| 1. |
- Rich, Rebecca L., et al.
(författare)
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A global benchmark study using affinity-based biosensors
- 2009
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Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 386:2, s. 194-216
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Tidskriftsartikel (refereegranskat)abstract
- To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
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| 2. |
- Jones, Owen R., et al.
(författare)
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Senescence rates are determined by ranking on the fast-slow life-history continuum
- 2008
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 11:7, s. 664-673
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analyses of survival senescence by using life tables have identified generalizations including the observation that mammals senesce faster than similar-sized birds. These generalizations have been challenged because of limitations of life-table approaches and the growing appreciation that senescence is more than an increasing probability of death. Without using life tables, we examine senescence rates in annual individual fitness using 20 individual-based data sets of terrestrial vertebrates with contrasting life histories and body size. We find that senescence is widespread in the wild and equally likely to occur in survival and reproduction. Additionally, mammals senesce faster than birds because they have a faster life history for a given body size. By allowing us to disentangle the effects of two major fitness components our methods allow an assessment of the robustness of the prevalent life-table approach. Focusing on one aspect of life history - survival or recruitment - can provide reliable information on overall senescence.
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| 3. |
- Karlsson, Laila, 1965-
(författare)
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Seed dormancy and germination in an ecological context : comparative studies of annual weeds
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Germination ecology studies, i.e. studies of interactions between characteristics of the seeds and environmental circumstances, provide understanding of spatial and temporal patterns of emergence of wild species, as weeds in the field. A large number of species have seed dormancy, i.e. seeds respond to circumstances not directly evoking germination. Thus, germination may occur only if specific environmental events have occurred in the seeds' past life story, and/or if a suitable time period has passed since ripening on mother plants. In this thesis, three characteristics, i.e. dormancy pattern, germination preferences and dormancy strength, hypothesised as mutually independent seed characteristics, are used to describe dormancy and germination in an ecological context. This conceptual model may be used for descriptions of differences between species, to understand emergence patterns in the field from controlled germination tests, and probably for increasing the understanding of evolution of ecological important properties of seed dormancy and germination.Fifteen annual weedy taxa were investigated: two groups of temperate climate weeds, Lamium and Papaver, and one group of tropical weeds, co-occurring Asteraceae species of different genera. Intra-species variations in germination occurred for all species, but species-specific germination responses within all groups were revealed in analyses. All species showed some kind of species-specific dormancy pattern that was expressed as increased germination in response to one or more environmental factor not required for the actual germination.For Lamium and Papaver, the general dormancy pattern was genus-specific. Germination preferences varied slightly within genus. Dormancy strength was to some extent species-specific, but highly variable. The species belonging to Asteraceae showed differences in dormancy pattern. It is shown how such differences can be visualized and compared by plotting response time and achieved germination in two-dimensional graphs, giving species-specific pictures.Dormancy pattern and germination preferences explained how Papaver can perform as winter annuals in warmer climates, but substantially as summer annuals in colder climates, without local adaptations. For Lamium, the results indicate a local adaptation of increasing dormancy strength: in relatively cold climate in Sweden, a strong dormancy restricted a part of each cohort from germinating during autumn, thus preventing from winter mortality. For the Asteraceae, five of six species clearly responded to cold pretreatment, which is noteworthy considering the small seasonal temperature differences in the study area and in the areas of origin for the species. The six Asteraceae achieved similar emergence timing in the field by responding to different environmental factors.Together, the results from these fifteen species indicate that dormancy pattern is an evolutionary conservative characteristic, dormancy strength is relatively easily changed, and germination preference is intermediate.
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| 4. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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