| 1. |
- Ahmadpour, Doryaneh, 1973, et al.
(författare)
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Robustness analysis of HOG pathway genes in Saccharomyces cerevisiae
- 2006
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Ingår i: YSBN Meeting Nov. 14-16, 2006- Vienna- Austria.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Robustness analysis of HOG pathway genes in Saccharomyces cerevisiae Doryaneh Ahmadpour1, Lars-Göran Ottosson1, Markus Krantz2, Jonas Warringer1, Anders Blomberg1 and Stefan Hohmann1* 1Department of Cell and Molecular Biology/Microbiology, Göteborg University, S-405 30 Göteborg, Sweden 2 The Systems Biology Institute (SBI), Shibuya, Tokyo, Japan E-mail: doryaneh.ahmadpour@gmm.gu.se Robustness is a fundamental property of biological systems and crucial for their effective function under internal or external perturbations. For instance, it has been proposed that internal parameters such as gene expression have been optimized during evolution such that a given system has the observed robustness. The permissible ranges of internal parameters in the cells are not comprehensively understood since there has not been a technique to measure such parameters. “Genetic tug-of-war” (gTOW) [1] is a genetic screening method that allows the investigation of the upper limit copy number of genes, and thereby the upper permissible range of gene expression level. This method is based on a 2-micron plasmid vector containing the leu2d allele with a very weak complementation activity and the gene of interest inserted as target gene. When the leu2ura3 deletion yeast cells transformed with pTOW plasmid are cultured under leucine-limiting conditions, there will be a bias toward increasing the plasmid copy number to compensate for the lack of leucine. On the other hand there will be an opposing bias toward decreasing the plasmid copy number if the target gene inhibits growth or has a toxic effect when a certain copy number is exceeded (it reaches to its upper limit). Eventually as a result of the “tug-of-war” between these two selection biases cells with optimized plasmid copy number will be concentrated. In this study we have applied the gTOW method on 29 HOG pathway related genes in Saccharomyces cerevisiae. The high osmolarity glycerol (HOG) MAPK pathway is essential for yeast survival in high osmolarity condition and consists of two branches that activate a MAPK (Hog1) via a MAPKK (Pbs2) to orchestrate part of the transcriptional response. The HOG pathway is the best understood osmoresponsive system in eukaryotes and the quantitative data provided by the gTOW method collating with the existing computational models could be used to analyze the robustness and fragility of the pathway. 1. Hisao Moriya, Yuki Shimizu-Yoshida and Hiroaki Kitano, 2006, PLoS Genetics, 2:7
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| 2. |
- Ahmadpour, Doryaneh, 1973, et al.
(författare)
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Robustness analysis of HOG pathway related genes in Saccharomyces cerevisiae
- 2007
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Ingår i: FEBS-SysBio March 10-16, 2007- Gosau, Austria.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Robustness analysis of HOG pathway related genes in Saccharomyces cerevisiae Doryaneh Ahmadpour1, Lars-Göran Ottosson1, Markus Krantz2, Jonas Warringer1, Anders Blomberg1 and Stefan Hohmann1* 1Department of Cell and Molecular Biology/Microbiology, Göteborg University, S-405 30 Göteborg, Sweden 2 The Systems Biology Institute (SBI), Shibuya, Tokyo, Japan E-mail: doryaneh.ahmadpour@gmm.gu.se Robustness is a fundamental property of biological systems and crucial for their effective function under internal or external perturbations. For instance, it has been proposed that internal parameters such as gene expression have been optimized during evolution such that a given system has the observed robustness. The permissible ranges of internal parameters in the cells are not comprehensively understood since there has not been a technique to measure such parameters. “Genetic tug-of-war” (gTOW) [1] is a genetic screening approach that allows the determination of the upper limit copy number of genes, and thereby the upper permissible range of the level of gene expression. This method is based on a 2-micron plasmid vector containing the LEU2d allele with a very weak complementation activity and the gene of interest inserted as target gene. When the leu2 ura3 mutant yeast transformed with pTOW plasmids is cultured under leucine-limiting conditions, there will be a bias toward increasing the plasmid copy number to satisfy the requirement for leucine. On the other hand there will be an opposing bias toward decreasing the plasmid copy number if the target gene inhibits growth when a certain copy number is exceeded (i.e. it reaches its upper limit). Eventually as a result of the “tug-of-war” between these two selection biases cells with optimized plasmid copy number will accumulate. In this study we have applied the gTOW method on 29 HOG pathway genes in S. cerevisiae. The high osmolarity glycerol (HOG) MAPK pathway is essential for yeast survival in high osmolarity condition [2]. It consists of two branches that activate a MAPK (Hog1) to orchestrate part of the transcriptional response. The HOG pathway is the best understood osmoresponsive system in eukaryotes. The quantitative data provided by the gTOW method collating with the existing computational models [3] could be used to analyze the robustness and fragility of the pathway. 1. Moriya H, et al., (2006), PLoS Genet 2(7): e111 2. Hohmann S (2002), Microbiol Mol Biol Rev 66:300 3. Klipp E, et al., (2005), Nat Biotechnol 23:975
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| 3. |
- Bendroth, Peter, et al.
