage of Dementia as Measured by Semantic Differentials
- 1993
-
Ingår i: The International Journal of Aging & Human Development. - 0091-4150 .- 1541-3535. ; 37:3, s. 205-215
-
Tidskriftsartikel (refereegranskat)abstract
- The semantic differential (SeD) technique was applied to 158 caregivers from a nursing home in the northern part of Sweden. The questionnaire contained fifty-eight bipolar scales of adjective pairs and the interviewees indicated then-reactions to a described picture of a severely demented person: A factor analysis revealed three dimensions; an ethical one, an esthetical one, and one about the person's own feelings. The fifty-eight scales were mostly rated toward the negative poles. The severely demented person was rated as painful, apathetic, suffering, weak, afraid, sad, cold, dark, rough, and ugly.Four years later a comparable group of caregivers (n = 93) answered a revised questionnaire containing the 26 SeD scales with factor loadings > .50 for the picture of the severely demented person. The result was nearly identical and alternative interpretations are discussed.
|
|
| 9. |
- Asplund, Kenneth, et al.
(författare)
-
Caregivers' Reactions to the Physical Appearance of a Person in the Final Stage of Dementia as Measured by Semantic Differentials
- 1993
-
Ingår i: International Journal of Aging and Human Development. - 0091-4150. ; 37:3, s. 205-216
-
Tidskriftsartikel (refereegranskat)abstract
- Caregivers (n=158) from Swedish nursing home rated severely demented person as painful, apathetic, suffering, weak, afraid, sad, cold, dark, rough, and ugly. Four years later, comparable group of 93 caregivers answered revised questionnaire. Results were nearly identical to first administration.
|
|
| 10. |
|
|
