| 1. |
- Alpkvist, Erik, et al.
(author)
-
A new mathematical model for chemotactic bacterial colony growth
- 2004
-
In: Water Science and Technology. - : Biriwa Education Services. - 0273-1223 .- 1996-9732. ; 49:11-12, s. 187-192
-
Journal article (peer-reviewed)abstract
- A new continuum model for the growth of a single species biofilm is proposed. The geometry of the biofilm is described by the interface between the biomass and the surrounding liquid. Nutrient transport is given by the solution of a semi-linear Poisson equation. In this model we study the morphology of a chemotactic bacterial colony, which grows in the direction of increasing nutrient concentration. Numerical simulations using the level set method and finite difference schemes are presented. The results show rich heterogeneous morphology.
|
|
| 2. |
- Andersson, Anders, et al.
(author)
-
A transcriptional timetable of autumn senescence
- 2004
-
In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 5:4, s. R24-
-
Journal article (peer-reviewed)abstract
- Background We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.
|
|
| 3. |
- Björklund, Stefan, et al.
(author)
-
The mediator complex
- 2004
-
In: Advances in protein chemistry. - 0065-3233 .- 1557-8941. ; 67, s. 43-65
-
Journal article (peer-reviewed)
|
|
| 4. |
|
|
| 5. |
- Elbing, Karin, 1974, et al.
(author)
-
Role of hexose transport in control of glycolytic flux in Saccharomyces cerevisiae
- 2004
-
In: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 70:9, s. 5323-5330
-
Journal article (peer-reviewed)abstract
- The yeast Saccharomyces cerevisiae predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose concentrations and in the presence of oxygen, as in a glucose-limited chemostat, no ethanol is produced. The importance of the external glucose concentration suggests a central role for the affinity and maximal transport rates of yeast's glucose transporters in the control of ethanol production. Here we present a series of strains producing functional chimeras between the hexose transporters Hxt1 and Hxt7, each of which has distinct glucose transport characteristics. The strains display a range of decreasing glycollytic rates resulting in a proportional decrease in ethanol production. Using these strains, we show for the first time that at high glucose levels, the glucose uptake capacity of wild-type S. cerevisiae does not control glycolytic flux during exponential batch growth. In contrast, our chimeric Hxt transporters control the rate of glycollysis to a high degree. Strains whose glucose uptake is mediated by these chimeric transporters will undoubtedly provide a powerful tool with which to examine in detail the mechanism underlying the switch between fermentation and respiration in S. cerevisiae and will provide new tools for the control of industrial fermentations.
|
|
| 6. |
- Elbing, Karin, 1974, et al.
(author)
-
Transcriptional responses to glucose at different glycolytic rates in Saccharomyces cerevisiae
- 2004
-
In: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 271:23-24, s. 4855-4864
-
Journal article (peer-reviewed)abstract
- The addition of glucose to Saccharomyces cerevisiae cells causes reprogramming of gene expression. Glucose is sensed by membrane receptors as well as (so far elusive) intracellular sensing mechanisms. The availability of four yeast strains that display different hexose uptake capacities allowed us to study glucose-induced effects at different glycolytic rates. Rapid glucose responses were observed in all strains able to take up glucose, consistent with intracellular sensing. The degree of long-term responses, however, clearly correlated with the glycolytic rate: glucose-stimulated expression of genes encoding enzymes of the lower part of glycolysis showed an almost linear correlation with the glycolytic rate, while expression levels of genes encoding gluconeogenic enzymes and invertase (SUC2) showed an inverse correlation. Glucose control of SUC2 expression is mediated by the Snf1-Mig1 pathway. Mig1 dephosphorylation upon glucose addition is known to lead to repression of target genes. Mig1 was initially dephosphorylated upon glucose addition in all strains able to take up glucose, but remained dephosphorylated only at high glycolytic rates. Remarkably, transient Mig1-dephosphorylation was accompanied by the repression of SUC2 expression at high glycolytic rates, but stimulated SUC2 expression at low glycolytic rates. This suggests that Mig1-mediated repression can be overruled by factors mediating induction via a low glucose signal. At low and moderate glycolytic rates, Mig1 was partly dephosphorylated both in the presence of phosphorylated, active Snf1, and unphosphorylated, inactive Snf1, indicating that Mig1 was actively phosphorylated and dephosphorylated simultaneously, suggesting independent control of both processes. Taken together, it appears that glucose addition affects the expression of SUC2 as well as Mig1 activity by both Snf1-dependent and -independent mechanisms that can now be dissected and resolved as early and late/sustained responses.
|
|
| 7. |
- Gustafsson, Erik, et al.
