Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands.

BACKGROUND: The affinities of DNA binding proteins for target sites can be used to model the regulation of gene expression. These proteins can bind to DNA cooperatively, strongly impacting their affinity and specificity. However, current methods for measuring cooperativity do not provide the means to accurately predict binding behavior over a wide range of concentrations. METHODS: We use standard computational and mathematical methods, and develop novel methods as described in Results. RESULTS: We explore some complexities of cooperative binding, and develop an improved method for relating in vitro measurements to in vivo function, based on ternary complex formation. We derive expressions for the equilibria among the various complexes, and explore the limitations of binding experiments that model the system using a single parameter. We describe how to use single-ligand binding and ternary complex formation in tandem to determine parameters that have thermodynamic relevance. We develop an improved method for finding both single-ligand dissociation constants and concentrations simultaneously. We show how the cooperativity factor can be found when only one of the single-ligand dissociation constants can be measured. CONCLUSIONS: The methods that we develop constitute an optimized approach to accurately model cooperative binding. GENERAL SIGNIFICANCE: The expressions and methods we develop for modeling and analyzing DNA binding and cooperativity are applicable to most cases where multiple ligands bind to distinct sites on a common substrate. The parameters determined using these methods can be fed into models of higher-order cooperativity to increase their predictive power

Quantum statistics on graphs

Quantum graphs are commonly used as models of complex quantum systems, for example molecules, networks of wires, and states of condensed matter. We consider quantum statistics for indistinguishable spinless particles on a graph, concentrating on the simplest case of abelian statistics for two particles. In spite of the fact that graphs are locally one-dimensional, anyon statistics emerge in a generalized form. A given graph may support a family of independent anyon phases associated with topologically inequivalent exchange processes. In addition, for sufficiently complex graphs, there appear new discrete-valued phases. Our analysis is simplified by considering combinatorial rather than metric graphs -- equivalently, a many-particle tight-binding model. The results demonstrate that graphs provide an arena in which to study new manifestations of quantum statistics. Possible applications include topological quantum computing, topological insulators, the fractional quantum Hall effect, superconductivity and molecular physics.Comment: 21 pages, 6 figure

Pre- and pro-biotics may improve mineral absorption and retention in the growing male rat : a thesis submitted in partial fulfilment of the requirements for the degree of Master of Science in Nutritional Science at Massey University, Turitea, Palmerston North, New Zealand

Probiotics are bacteria, which reside in the large intestine and concur beneficial health effects on their host. Their abundance can be selectively-stimulated by prebiotics, such as fructo-oligosaccharide (FOS); prebiotics are oligosaccharides, which are not digested in the small intestine, but pass into the large intestine where they are fermented into short-chain fatty acids. Several studies have suggested that prebiotics may improve mineral absorption. This study aimed to determine the effects of pro- and pre-biotic supplementation on mineral absorption and bone quality in growing male rats. Sixty three-week old male Sprague-Dawley rats were randomised into five groups and fed either a high-calcium milk powder (HCMP) with or without a probiotic added (groups were subsequently named HCMP - and HCMP + respectively), or HCMP and vitamin K with or without the probiotic (HCMPK - and HCMPK +), or the HCMP with FOS replacing the sucrose in other diets, and the probiotic (the dietary group was named FOS). Animals were maintained on diets for 10 weeks. Balance studies were carried out during weeks 3 - 4 and 8 - 9 of the study. The earlier balance study suggested that dietary interventions may affect mineral absorption. The latter balance study, however, showed no discernable differences between groups. Several reasons were postulated for this. Active-absorption may have been down-regulated as a result of long-term supplementation, or an increased abundance of probiotics could cause an elevation of nutritional demands. Alternatively, supplementation may not prove beneficial once animals had passed their period of peak absorption. Bone resorption and formation did not appear to have been altered as a result of dietary intervention, when measured after 10-weeks. Bone mineral density and content, calcium, magnesium, zinc and ash contents and bone biomechanical testing also showed no significant differences between dietary groups. Further research is required to determine whether results obtained were due to long-term supplementation and / or due to the joint-supplementation of pre- and pro-biotics

Upregulation of cardioprotective SUR2A by sub-hypoxic drop in oxygen

AbstractThe effects of hypoxia on gene expression have been vigorously studied, but possible effects of small changes in oxygen tension have never been addressed. SUR2A is an atypical ABC protein serving as a regulatory subunit of sarcolemmal ATP-sensitive K+ (KATP) channels. Up-regulation of SUR2A is associated with cardioprotection and improved physical endurance. Here, we have found that a 24h-long exposure to slightly decreased ambient fractional concentration of oxygen (20% oxygen), which is an equivalent to oxygen tension at 350m above sea level, significantly increased levels of SUR2A in the heart despite that this drop of oxygen did not affect levels of O2, CO2 and hematocrit in the blood or myocardial levels of ATP, lactate and NAD/NADH/NAD+. Hearts from mice exposed to 20% oxygen were significantly more resistant to ischaemia-reperfusion when compared to control ones. Decrease in fractional oxygen concentration of just 0.9% was associated with phosphorylation of ERK1/2, but not Akt, which was essential for up-regulation of SUR2A. These findings indicate that a small drop in oxygen tension up-regulates SUR2A in the heart by activating ERK signaling pathway. This is the first report to suggest that a minimal change in oxygen tension could have a profound signaling effect

Collisions of protons with light nuclei shed new light on nucleon structure

The high rates of multi-parton interactions at the LHC can provide a unique opportunity to study the multi-parton structure of the hadron. To this purpose high energy collisions of protons with nuclei are particularly suitable. The rates of multi-parton interactions depend in fact both on the partonic multiplicities and on the distributions of partons in transverse space, which produce different effects on the cross section in pA collisions, as a function of the atomic mass number A. Differently with respect to the case of multi-parton interactions in pp collisions, the possibility of changing the atomic mass number provides thus an additional handle to distinguish the diverse contributions. Some relevant features of double parton interactions in pD collisions have been discussed in a previous paper. In the present paper we show how the effects of double and triple correlation terms of the multi-parton structure can be disentangled, by comparing the rates of multiple parton interactions in collisions of protons with D, Tritium and 3He.Comment: 50 pages, 13 figure

Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn