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The Seven Stones details
Listing ID: 377
Title: The Seven Stones
Description: This blog of the Molecular Systems Biology Journal Covers systems biology at the molecular level.
Owner:
listed on: May 01, 2008 08:25:22 AM
Number Hits: 2 times
Recent Posts:
| [Research highlight] NF-kappaB signaling goes digital - 2010-07-09 12:49:48 | ||||||||||||||||||||||||||||||||||||||||||||
| In a report published this week at Nature, Tay et al. reveal that populations of mouse 3T3 cells exposed to TNF-α show a digital NF-κB response, where increasing TNF-α concentrations lead to a higher proportion of cells with nuclear localized NF-κB — an effect that depends, in part, on pre-existing heterogeneity within the cell population. These results provide another compelling example of the way that studies using single cell measurements are transforming our understanding of cellular signaling mechanisms. Interestingly, these results seem to contrast with another recent single-cell-based study of NF-κB dynamics (Giorgetti et al. 2010), which observed a relatively uniform population-level NF-κB response to TNF-α in human HCT116 cells, indicating that there is still much to learn about the dynamics of NF-κB signaling.Giorgetti L, Siggers T, Tiana G, Caprara G, Notarbartolo S, Corona T,Pasparakis M, Milani P, Bulyk ML, Natoli G (2010) Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol Cell 37:418-28Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW (2010) Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 466:267-71→ Also, see Cheong et al. for a history of systems biology modeling of NF-κB signaling:Cheong R, Hoffmann A, Levchenko A (2008) Understanding NF-kappaB signaling via mathematical modeling. Mol Syst Biol 4:192.In a report published this week at Nature, Tay et al. reveal that populations of mouse 3T3 cells exposed to TNF-α show a digital NF-κB response, where increasing TNF-α concentrations lead to a higher proportion of cells with nuclear localized NF-κB — an effect that depends, in part, on pre-existing heterogeneity within the cell population. These results provide another compelling example of the way that studies using single cell measurements are transforming our understanding of cellular signaling mechanisms. Interestingly, these results seem to contrast with another recent single-cell-based study of NF-κB dynamics (Giorgetti et al. 2010), which observed a relatively uniform population-level NF-κB response to TNF-α in human HCT116 cells, indicating that there is still much to learn about the dynamics of NF-κB signaling. Giorgetti L, Siggers T, Tiana G, Caprara G, Notarbartolo S, Corona T,Pasparakis M, Milani P, Bulyk ML, Natoli G (2010) Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol Cell 37:418-28 Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW (2010) Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 466:267-71 → Also, see Cheong et al. for a history of systems biology modeling of NF-κB signaling: | ||||||||||||||||||||||||||||||||||||||||||||
| [Research highlight] Cis-regulatory evolution, not so mysterious after all? - 2010-06-04 10:33:43 | ||||||||||||||||||||||||||||||||||||||||||||
| Animal genomes are littered with conserved non-coding elements (CNEs)—most of which represent evolutionarily constrained cis-regulatory sequences—however, it is often not clear why these sequences are so exceptionally conserved, since anecdotal examples have shown that orthologous CNEs can have divergent functions in vivo (Strähle and Rastegar 2008; Elgar and Vavouri 2008). In an article recently published in Molecular Biology & Evolution, Ritter et al. compare the functional activities of 41 pairs of orthologous conserved non-coding elements (CNEs) from humans and zebrafish (2010). Interestingly, sequence similarity was found to be a poor predictor of which CNEs had conserved function. In contrast, the authors found that measuring transcription factor binding site change, instead of simple sequence divergence, improves their ability to predict functional conservation. While this set of tested CNEs remains relatively small, these results are encouraging because they suggest that as scientists move from phenomenological measures of CNE evolution to models based explicitly on binding site evolution, the patterns of cis-regulatory evolution observed within animal genomes should become far less mysterious.Elgar G, Vavouri T (2008) Tuning in to the signals: noncoding sequence