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- Dixon, Laura E., et al.
(författare)
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Light and circadian regulation of clock components aids flexible responses to environmental signals
- 2014
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Ingår i: New Phytologist. - : Wiley. - 1469-8137 .- 0028-646X. ; 203:2, s. 568-577
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Tidskriftsartikel (refereegranskat)abstract
- The circadian clock measures time across a 24h period, increasing fitness by phasing biological processes to the most appropriate time of day. The interlocking feedback loop mechanism of the clock is conserved across species; however, the number of loops varies. Mathematical and computational analyses have suggested that loop complexity affects the overall flexibility of the oscillator, including its responses to entrainment signals. We used a discriminating experimental assay, at the transition between different photoperiods, in order to test this proposal in a minimal circadian network (in Ostreococcus tauri) and a more complex network (in Arabidopsis thaliana). Transcriptional and translational reporters in O.tauri primarily tracked dawn or dusk, whereas in A.thaliana, a wider range of responses were observed, consistent with its more flexible clock. Model analysis supported the requirement for this diversity of responses among the components of the more complex network. However, these and earlier data showed that the O.tauri network retains surprising flexibility, despite its simple circuit. We found that models constructed from experimental data can show flexibility either from multiple loops and/or from multiple light inputs. Our results suggest that O.tauri has adopted the latter strategy, possibly as a consequence of genomic reduction.
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| 2. |
- Dubernet, M. L., et al.
(författare)
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Virtual atomic and molecular data centre
- 2010
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Ingår i: Journal of Quantitative Spectroscopy and Radiative Transfer. - 0022-4073 .- 1879-1352. ; 111:15, s. 2151-2159
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Tidskriftsartikel (refereegranskat)abstract
- The Virtual Atomic and Molecular Data Centre (VAMDC, http://www.vamdc.eu) is a European Union funded collaboration between groups involved in the generation, evaluation, and use of atomic and molecular data. VAMDC aims to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data. The project will cover establishing the core consortium, the development and deployment of the infrastructure and the development of interfaces to the existing atomic and molecular databases. It will also provide a forum for training potential users and dissemination of expertise worldwide. This review describes the scope of the VAMDC project; it provides a survey of the atomic and molecular data sets that will be included plus a discussion of how they will be integrated. Some applications of these data are also discussed.
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| 3. |
- Johansson, Mikael, 1981-, et al.
(författare)
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Partners in time : early bird associates with zeitlupe and regulates the speed of the arabidopsis clock
- 2011
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 155:4, s. 2108-2122
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Tidskriftsartikel (refereegranskat)abstract
- The circadian clock of the model plant Arabidopsis (Arabidopsis thaliana) is made up of a complex series of interacting feedback loops whereby proteins regulate their own expression across day and night. early bird (ebi) is a circadian mutation that causes the clock to speed up: ebi plants have short circadian periods, early phase of clock gene expression, and are early flowering. We show that EBI associates with ZEITLUPE (ZTL), known to act in the plant clock as a posttranslational mediator of protein degradation. However, EBI is not degraded by its interaction with ZTL. Instead, ZTL counteracts the effect of EBI during the day and increases it at night, modulating the expression of key circadian components. The partnership of EBI with ZTL reveals a novel mechanism involved in controlling the complex transcription-translation feedback loops of the clock. This work highlights the importance of cross talk between the ubiquitination pathway and transcriptional control for regulation of the plant clock.
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| 7. |
- Ashelford, Kevin, et al.
(författare)
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Full genome re-sequencing reveals a novel circadian clock mutationin Arabidopsis
- 2011
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 12, s. R28-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process,specifically if the phenotype is subtle and scoring labour intensive. An alternative to map basedcloning would be to directly sequence the whole genome of a mutant to uncover the mutationresponsible for the phenotype. Results: Here, we have re-sequenced the 120 Mb genome of a novel Arabidopsis clock mutant earlybird (ebi-1), using massively parallel sequencing by ligation. This process was further complicated by the fact that ebi-1 is in Wassilewskija (Ws-2), not the reference accession ofArabidopsis. The approach reveals evidence of DNA strand bias in the ethyl methanesulfonate(EMS) mutation process. We have demonstrated the utility of sequencing a backcrossed line andusing gene expression data to limit the number of SNP considered. Using new SNP informationwe have excluded a previously identified clock gene, PRR7. Finally, we have identified a SNPin the gene AtNFXL-2 as the likely cause of the ebi-1 phenotype and validated this bycharacterising a further allele. Conclusion: In Arabidopsis, as in other organisms, the (EMS) mutation load can be high. Here wedescribe how sequencing a backcrossed line, using functional genomics and analysing new SNPinformation can be used to reduce the number EMS mutations for consideration. Moreover, theapproach we describe here does not require out-crossing and scoring F2 mapping populations, anapproach which can be compromised by background effects. The strategy has broad utility andwill be an extremely useful tool to identify causative SNP in other organisms.
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