| 1. |
- Bylesjö, Max, et al.
(författare)
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Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen
- 2009
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 8:1, s. 199-210
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Tidskriftsartikel (refereegranskat)abstract
- Tree biotechnology will soon reach a mature state where it will influence the overall supply of fiber, energy and wood products. We are now ready to make the transition from identifying candidate genes, controlling important biological processes, to discovering the detailed molecular function of these genes on a broader, more holistic, systems biology level. In this paper, a strategy is outlined for informative data generation and integrated modeling of systematic changes in transcript, protein and metabolite profiles measured from hybrid aspen samples. The aim is to study characteristics of common changes in relation to genotype-specific perturbations affecting the lignin biosynthesis and growth. We show that a considerable part of the systematic effects in the system can be tracked across all platforms and that the approach has a high potential value in functional characterization of candidate genes.
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| 2. |
- Funehag, Johan, et al.
(författare)
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Rock Excavation Cycle and Its Effect on Grouting
- 2019
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Ingår i: ISRM 9th Nordic Grouting Symposium. - : International Society for Rock Mechanics and Rock Engineering. - 9789517586481 ; , s. 47-59
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The drill and blast rock excavation cycle involves several processes that affects the grouting; vibration from drilling, borehole flushing, the blasting itself and water-loss measurements in boreholes. This research project focused on the effects of water-loss measurements, drilling (both vibration and flushing) and blasting on the grout and during the first five hours of the hardening process. A conceptual model was derived to explain what forces acts on the grout and how the forces can be interpreted in order to reveal how these forces effects the grout. The model suggests that the shear modulus of the grout is a key parameter for understanding the degradation of the grout. The different forces/stresses during an excavation effects the grout differently but the blasting is by far the most difficult process to describe. One starting point of the project is that the grout does not reinforce the rock and by that should not hinder the gas expansion. The blasting should generate new fractures around the blast hole and the gas will penetrate these cracks and finally the expansion of gases should cause fragmentation and movement in the rock mass. The paper describes the results from the field test and how the grout has been characterized using a rheometer. The field test was conducted in a short tunnel niche. The effects from the drill- and blast cycle were studied i.e. vibrations from drilling, boreholes flushing/water-loss measurements and vibrations from blasting. Five boreholes with a centrum distance of 1 m were chosen to be monitored, due to its hydraulic connectivity between the boreholes. Four of these boreholes were successfully grouted by following a grouting design and one borehole was left un-grouted and used for blasting. The effect on grouting in the rock mass from hole of blasting was measured using water-loss measurements in adjacent boreholes. One result of the field test is that the grout was not affected by the blasting under the circumstances used. Instead the study revealed that the water loss measurements affected the connected boreholes negatively.
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| 3. |
- Srivastava, Vaibhav, et al.
(författare)
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OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants
- 2013
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Ingår i: BMC Genomics. - : BioMed Central. - 1471-2164. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.RESULTS: The main categories that appear to be significantly influenced in the transgenic plants were pathways related to redox regulation, carbon metabolism and protein degradation, e.g. the glycolysis and pentose phosphate pathways (PPP). The results provide system-level information on ROS metabolism and responses to oxidative stress, and indicate that some initial responses to oxidative stress may share common pathways.CONCLUSION: The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.
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