conservation in vertebrate genomes. Trends Genet 24: 344–352Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH (2010) The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity. Mol Biol Evol advance online publication May 21Strähle U, Rastegar S (2008) Conserved non-coding sequences and transcriptional regulation. Brain Res Bull 75: 225–230 Animal genomes are littered with conserved non-coding elements (CNEs)—most of which represent evolutionarily constrained cis-regulatory sequences—however, it is often not clear why these sequences are so exceptionally conserved, since anecdotal examples have shown that orthologous CNEs can have divergent functions in vivo (Strähle and Rastegar 2008; Elgar and Vavouri 2008). In an article recently published in Molecular Biology & Evolution, Ritter et al. compare the functional activities of 41 pairs of orthologous conserved non-coding elements (CNEs) from humans and zebrafish (2010). Interestingly, sequence similarity was found to be a poor predictor of which CNEs had conserved function. In contrast, the authors found that measuring transcription factor binding site change, instead of simple sequence divergence, improves their ability to predict functional conservation. While this set of tested CNEs remains relatively small, these results are encouraging because they suggest that as scientists move from phenomenological measures of CNE evolution to models based explicitly on binding site evolution, the patterns of cis-regulatory evolution observed within animal genomes should become far less mysterious. Elgar G, Vavouri T (2008) Tuning in to the signals: noncoding sequence conservation in vertebrate genomes. Trends Genet 24: 344–352 Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH (2010) The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity. Mol Biol Evol advance online publication May 21 Strähle U, Rastegar S (2008) Conserved non-coding sequences and transcriptional regulation. Brain Res Bull 75: 225–230 | ||||||||||||||||||||||||||||||||||||||||||||
| Editors'conference agenda - 2010-05-25 17:53:00 | ||||||||||||||||||||||||||||||||||||||||||||
| I spent May 14-15th at the Symposium on Integrative Network Biology and Cancer, hosted by the Institute of Cancer Research in London. The organizers, Chris Bakal and Rune Linding, managed to attract a stellar speakers list, and I had great discussions with many of the attendees. Inspired by this, I thought it could be useful to share a tentative list of conferences in 2010 that will be attended by the Molecular Systems Biology editors. If you happen to be at one these conferences, we would be delighted to meet you in person and hear about your research.Please note that this is a tentative schedule. Moreover, please do not feel slighted if your favorite conference is not on this list. There are many high-quality conferences that we will not be able to attend this year due to scheduling limitations.ConferencePlaceDateWhoSystems Biology&New Sequencing TechnologiesBarcelonaJune 16-18TL8th International Conference on Pathways, Networks, and Systems MedicineRhodesJuly 9-14TLISMB 2010BostonJuly 11-13ALHq-bio Conference on Cellular Information ProcessingSanta FeAugust 11-14ALHThe EMBO Meeting 2010BarcelonaSept. 4-7TLCSHL Personal GenomesCold Spring HarborSept. 10-12ALHHUPO2010SydneySept. 19-23TL11th International Conference on Systems BiologyEdinburghOct. 11-14TLEMBO Conference: From Functional Genomics to Systems BiologyHeidelbergNov. 13-16ALHPharmacogenomics&Personalized TherapyCold Spring HarborNov. 17-21TLTL: Thomas Lemberger, ALH: Andrew L. Hufton I spent May 14-15th at the Symposium on Integrative Network Biology and Cancer, hosted by the Institute of Cancer Research in London. The organizers, Chris Bakal and Rune Linding, managed to attract a stellar speakers list, and I had great discussions with many of the attendees. Inspired by this, I thought it could be useful to share a tentative list of conferences in 2010 that will be attended by the Molecular Systems Biology editors. If you happen to be at one these conferences, we would be delighted to meet you in person and hear about your research. Please note that this is a tentative schedule. Moreover, please do not feel slighted if your favorite conference is not on this list. There are many high-quality conferences that we will not be able to attend this year due to scheduling limitations.
TL: Thomas Lemberger, ALH: Andrew L. Hufton | ||||||||||||||||||||||||||||||||||||||||||||