| 1. |
- Habuka, Masato, et al.
(författare)
-
The Kidney Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling
- 2014
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:12, s. e116125-
-
Tidskriftsartikel (refereegranskat)abstract
- To understand renal functions and disease, it is important to define the molecular constituents of the various compartments of the kidney. Here, we used comparative transcriptomic analysis of all major organs and tissues in the human body, in combination with kidney tissue micro array based immunohistochemistry, to generate a comprehensive description of the kidney-specific transcriptome and proteome. A special emphasis was placed on the identification of genes and proteins that were elevated in specific kidney subcompartments. Our analysis identified close to 400 genes that had elevated expression in the kidney, as compared to the other analysed tissues, and these were further subdivided, depending on expression levels, into tissue enriched, group enriched or tissue enhanced. Immunohistochemistry allowed us to identify proteins with distinct localisation to the glomeruli (n=11), proximal tubules (n=120), distal tubules (n=9) or collecting ducts (n=8). Among the identified kidney elevated transcripts, we found several proteins not previously characterised or identified as elevated in kidney. This description of the kidney specific transcriptome and proteome provides a resource for basic and clinical research to facilitate studies to understand kidney biology and disease.
|
|
| 2. |
- Habuka, Masato, et al.
(författare)
-
The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling
- 2015
-
Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 10:12
-
Tidskriftsartikel (refereegranskat)abstract
- To understand functions and diseases of urinary bladder, it is important to define its molecular constituents and their roles in urinary bladder biology. Here, we performed genome-wide deep RNA sequencing analysis of human urinary bladder samples and identified genes upregulated in the urinary bladder by comparing the transcriptome data to those of all other major human tissue types. 90 protein-coding genes were elevated in the urinary bladder, either with enhanced expression uniquely in the urinary bladder or elevated expression together with at least one other tissue (group enriched). We further examined the localization of these proteins by immunohistochemistry and tissue microarrays and 20 of these 90 proteins were localized to the whole urothelium with a majority not yet described in the context of the urinary bladder. Four additional proteins were found specifically in the umbrella cells (Uroplakin 1a, 2, 3a, and 3b), and three in the intermediate/basal cells (KRT17, PCP4L1 and ATP1A4). 61 of the 90 elevated genes have not been previously described in the context of urinary bladder and the corresponding proteins are interesting targets for more in-depth studies. In summary, an integrated omics approach using transcriptomics and antibody-based profiling has been used to define a comprehensive list of proteins elevated in the urinary bladder.
|
|
| 3. |
- Horvatovich, Peter, et al.
(författare)
-
Quest for Missing Proteins : Update 2015 on Chromosome-Centric Human Proteome Project
- 2015
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 14:9, s. 3415-3431
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities; therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper's content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wild (http://c-hpp.webhosting.rug.nl/) and in the Supporting Information.
|
|
| 4. |
|
|
| 5. |
- Legrain, Pierre, et al.
(författare)
-
The Human Proteome Project : Current State and Future Direction
- 2011
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 10:7
-
Tidskriftsartikel (refereegranskat)abstract
- After the successful completion of the Human Genome Project, the Human Proteome Organization has recently officially launched a global Human Proteome Project (HPP), which is designed to map the entire human protein set. Given the lack of protein-level evidence for about 30% of the estimated 20,300 protein-coding genes, a systematic global effort will be necessary to achieve this goal with respect to protein abundance, distribution, subcellular localization, interaction with other biomolecules, and functions at specific time points. As a general experimental strategy, HPP research groups will use the three working pillars for HPP: mass spectrometry, antibody capture, and bioinformatics tools and knowledge bases. The HPP participants will take advantage of the output and cross-analyses from the ongoing Human Proteome Organization initiatives and a chromosome-centric protein mapping strategy, termed C-HPP, with which many national teams are currently engaged. In addition, numerous biologically driven and disease-oriented projects will be stimulated and facilitated by the HPP. Timely planning with proper governance of HPP will deliver a protein parts list, reagents, and tools for protein studies and analyses, and a stronger basis for personalized medicine. The Human Proteome Organization urges each national research funding agency and the scientific community at large to identify their preferred pathways to participate in aspects of this highly promising project in a HPP consortium of funders and investigators.
|
|
| 6. |
- Lin, Xue, et al.
(författare)
-
Controlled release of matrix metalloproteinase 1 with or without skeletal myoblasts transplantation improves cardiac function of rat hearts with chronic myocardial infarction.