(författare)
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Comparison of ethyl glucuronide in hair with phosphatidylethanol in whole blood as post-mortem markers of alcohol abuse
- 2008
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Ingår i: Forensic Science International. - : Elsevier BV. - 0379-0738 .- 1872-6283. ; 176:1, s. 76-81
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Tidskriftsartikel (refereegranskat)abstract
- Ethyl glucuronide (EtG) is a direct metabolite of ethanol and has been used as a marker of alcohol abuse in both urine and hair. This study investigated the value of EtG testing in post-mortem hair for diagnostic improvement of alcohol abuse in forensic medicine. Material from 70 consecutive medico-legal autopsies was collected in accordance with the recommendations on ethics by the Swedish National Board of Forensic Medicine. A method for determination of EtG in hair samples was developed using ultra performance liquid chromatography/electrospray tandem mass spectrometry (UPLC/ESI-MS/MS; LOQ, 2.5 pg/mg). The result of the EtG analysis was compared with the findings of phosphatidylethanol (PEth) in femoral whole blood, as measured by high performance liquid chromatography with an evaporative light-scattering detector (HPLC–ELSD; LOQ, 0.22 μmol/l). Evaluation of liver histology and anamnestic evidence of alcohol abuse of the deceased were taken in consideration for the interpretation. Measurable levels of EtG were present in 49 of the 70 autopsy cases whereas PEth was present in 36. Thirty-nine cases had EtG levels above the cutoff limit (≥30 pg/mg) compared with 29 for PEth (≥0.7 μmol/l). Fifteen cases had EtG as exclusive indicator for alcohol abuse compared with four cases for PEth. These findings suggest that measurements of EtG in hair may provide improved diagnostic information on alcohol abuse, due to a long retrospective time-window for detection and stability of EtG in hair in the decaying cadaver. However, an EtG level below the cutoff does not completely exclude previous alcohol abuse.
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| 4. |
- Hovelius, Lennart, et al.
(författare)
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Non-operative treatment of primary anterior shoulder dislocation in patients forty years of age and younger : a prospective twenty-five-year follow-up
- 2008
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Ingår i: Journal of Bone and Joint Surgery. American volume. - : Journal of Bone and Joint Surgery. - 0021-9355 .- 1535-1386. ; 90:5, s. 945-952
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Tidskriftsartikel (refereegranskat)abstract
- Background: During 1978 and 1979, we initiated a prospective multicenter study to evaluate the results of nonoperative treatment of primary anterior shoulder dislocation. In the current report, we present the outcome after twenty-five years.Methods: Two hundred and fifty-five patients (257 shoulders) with an age of twelve to forty years who had a primary anterior shoulder dislocation were managed with immobilization (achieved by tying the arm to the torso with use of a bandage) or without immobilization. All 227 living patients (229 shoulders) completed the follow-up questionnaire, and 214 patients completed the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire.Results: Ninety-nine (43%) of 229 shoulders had not redislocated, and seventeen (7%) redislocated once. Thirty-three recurrent dislocations had become stable over time (14.4%), and eighteen were considered to be still recurrent (7.9%). Sixty-two shoulders (27%) had undergone surgery for the treatment of recurrent instability. Immobilization after the primary dislocation did not change the prognosis. Only two of twenty-four shoulders with a fracture of the greater tuberosity at the time of the primary dislocation redislocated (p < 0.001). When shoulders with a fracture of the greater tuberosity were excluded, forty-four (38%) of 115 shoulders in patients who had been twelve to twenty-five years of age at the time of the original dislocation and sixteen (18%) of ninety shoulders in patients who had been twenty-six to forty years of age had undergone surgical stabilization. At twenty-five years, fourteen (23%) of sixty-two shoulders that had undergone surgical stabilization were in patients who subsequently had a contralateral dislocation, compared with seven (7%) of ninety-nine shoulders in patients in whom the index dislocation had been classified as solitary (p = 0.01). Gender and athletic activity did not appear to affect the redislocation rate; however, women had worse DASH scores than men did (p = 0.006).Conclusions: After twenty-five years, half of the primary anterior shoulder dislocations that had been treated nonoperatively in patients with an age of twelve to twenty-five years had not recurred or had become stable over time.Level of Evidence: Prognostic Level I. See Instructions to Authors for a complete description of levels of evidence.
