- Email: [email protected]
Systems biology of homeodynamics: Neuronal adaptive compensation
S44
Abstracts / Comparative Biochemistry and Physiology, Part A 150 (2008) S42–S48
CSS.7 The chemotaxis receptor cluster revisited
CSS.9 New view on Drosophila transcriptome
D. Bray (University of Cambridge)
J. Wang, V. Chintapalli, P. Herzyk, J. Dow (University of Glasgow)
The cluster of receptors and associated proteins at the ‘front end’ of the E. coli chemotaxis pathway is a paradigm for membrane complexes in cells. Like focal adhesions and synapses, it acts as a solid-state computational device that amplifies, integrates, and parses chemical signals from the environment and relays the output to the rest of the cell. Ten years ago we proposed a structure for this receptor cluster and suggested how it might provide a basis for the very high sensitivity of cells to certain attractants. In this talk I will revisit the lattice architecture in the light of recent findings and present a radically different mechanism for its amplification. The new model is more firmly based on known molecular events and gives a better understanding of how the cell responds to mixed signals.
The Drosophila expression array targets 3′ end of the known and predicated genes. However it is biased towards the 3′ end of the known genes. Drosophila tiling arrays are a discovery tools to study genes regulation. We performed the Drosophila tubules against whole flies experiment on the Drosophila Genome 1 Array in 2004. We were able to find out the tubule specific genes. Further more we set up a FlyAtlas, a new online resource, providing the most comprehensive view yet of expression in multiple tissues of Drosophila melanogaster in 2007 using Drosophila Genome 2.0. We ran the Drosophila tubules against whole flies on the Drosophila tiling array in 2008. We were able to compare the tiling array with Drosophila Genome 2.0 array; where we found the same and the new views:
doi:10.1016/j.cbpa.2008.04.015
1. The top 35 of 50 hits of Drosophila tiling array match the top 18 of 50 genes of Drosophila Genome 2.0. 2. The new transcribe fragments locate in the intronic and intergenic regions detected by tiling array. Are these new genes or new transcriptional start sites?
CSS.8 Systems biology of homeodynamics: Neuronal adaptive compensation J. Schwaber (Thomas Jefferson University); R. Vadigepalli (Thomas Jefferson University); R. Khan (Thomas Jefferson University/University of Delaware); R. Rogers (University of Delaware); M. Macdonald (University of Delaware) Recent reports indicate that the central nervous system plays a significant role in long term regulation of blood pressure, including the development and maintenance of hypertension, by baroreflex resetting to a higher mean arterial pressure range. The molecular mechanisms underlying these surprising but potentially very important cardiovascular homeodynamics are largely unknown. We hypothesize that the nucleus tractus solitarius (NTS), a major center mediating central and peripheral integration in cardiovascular control, adapts to peripheral blood pressure disturbance with a molecular remodeling that may contribute to alterations of regulatory function. We have mounted a systems-level study of the cardiovascular NTS response to hypertension involving examination of system-wide transcriptional regulation, short- and longer-term signaling behavior, and the relation of these events to neuronal outputs including electrical behavior of the neuronal membrane. Our approach involves examining these processes together as a single cellular system. The behavior of this complex system involves dynamic interactions that are difficult to predict using qualitative reasoning and there is a need for experimentally validated computational modeling approaches at the systems level. In our models we are developing feedbacks or functional links between levels of analysis. These approaches are valuable in generation of hypotheses and provide a framework for the systematic comparison of data collected across experiments. The present talk is a report on progress in development of these systems biology approaches, and contemplation of the significant remaining challenges.
doi:10.1016/j.cbpa.2008.04.016
3. 5′extension or alternative 5′end? 3′extention or alternative 3′end detected on the tiling array? 4. Unannotated tubule transcribed fragments may play an important role in the tubule function. In conclusion, the combination of array evidence, gene models, RT-PCR or High-throughput cDNA sequencing will help us to improve the accuracy of the gene models, and to explore the function of the unannotated transcribed area or discover the new genes. We hope a pipeline will be created to link the Drosophila expression array and Tiling Array data to further view the function of Drosophila tubules. The above work was partly funded by BBSRC, UK.
doi:10.1016/j.cbpa.2008.04.017
CSS.10 Digital Circuit Emulation of Gene Expression Alberto Delgado (National University of Colombia at Bogota)
The paper presents four digital circuit models inspired by biological gene expression, these circuits have been used successfully as controllers for mobile robots. The paper is developed in two parts: The first one, presents the fundamentals of gene expression, from an engineering perspective, including concepts such as: regulating region, motif, transcription factor, coding region, exon, intron, DNA transcription and translation. The second part describes the biomimetic digital circuits and its applications in mobile robotics.