- 2009
-
Ingår i: Tissue engineering. Part A. - : Mary Ann Liebert Inc. - 1937-335X .- 1937-3341. ; 15:9, s. 2699-706
-
Tidskriftsartikel (refereegranskat)abstract
- Skeletal myoblast transplantation has been applied clinically for severe ischemic cardiomyopathy. Matrix metalloproteinase 1 (MMP-1) reduces fibrosis and prevents the progress of heart failure. We hypothesized that MMP-1 administration to the infarct area enhances the efficacy of skeletal myoblast transplantation. The controlled release of MMP-1 improved cardiac functions of rats with chronic myocardiac infarction with or without transplantation of skeletal myoblasts. Improvement in cardiac function and small fibrotic area inside the infarcted area were observed compared with those of myoblast transplantation. In conclusion, controlled release of MMP-1 was effective in cardioprotection in postmyocardial infarction although the combination with cell transplantation showed the similar effect.
|
|
| 7. |
- Naruse, Makoto, et al.
(författare)
-
Energy dissipation in energy transfer mediated by optical near-field interactions and their interfaces with optical far-fields
- 2012
-
Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 100:24, s. 241102-
-
Tidskriftsartikel (refereegranskat)abstract
- We theoretically and experimentally evaluated energy dissipation of nanophotonic devices based on energy transfer via near-field interactions and their interfaces with optical far-fields. The lower bound is about 10(4) times more energy-efficient than electronic devices. We also examined some fundamental differences between near-field-mediated optical energy transfer logic and electrical logic in terms of energy dissipation.
|
|
| 8. |
- Paik, Young-Ki, et al.
(författare)
-
Standard Guidelines for the Chromosome-Centric Human Proteome Project
- 2012
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 11:4, s. 2005-2013
-
Tidskriftsartikel (refereegranskat)abstract
- The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-FIPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, introduce topics associated with experimental approaches, data production, quality control, treatment, and transparency of data, governance of the consortium, and collaborative benefits. A companion approach for the Biology and Disease-Driven HPP (B/D-HPP) component of the Human Proteome Project is currently being organized, building upon the Human Proteome Organization's organ-based and biofluid-based initiatives (www.hupo.org/research). The common application of these guidelines in the participating laboratories is expected to facilitate the goal of a comprehensive analysis of the human proteome.
|
|
| 9. |
- Uhlen, Mathias, et al.
(författare)
-
A proposal for validation of antibodies
- 2016
-
Ingår i: Nature Methods. - : Nature Publishing Group. - 1548-7091 .- 1548-7105. ; 13:10, s. 823-
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We convened an ad hoc International Working Group for Antibody Validation in order to formulate the best approaches for validating antibodies used in common research applications and to provide guidelines that ensure antibody reproducibility. We recommend five conceptual 'pillars' for antibody validation to be used in an application-specific manner.
|
|
| 10. |
- Yamamoto, Kohei, et al.
(författare)
-
Ultrafast demagnetization of Pt magnetic moment in L1(0)-FePt probed by magnetic circular dichroism at a hard x-ray free electron laser
- 2019
-
Ingår i: New Journal of Physics. - : IOP PUBLISHING LTD. - 1367-2630. ; 21:12
-
Tidskriftsartikel (refereegranskat)abstract
- Unraveling the origin of ultrafast demagnetization in multisublattice ferromagnetic materials requires femtosecond x-ray techniques to trace the magnetic moment dynamics on individual elements, but this could not yet be achieved in the hard x-ray regime. We demonstrate here the first ultrafast demagnetization dynamics in the ferromagnetic heavy 5d-transition metal Pt using circularly-polarized hard x-rays at an x-ray free electron laser (XFEL). The decay time of laser-induced demagnetization of L1(0)-FePt is determined to be tau(Pt) = 0.61 +/- 0.04 ps using time-resolved x-ray magnetic circular dichroism at the Pt L-3 edge, whereas magneto-optical Kerr measurements indicate the decay time for the total magnetization as tau(total) < 0.1 ps. A transient magnetic state with a photomodulated ratio of the 3d and 5d magnetic moments is demonstrated for pump-probe delays larger than 1 ps. We explain this distinct photo-modulated transient magnetic state by the induced-moment behavior of the Pt atom and the x-ray probing depth. Our findings pave the way for the future use of XFELs to disentangle atomic spin dynamics contributions.
|
|
