http://www.dspace.cam.ac.uk:80/handle/1810/227536 Sun, 26 May 2013 04:12:57 GMT 2013-05-26T04:12:57Z http://www.dspace.cam.ac.uk:80/handle/1810/241920 Title: DnaA and the timing of chromosome replication in Escherichia coli as a function of growth rate Authors: Grant, Matthew AA; Saggioro, Chiara; Ferrari, Ulisse; Bassetti, Bruno; Sclavi, Bianca; Cosentino Lagomarsino, Marco Abstract: Abstract Background In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory circuit that depends on the binding of a critical number of ATP-bound DnaA proteins at the origin of replication, resulting in the melting of the DNA and the assembly of the replication complex. The synthesis of DnaA in the cell is controlled by a growth-rate dependent, negatively autoregulated gene found near the origin of replication. Both the regulatory and initiation activity of DnaA depend on its nucleotide bound state and its availability. Results In order to investigate the contributions of the different regulatory processes to the timing of initiation of DNA replication at varying growth rates, we formulate a minimal quantitative model of the initiator circuit that includes the key ingredients known to regulate the activity of the DnaA protein. This model describes the average-cell oscillations in DnaA-ATP/DNA during the cell cycle, for varying growth rates. We evaluate the conditions under which this ratio attains the same threshold value at the time of initiation, independently of the growth rate. Conclusions We find that a quantitative description of replication initiation by DnaA must rely on the dependency of the basic parameters on growth rate, in order to account for the timing of initiation of DNA replication at different cell doubling times. We isolate two main possible scenarios for this, depending on the roles of DnaA autoregulation and DnaA ATP-hydrolysis regulatory process. One possibility is that the basal rate of regulatory inactivation by ATP hydrolysis must vary with growth rate. Alternatively, some parameters defining promoter activity need to be a function of the growth rate. In either case, the basal rate of gene expression needs to increase with the growth rate, in accordance with the known characteristics of the dnaA promoter. Furthermore, both inactivation and autorepression reduce the amplitude of the cell-cycle oscillations of DnaA-ATP/DNA. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 21 Dec 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241920 2011-12-21T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237819 Title: Detecting separate time scales in genetic expression data Authors: Orlando, David A; Brady, Siobhan M; Fink, Thomas M A; Benfey, Philip N; Ahnert, Sebastian E Abstract: Abstract Background Biological processes occur on a vast range of time scales, and many of them occur concurrently. As a result, system-wide measurements of gene expression have the potential to capture many of these processes simultaneously. The challenge however, is to separate these processes and time scales in the data. In many cases the number of processes and their time scales is unknown. This issue is particularly relevant to developmental biologists, who are interested in processes such as growth, segmentation and differentiation, which can all take place simultaneously, but on different time scales. Results We introduce a flexible and statistically rigorous method for detecting different time scales in time-series gene expression data, by identifying expression patterns that are temporally shifted between replicate datasets. We apply our approach to a Saccharomyces cerevisiae cell-cycle dataset and an Arabidopsis thaliana root developmental dataset. In both datasets our method successfully detects processes operating on several different time scales. Furthermore we show that many of these time scales can be associated with particular biological functions. Conclusions The spatiotemporal modules identified by our method suggest the presence of multiple biological processes, acting at distinct time scales in both the Arabidopsis root and yeast. Using similar large-scale expression datasets, the identification of biological processes acting at multiple time scales in many organisms is now possible. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Tue, 15 Jun 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237819 2010-06-15T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237595 Title: On the direct insulator-quantum Hall transition in two-dimensional electron systems in the vicinity of nanoscaled scatterers Authors: Liang, Chi-Te; Lin, Li-Hung; Chen, Kuang Yao; Lo, Shun-Tsung; Wang, Yi-Ting; Lo, Dong-Sheng; Kim, Gil-Ho; Chang, Yuan Huei; Ochiai, Yuichi; Aoki, Nobuyuki; Chen, Jeng Chung; Lin, Yiping; Huang, Chun Feng; Lin, Sheng-Di; Richie, David A Abstract: Abstract A direct insulator-quantum Hall (I-QH) transition corresponds to a crossover/transition from the insulating regime to a high Landau level filling factor ν > 2 QH state. Such a transition has been attracting a great deal of both experimental and theoretical interests. In this study, we present three different two-dimensional electron systems (2DESs) which are in the vicinity of nanoscaled scatterers. All these three devices exhibit a direct I-QH transition, and the transport properties under different nanaoscaled scatterers are discussed. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Fri, 11 Feb 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237595 2011-02-11T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237568 Title: Neural networks with small-world topology are optimal for encoding based on spatiotemporal patterns of spikes Abstract: Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 12 Jul 2009 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237568 2009-07-12T23:00:00Z