doi:10.1016/j.cbpa.2008.04.018
Abstracts / Comparative Biochemistry and Physiology, Part A 150 (2008) S42–S48
CSS.7 The chemotaxis receptor cluster revisited
CSS.9 New view on Drosophila transcriptome
D. Bray (University of Cambridge)
J. Wang, V. Chintapalli, P. Herzyk, J. Dow (University of Glasgow)
The cluster of receptors and associated proteins at the ‘front end’ of the E. coli chemotaxis pathway is a paradigm for membrane complexes in cells. Like focal adhesions and synapses, it acts as a solid-state computational device that amplifies, integrates, and parses chemical signals from the environment and relays the output to the rest of the cell. Ten years ago we proposed a structure for this receptor cluster and suggested how it might provide a basis for the very high sensitivity of cells to certain attractants. In this talk I will revisit the lattice architecture in the light of recent findings and present a radically different mechanism for its amplification. The new model is more firmly based on known molecular events and gives a better understanding of how the cell responds to mixed signals.
The Drosophila expression array targets 3′ end of the known and predicated genes. However it is biased towards the 3′ end of the known genes. Drosophila tiling arrays are a discovery tools to study genes regulation. We performed the Drosophila tubules against whole flies experiment on the Drosophila Genome 1 Array in 2004. We were able to find out the tubule specific genes. Further more we set up a FlyAtlas, a new online resource, providing the most comprehensive view yet of expression in multiple tissues of Drosophila melanogaster in 2007 using Drosophila Genome 2.0. We ran the Drosophila tubules against whole flies on the Drosophila tiling array in 2008. We were able to compare the tiling array with Drosophila Genome 2.0 array; where we found the same and the new views:
doi:10.1016/j.cbpa.2008.04.015
1. The top 35 of 50 hits of Drosophila tiling array match the top 18 of 50 genes of Drosophila Genome 2.0. 2. The new transcribe fragments locate in the intronic and intergenic regions detected by tiling array. Are these new genes or new transcriptional start sites?
CSS.8 Systems biology of homeodynamics: Neuronal adaptive compensation J. Schwaber (Thomas Jefferson University); R. Vadigepalli (Thomas Jefferson University); R. Khan (Thomas Jefferson University/University of Delaware); R. Rogers (University of Delaware); M. Macdonald (University of Delaware) Recent reports indicate that the central nervous system plays a significant role in long term regulation of blood pressure, including the development and maintenance of hypertension, by baroreflex resetting to a higher mean arterial pressure range. The molecular mechanisms underlying these surprising but potentially very important cardiovascular homeodynamics are largely unknown. We hypothesize that the nucleus tractus solitarius (NTS), a major center mediating central and peripheral integration in cardiovascular control, adapts to peripheral blood pressure disturbance with a molecular remodeling that may contribute to alterations of regulatory function. We have mounted a systems-level study of the cardiovascular NTS response to hypertension involving examination of system-wide transcriptional regulation, short- and longer-term signaling behavior, and the relation of these events to neuronal outputs including electrical behavior of the neuronal membrane. Our approach involves examining these processes together as a single cellular system. The behavior of this complex system involves dynamic interactions that are difficult to predict using qualitative reasoning and there is a need for experimentally validated computational modeling approaches at the systems level. In our models we are developing feedbacks or functional links between levels of analysis. These approaches are valuable in generation of hypotheses and provide a framework for the systematic comparison of data collected across experiments. The present talk is a report on progress in development of these systems biology approaches, and contemplation of the significant remaining challenges.
doi:10.1016/j.cbpa.2008.04.016
3. 5′extension or alternative 5′end? 3′extention or alternative 3′end detected on the tiling array? 4. Unannotated tubule transcribed fragments may play an important role in the tubule function. In conclusion, the combination of array evidence, gene models, RT-PCR or High-throughput cDNA sequencing will help us to improve the accuracy of the gene models, and to explore the function of the unannotated transcribed area or discover the new genes. We hope a pipeline will be created to link the Drosophila expression array and Tiling Array data to further view the function of Drosophila tubules. The above work was partly funded by BBSRC, UK.
doi:10.1016/j.cbpa.2008.04.017
CSS.10 Digital Circuit Emulation of Gene Expression Alberto Delgado (National University of Colombia at Bogota)
The paper presents four digital circuit models inspired by biological gene expression, these circuits have been used successfully as controllers for mobile robots. The paper is developed in two parts: The first one, presents the fundamentals of gene expression, from an engineering perspective, including concepts such as: regulating region, motif, transcription factor, coding region, exon, intron, DNA transcription and translation. The second part describes the biomimetic digital circuits and its applications in mobile robotics.
doi:10.1016/j.cbpa.2008.04.018