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| 2. |
- Andersson, Anders, et al.
(author)
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Global analysis of mRNA stability in the archaeon Sulfolobus
- 2006
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In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 7:10, s. R99-
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Journal article (peer-reviewed)abstract
- Background: Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known about RNA stability in the third domain of life, Archaea. Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea. Results: The two transcriptomes displayed similar half-life distributions, with medians of about five minutes. Growth-related genes, such as those involved in transcription, translation and energy production, were over-represented among unstable transcripts, whereas uncharacterized genes were over-represented among the most stable. Half-life was negatively correlated with transcript abundance and, unlike the situation in other organisms, also negatively correlated with transcript length. Conclusion: The mRNA half-life distribution of Sulfolobus species is similar to those of much faster growing bacteria, contrasting with the earlier observation that median mRNA half-life is proportional to the minimal length of the cell cycle. Instead, short half-lives may be a general feature of prokaryotic transcriptomes, possibly related to the absence of a nucleus and/or more limited post-transcriptional regulatory mechanisms. The pattern of growth-related transcripts being among the least stable in Sulfolobus may also indicate that the short half-lives reflect a necessity to rapidly reprogram gene expression upon sudden changes in environmental conditions.
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| 3. |
- Andersson, Anders, et al.
(author)
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Replication-biased genome organisation in the crenarchaeon Sulfolobus
- 2010
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11, s. 454-
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Journal article (peer-reviewed)abstract
- Background: Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. Results: We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements. Conclusion: The strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.
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| 5. |
- Bernander, Rolf, et al.
(author)
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Comparative and functional analysis of the archaeal cell cycle
- 2010
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In: Cell Cycle. - : Informa UK Limited. - 1538-4101 .- 1551-4005. ; 9:4, s. 795-806
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Journal article (peer-reviewed)abstract
- The temporal and spatial organization of the chromosome replication, genome segregation and cell division processes is less well understood in species belonging to the Archaea, than in those from the Bacteria and Eukarya domains. Novel insights into the regulation and key components of the Sulfolobus acidocaldarius cell cycle have been obtained through genome-wide analysis of cell cycle-specific gene expression, followed by cloning and characterization of gene products expressed at different cell cycle stages. Here, the results of the transcript profiling are further explored, and potential key players in archaeal cell cycle progression are highlighted in an evolutionary context, by comparing gene expression patterns and gene conservation between three selected microbial species from different domains of life. We draw attention to novel putative nucleases and helicases implicated in DNA replication, recombination and repair, as well as to potential genome segregation factors. Focus is also placed upon regulatory features, including transcription factors and protein kinases inferred to be involved in the execution of specific cell cycle stages, and regulation through metabolic coupling is discussed.
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| 6. |
- Björkqvist, Maria, et al.
(author)
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Somatostatin, misoprostol and galanin inhibit gastrin- and PACAP-stimulated secretion of histamine and pancreastatin from ECL cells by blocking specific Ca(2+) channels.