(author)
-
Characterizing the dynamics of the quorum-sensing system in Staphylococcus aureus
- 2004
-
In: Journal of molecular microbiology and biotechnology. - : S. Karger AG. - 1464-1801. ; 8:4, s. 232-242
-
Journal article (peer-reviewed)abstract
- The virulence determinants of <i>Staphylococcus aureus</i> are expressed in a growth phase-dependent manner governed by the autoinducible quorum-sensing system <i>agr</i>. Activation of the <i>agr</i> system results in a rapid increase in the regulator RNAIII and occurs in response to accumulation of AIP. In order to activate the <i>agr</i> system, a basal transcription of <i>agr</i> components must be assumed. This basal transcription of <i>agr</i> components seems to be stimulated by <i>sarA</i>. To better understand how SarA would affect activation of the <i>agr</i> system by modulating the basal <i>agr</i> activity, a mathematical model for autoactivation of the <i>agr</i> system was set up. The model predicted that the <i>agr</i> system is hysteretic, meaning that the <i>agr</i> system is activated at a specific concentration of autoinducing peptide (AIP), whereas it is inactivated at a specific lower concentration of AIP. According to the model, changing the basal <i>agr</i> activity only had a marginal effect on steady-state levels of RNAIII but changed the sensitivity of the cells to AIP. This was supported by Northern blot analysis of RNAIII in <i>S. aureus</i> mutants with different levels of SarA expression. Since natural antagonistic AIPs have been demonstrated, the effect of adding inhibitors to the system was analyzed.
|
|
| 8. |
- Gustafsson, Ewa, et al.
(author)
-
Juridiken i hälso- och sjukvården
- 2004
-
In: Kliniska färdigheter: informationsutbytet mellan patient och läkare (2 uppl.). - 9789144023755 ; , s. 199-214
-
Book chapter (other academic/artistic)
|
|
| 9. |
|
|
| 10. |
- Krantz, Marcus, 1975, et al.
(author)
-
Anaerobicity prepares Saccharomyces cerevisiae cells for faster adaptation to osmotic shock
- 2004
-
In: Eukaryotic Cell. - 1535-9786 .- 1535-9778. ; 3:6, s. 1381-1390
-
Journal article (peer-reviewed)abstract
- Yeast cells adapt to hyperosmotic shock by accumulating glycerol and altering expression of hundreds of genes. This transcriptional response of Saccharomyces cerevisiae to osmotic shock encompasses genes whose products are implicated in protection from oxidative damage. We addressed the question of whether osmotic shock caused oxidative stress. Osmotic shock did not result in the generation of detectable levels of reactive oxygen species (ROS). To preclude any generation of ROS, osmotic shock treatments were performed in anaerobic cultures. Global gene expression response profiles were compared by employing a novel two-dimensional cluster analysis. The transcriptional profiles following osmotic shock under anaerobic and aerobic conditions were qualitatively very similar. In particular, it appeared that expression of the oxidative stress genes was stimulated upon osmotic shock even if there was no apparent need for their function. Interestingly, cells adapted to osmotic shock much more rapidly under anaerobiosis, and the signaling as well as the transcriptional response was clearly attenuated under these conditions. This more rapid adaptation is due to an enhanced glycerol production capacity in anaerobic cells, which is caused by the need for glycerol production in redox balancing. Artificially enhanced glycerol production led to an attenuated response even under aerobic conditions. These observations demonstrate the crucial role of glycerol accumulation and turgor recovery in determining the period of osmotic shock-induced signaling and the profile of cellular adaptation to osmotic shock.
|
|