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| 5. |
- Krantz, Marcus, 1975, et al.
(författare)
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Robustness and fragility in the high osmolarity glycerol (HOG) pathway in S. cerevisiae
- 2009
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Ingår i: 10th International Conference on Systems Biology (ICSB2009) proceedings, 10th International Conference on Systems Biology (ICSB2009), Aug 30 - Sep 4, Stanford, California, USA.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Cellular signalling networks integrate environmental stimuli with information on cellular status. These networks must be robust against stochastic fluctuations in external stimuli as well as in the amounts of signalling components. Here [1], we challenge the yeast HOG signal transduction pathway with systematic perturbations in components’ expression levels implemented by a “genetic tug-of-war” methodology under various external conditions in search of nodes of fragilities. We observe a substantially higher frequency of fragile nodes in this signal transduction pathway than has been observed for other cellular processes. These fragilities disperse without any clear pattern over biochemical functions or location in pathway topology, with the most sensitive nodes being the proteins PBS2 and SSK1. They are also largely independent of pathway activation by external stimuli. However, the strongest toxicities are caused by pathway hyperactivation. We studied the influence of seven regulatory motifs around these HOG pathway components in silico through ODE models. Based on the SLN1 and the MAPK modules of a mathematical model of osmoregulation in budding yeast by Klipp et al. [2] we included new motifs and fitted the affected parameters to time courses of dually phosphorylated Hog1p generated by the original model under stress and stress-free conditions. The regulations taken into account by our analysis include Pbs2p scaffolding, Ssk1p and Pbs2p autoactivation, and the formation of a stable dimer between Ssk2p and Ssk1p. A subsequent sensitivity analysis identified Pbs2's role as a scaffold protein and Ssk1p-Ssk2p dimerization as the important contributors to the observed robustness pattern in silico. Thus, in vivo robustness data can be used to discriminate and improve mathematical models.
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| 6. |
- Krantz, Marcus, 1975, et al.
(författare)
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Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway.
- 2009
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Ingår i: Molecular systems biology. - : EMBO. - 1744-4292. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Cellular signalling networks integrate environmental stimuli with the information on cellular status. These networks must be robust against stochastic fluctuations in stimuli as well as in the amounts of signalling components. Here, we challenge the yeast HOG signal-transduction pathway with systematic perturbations in components' expression levels under various external conditions in search for nodes of fragility. We observe a substantially higher frequency of fragile nodes in this signal-transduction pathway than that has been observed for other cellular processes. These fragilities disperse without any clear pattern over biochemical functions or location in pathway topology and they are largely independent of pathway activation by external stimuli. However, the strongest toxicities are caused by pathway hyperactivation. In silico analysis highlights the impact of model structure on in silico robustness, and suggests complex formation and scaffolding as important contributors to the observed fragility patterns. Thus, in vivo robustness data can be used to discriminate and improve mathematical models.
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| 7. |
- Krantz, Marcus, 1975, et al.
