| 1. |
- Fagerberg, Linn, et al.
(författare)
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Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
- 2014
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 13:2, s. 397-406
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Tidskriftsartikel (refereegranskat)abstract
- Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody- based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to 80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.
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| 2. |
- Duggen, S., et al.
(författare)
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The role of airborne volcanic ash for the surface ocean biogeochemical iron-cycle: a review
- 2010
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Ingår i: BIOGEOSCIENCES. - 1726-4170. ; 7:3, s. 827-844
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Forskningsöversikt (refereegranskat)abstract
- Iron is a key micronutrient for phytoplankton growth in the surface ocean. Yet the significance of volcanism for the marine biogeochemical iron-cycle is poorly constrained. Recent studies, however, suggest that offshore deposition of airborne ash from volcanic eruptions is a way to inject significant amounts of bio-available iron into the surface ocean. Volcanic ash may be transported up to several tens of kilometers high into the atmosphere during large-scale eruptions and fine ash may stay aloft for days to weeks, thereby reaching even the remotest and most iron-starved oceanic regions. Scientific ocean drilling demonstrates that volcanic ash layers and dispersed ash particles are frequently found in marine sediments and that therefore volcanic ash deposition and iron-injection into the oceans took place throughout much of the Earth's history. Natural evidence and the data now available from geochemical and biological experiments and satellite techniques suggest that volcanic ash is a so far underestimated source for iron in the surface ocean, possibly of similar importance as aeolian dust. Here we summarise the development of and the knowledge in this fairly young research field. The paper covers a wide range of chemical and biological issues and we make recommendations for future directions in these areas. The review paper may thus be helpful to improve our understanding of the role of volcanic ash for the marine biogeochemical iron-cycle, marine primary productivity and the ocean-atmosphere exchange of CO(2) and other gases relevant for climate in the Earth's history.
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| 3. |
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| 4. |
- Fagerberg, Linn, et al.
(författare)
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Contribution of antibody-based protein profiling to the human chromosome-centric proteome project (C-HPP)
- 2013
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:6, s. 2439-2448
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Tidskriftsartikel (refereegranskat)abstract
- A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas (www.proteinatlas.org).
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| 5. |
- MacLeod, Matthew, et al.
(författare)
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Identifying Chemicals That Are Planetary Boundary Threats
- 2014
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 48:19, s. 11057-11063
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Tidskriftsartikel (refereegranskat)abstract
- Rockstrom et al. proposed a set of planetary boundaries that delimit a safe operating space for humanity Many of the planetary boundaries that have so far been identified are determined by chemical agents. Other chemical pollution-related planetary boundaries likely exist, but are currently unknown. A chemical posed an unknown planetary boundary threat if it simultaneously fulfills three conditions (1) it has an unknown disruptive effect on a vital Earth system process; (2) the disruptive effect is not discovered until it is a problem at the global scale, and (3) the effect is not readily reversible. In this paper, we outline scenarios in which chemical could fulfill each of the three conditions, then use the scenarios as the basis to define chemical profiles that fit each scenario. The chemical profiles are defined in terms of the nature of the effect of the chemical and the nature of exposure of the environment to the chemical. Priortization of chemicals in commerce against some of the profiles appears feasible, but there are considerable uncertainites and scientific challenges that must be addressed. Most challenging is prioritizing chemicals for the potential to have a currently unknown effect on a vital. Earth system process. We conclude that the most effective strategy currently available to identify chemicals that are planetary boundary threats is prioritization against profiles defined in terms of environmental exposure combined with monitoring and study of the biogeochemical process that underlie vital Earth system processes to identify currently unknown disruptive effects.
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| 6. |
- Persson, Linn, et al.
(författare)
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Confronting Unknown Planetary Boundary Threats from Chemical Pollution
- 2013
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 47:22, s. 12619-12622
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Tidskriftsartikel (refereegranskat)abstract
- Rockström et al. proposed a set of planetary boundaries that delimitate a “safe operating space for humanity”. One of the planetary boundaries is determined by “chemical pollution”, however no clear definition was provided. Here, we propose that there is no single chemical pollution planetary boundary, but rather that many planetary boundary issues governed by chemical pollution exist. We identify three conditions that must be simultaneously met for chemical pollution to pose a planetary boundary threat. We then discuss approaches to identify chemicals that could fulfill those conditions, and outline a proactive hazard identification strategy that considers long-range transport and the reversibility of chemical pollution.
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| 7. |
- Vaag, Allan, et al.
(författare)
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Genetic, non-genetic and epigenetic risk determinants in developmental programming of type 2 diabetes.
- 2014
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Ingår i: Acta Obstetricia et Gynecologica Scandinavica. - : Wiley. - 1600-0412 .- 0001-6349. ; 93:11, s. 1099-1108
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Forskningsöversikt (refereegranskat)abstract
- Low birthweight (LBW) individuals and offspring of women with gestational diabetes mellitus (GDM) exhibit increased risk of developing type 2 diabetes (T2D) and associated cardiometabolic traits in adulthood, which for both groups may be mediated by adverse events and developmental changes in fetal life. T2D is a multifactorial disease occurring as a result of complicated interplay between genetic and both pre- as well as postnatal non-genetic factors, and it remains unknown to which extent the increased risk of T2D associated with LBW or GDM in the mother may be due to, or confounded by, genetic factors. Indeed, it has been shown that genetic changes influencing risk of diabetes may also be associated with reduced fetal growth as a result of reduced insulin secretion and/or action. Similarly, increased risk of T2D among offspring could be explained by T2D susceptibility genes shared between the mother and her offspring. Epigenetic mechanisms may explain the link between factors operating in fetal life and later risk of developing T2D, but so far convincing evidence is lacking for epigenetic changes as a prime and direct cause of T2D. This review addresses recent literature on the early origins of adult disease hypothesis, with a special emphasis on the role of genetic compared to non-genetic and epigenetic risk determinants and disease mechanisms. This article is protected by copyright. All rights reserved.
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