Results 21 to 30 of about 37,884 (225)

The diffusive influx and carrier efflux have a strong effect on the bistability of the lac operon in Escherichia coli [PDF]

arXiv, 2008
In the presence of gratuitous inducers, the lac operon of Escherichia coli exhibits bistability. Most models in the literature assume that the inducer enters the cell via the carrier (permease), and exits by a diffusion-like process. The diffusive influx and carrier efflux are neglected.
Jason T. Noel, Sergei S. Pilyugin, Atul Narang   +2 more
arxiv   +3 more sources

Accurate prediction of gene expression by integration of DNA sequence statistics with detailed modeling of transcription regulation [PDF]

Biophys. J. 99, 2408-2413 (2010), 2010
Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based either on its quantitative connection with single-domain binding free energies or on empirical rules that combine ...
Alberts, Berg, Bussemaker, Bussemaker, Djordjevic, Hudson, Jacob, Jose M.G. Vilar, Liu, Liu, Markstein, Mossing, Müller, Müller-Hill, Oehler, Oehler, Roider, Saiz, Saiz, Saiz, Saiz, Saiz, Stormo, Tavazoie, Tronche, van Batenburg, van Nimwegen, Veprintsev, Vilar, Vilar, Wasserman, Zhao   +31 more
arxiv   +5 more sources

Stochastic dynamics of macromolecular-assembly networks [PDF]

Nature/EMBO Molecular Systems Biology 2, art. no. msb4100061, pp. 2006.0024 (2006), 2006
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components ...
Arkin A, Hill TL, Jose MG Vilar, Leonor Saiz, Ptashne M   +4 more
arxiv   +6 more sources

Development of a Lac Operon Concept Inventory (LOCI). [PDF]

CBE Life Sci Educ, 2016
Concept inventories (CIs) are valuable tools for educators that assess student achievement and identify misconceptions held by students. Results of student responses can be used to adjust or develop new instructional methods for a given topic. The regulation of gene expression in both prokaryotes and eukaryotes is an important concept in genetics and ...
Stefanski KM, Gardner GE, Seipelt-Thiemann RL.   +2 more
europepmc   +5 more sources

Boolean Models of Bistable Biological Systems [PDF]

, 2009
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex differential equations models. The motivation for this work comes from mathematical systems biology.
A. Novick, C. Conradi, E. Aurell, F. Jacob, L. Mendoza, M. Cohn, M. Ptashne, M. Santillán, N. Friedman, N. Yildirim, P. Wong, R. Albert, R. de Boer, R. Edwards, R. Laubenbacher, S. A. Kauffman, T. Tian   +16 more
arxiv   +3 more sources

The Location of the Repressor Binding Sites in the lac Operon [PDF]

Proceedings of the National Academy of Sciences, 1974
The affinity of various mutant lac DNAs for the lac repressor was examined by means of a competition binding assay. The results indicate that there exist at least two binding sites for the lac repressor.
William S. Reznikoff, Robert B. Winter, Carolyn Katovich Hurley   +2 more
openalex   +4 more sources

Origin of bistability in the lac Operon. [PDF]

Biophys J, 2007
Multistability is an emergent dynamic property that has been invoked to explain multiple coexisting biological states. In this work, we investigate the origin of bistability in the lac operon. To do this, we develop a mathematical model for the regulatory pathway in this system and compare the model predictions with other experimental results in which ...
Santillán M, Mackey MC, Zeron ES.
europepmc   +5 more sources

Wrapped-around models for the lac operon complex. [PDF]

Biophys J, 2010
The protein-DNA complex, involved in the lac operon of enteric bacteria, is paradigmatic in understanding the extent of DNA bending and plasticity due to interactions with protein assemblies acting as DNA regulators. For the lac operon, two classes of structures have been proposed: 1), with the protein tetramer lying away from the DNA loop (wrapped ...
La Penna G, Perico A.
europepmc   +7 more sources

Effect of DNA looping on the induction kinetics of the lac operon [PDF]

arXiv, 2007
The induction of the lac operon follows cooperative kinetics.The first mechanistic model of these kinetics is the de facto standard in the modeling literature (Yagil & Yagil, Biophys J, 11, 11-27, 1971). Yet, subsequent studies have shown that the model is based on incorrect assumptions.
Atul Narang
arxiv   +5 more sources

Understanding operon architecture using LEGO bricks [PDF]

Journal of Microbiology & Biology Education
Many undergraduates struggle to interpret abstract concepts in molecular biology. Modeling can facilitate learning by making these abstract concepts tangible.
Dena R. Hammond-Weinberger, Christopher W. Lennon   +1 more
doaj   +2 more sources