(författare)
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Robustness and fragility in the yeast High Osmolarity signal transduction pathway
- 2008
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Ingår i: 2008 Yeast Genetics and Molecular Biology Meeting Program and Abstract Book, 2008 Yeast Genetics and Molecular Biology Meeting, July 22-27, 2008.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The cellular signalling networks that integrate various environmental stimuli with information on cellular status must be robust to stimuli fluctuations as well as to stochastic differences in the amounts of signalling components. Here, we challenge the Hog signal transduction pathway with systematic disturbances in components’ expression levels implemented by a “genetic tug-of-war”, or gToW, methodology. The disturbances were performed under various external perturbations, including pathway activation by osmotic shock. Ideally, the obtained sensitivity profiles will allow us to impose parameter constraints. However, a more important aspect is the qualitative improvement of model structures, when local fragilities cannot be explained by the model structure. The resulting phenotypes in this particular study reflect a wide range of sensitivities, and disperse without any clear pattern over biochemical functions and pathway modules alike, with the most sensitive nodes being PBS2 and SSK1. Surprisingly, the “neighbouring” nodes HOG1 and SSK2 were affected to a much lesser extent, questioning our current understanding.
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| 8. |
- Krantz, Marcus, 1975, et al.
(författare)
-
Robustness and fragility in the yeast High Osmolarity signal transduction pathway
- 2008
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Ingår i: 9th International Conference on Systems Biology (ICSB2008) proceedings, 9th International Conference on Systems Biology (ICSB2008), August 22-28, Gothenburg.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Objective: The cellular signalling networks that integrate various environmental stimuli with information on cellular status must be robust to stimuli fluctuations as well as to stochastic differences in the amounts of signalling components. Here, we challenge the high osmolarity glycerol response (HOG) signal transduction pathway in the yeast Saccharomyces cerevisiae with systematic disturbances in components’ expression levels implemented by a “genetic tug-of-war”, or gTOW, methodology. Results: The disturbances were performed under various external perturbations, including pathway activation by osmotic shock. The resulting phenotypes in this particular study reflect a wide range of sensitivities, and disperse without any clear pattern over biochemical functions and pathway modules alike, with the most sensitive nodes being PBS2 and SSK1. Conclusions: Ideally, the obtained sensitivity profiles will allow us to impose parameter constraints. However, a more important aspect is the qualitative improvement of model structures, when local fragilities cannot be explained by the model structure. Surprisingly, the “neighboring” nodes HOG1 and SSK2 were affected to a much lesser extent, questioning our current understanding.
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| 9. |
- Ottosson, Lars-Göran, et al.
(författare)
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Robustness analysis of HOG pathway related genes in budding yeast
- 2007
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Ingår i: ICSB 2007 Conference Proceedings, 8th International Conference on Systems Biology (ICSB2007), October 1-6, 2007.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We applied a novel genetic screening method, named “genetic tug-of-war” (gTOW) to estimate the upper limit of gene copy numbers in Saccharomyces cerevisiae. The study involved 29 HOG pathway related genes which included kinases, phosphatases and transcription factors to cover different set of players in the signal transduction system. In addition a phenotypic profiling was conducted in four different growth conditions with three outputs: lag phase, growth phase and efficiency of growth. A number of interesting hits were identified, including PBS2 which had low numbers of gene copies. It will be of interest to expand the study to encompass the entire known signal transduction system in yeast to search for sensitive nodes.
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| 10. |
- Ottosson, Lars-Göran, et al.
(författare)
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Robustness and fragility in the yeast High Osmolarity Glycerol (HOG) signal transduction pathway
- 2009
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Ingår i: Abstracts of the 24th International Conference on Yeast Genetics and Molecular Biology (Supplement to Yeast Volume 26 Issue S1), 25th International Conference on Yeast Genetics & Molecular Biology, July 19-24, Manchester, UK. ; 26:Issue S1
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Konferensbidrag (refereegranskat)abstract
- Cellular signalling networks integrate environmental stimuli with information on cellular status. These networks must be robust against stochastic fluctuations in stimuli as well as in the amounts of signalling components. Here, we challenge the yeast HOG signal transduction pathway with systematic perturbations in components’ expression levels implemented by a “genetic tug-of-war” methodology under various external conditions in search of nodes of fragilities. We observe a substantially higher frequency of fragile nodes in this signal transduction pathway than has been observed for other cellular processes. These fragilities disperse without any clear pattern over biochemical functions or location in pathway topology, with the most sensitive node being the scaffold protein PBS2. They are also largely independent of pathway activation by external stimuli. However, the strongest toxicities are caused by pathway hyperactivation. In silico analysis highlights the impact of model structure on in silico robustness, and suggests complex formation and scaffolding as important contributors to the observed fragility patterns. Thus, in vivo robustness data can be used to discriminate and improve mathematical models.
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