- 2005
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In: Regulatory Peptides. - : Elsevier BV. - 1873-1686 .- 0167-0115. ; 130:1-2, s. 81-90
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Journal article (peer-reviewed)abstract
- The oxyntic mucosa is rich in ECL cells. They secrete histamine and chromogranin A-derived peptides, such as pancreastatin, in response to gastrin and pituitary adenylate cyclase-activating peptide (PACAP). Secretion is initiated by Ca2+ entry. While gastrin stimulates secretion by opening L-type and N-type Ca2+ channels, PACAP stimulates secretion by activating L-type and receptor-operated Ca2+ channels. Somatostatin, galanin and prostaglandin E2 (PGE2) inhibit gastrin- and PACAP-stimulated secretion from the ECL cells. In the present study, somatostatin and the PGE2 congener misoprostol inhibited gastrin- and PACAP-stimulated secretion 100%, while galanin inhibited at most 60–65%. Bay K 8644, a specific activator of L-type Ca2+ channels, stimulated ECL-cell secretion, an effect that was inhibited equally effectively by somatostatin, misoprostol and galanin (75–80% inhibition). Pretreatment with pertussis toxin, that inactivates inhibitory G-proteins, prevented all three agents from inhibiting stimulated secretion (regardless of the stimulus). Pretreatment with nifedipine (10 μM), an L-type Ca2+ channel blocker, reduced PACAP-evoked pancreastatin secretion by 50–60%, gastrin-evoked secretion by not, vert, similar 80% and abolished the response to Bay K 8644. The nifedipine-resistant response to PACAP was abolished by somatostatin and misoprostol but not by galanin. Gastrin and PACAP raised the intracellular Ca2+ concentration in a biphasic manner, believed to reflect mobilization of internal Ca2+ followed by Ca2+ entry. Somatostatin and misoprostol blocked Ca2+ entry (and histamine and pancreastatin secretion) but not mobilization of internal Ca2+. The present observations on isolated ECL cells suggest that Ca2+ entry rather than mobilization of internal Ca2+ triggers exocytosis, that gastrin and PACAP activate different (but over-lapping) Ca2+ channels, that somatostatin, misoprostol and galanin interact with inhibitory G-proteins to block Ca2+ entry via L-type Ca2+ channels, and that somatostatin and misoprostol (but not galanin) in addition block N-type and/or receptor-operated Ca2+ channels.
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| 8. |
- Bostian, Moriah B., et al.
(author)
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Prevention or cure? Optimal abatement mix
- 2022
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In: Environmental Economics and Policy Studies. - : Springer-Verlag Tokyo Inc.. - 1432-847X .- 1867-383X. ; 24, s. 503-531
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Journal article (peer-reviewed)abstract
- We develop a model for pollution abatement that distinguishes between prevention and treatment technologies, in order to better understand the optimal mix of abatement measures. Our model separates the production process into two stages, an initial production and prevention stage and a final treatment (or cure) stage. We allow for reallocation of abatement investment across the production stages, in order to improve overall abatement and production and to better understand the tradeoffs between abatement measures. This framework is relevant in practice for numerous industrial production processes, including manufacturing and energy, which employ different abatement measures at different stages of production. In our application to Sweden’s pulp and paper sector, we find the industry could achieve further gains to both production and emissions reductions, beyond those estimated using more common single-stage technology estimation methods, by reallocating abatement investments. These results could be used to improve firm environmental management decisions, and to better target policy incentives to specific forms of abatement.
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| 9. |
- Bostian, Moriah, et al.
(author)
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Environmental investment and firm performance : a network approach
- 2016
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In: Energy Economics. - : Elsevier. - 0140-9883 .- 1873-6181. ; 57, s. 243-255
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Journal article (peer-reviewed)abstract
- This study examines the role of investment in environmental production practices for both environmental performance and energy efficiency over time. We employ a network DEA approach that links successive production technologies through intertemporal investment decisions with a period by period estimation. This allows us to estimate energy efficiency and environmental performance separately, as well as productivity change and its associated decompositions into efficiency change and technology change. Incorporating a network model also allows us to account for both short-term environmental management practices and long-term environmental investments in each of our productivity measures. We apply this framework to a panel of detailed plant-level production data for Swedish manufacturing firms covering the years 2002-2008.
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| 10. |
- Bostian, Moriah, et al.
(author)
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Network Representations of Pollution-Generating Technologies
- 2017
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In: International Review of Environmental and Resource Economics. - : Now Publishers Inc.. - 1932-1465 .- 1932-1473. ; 11:3, s. 193-231
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Journal article (peer-reviewed)abstract
- We update developments on modeling technology including unintended outputs and show how these can, at least to a large extent, be incorporated in a network model framework. Recently there have been efforts to specify more detailed models which include multiple functions to separately capture intended and unintended products. Yet another recent strand of the recent literature has also explicitly tried to include a material balance condition in the model. We see this general evolution as beginning with what might be called a black box technology, with inputs entering the box, and good and bad outputs exiting the box. The more sophisticated models can be thought of as filling in the black box with the more detailed processes involved with production, prevention and abatement, with production accompanied by undesirable byproducts subject to legal regulations and laws of nature. This can be modeled as a network within the black box.
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