Bio-logic: gene expression and the laws of combinatorial logic

Original article can be found at: http://www.mitpressjournals.org/ Copyright MIT Press DOI: 10.1162/artl.2008.14.1.121At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multi-cellular organisms, signal selection and multiplexing is performed at the cis-regulatory domains of genes, where combinations of transcription factors (TFs) regulate the rates at which the genes are transcribed into mRNA. To be able to act as activators or repressors of gene transcription, TFs must first bind to target sequences on the regulatory domains. Two TFs that act in concert may bind entirely independently of each other, but more often binding of the first one will alter the affinity of the other for its binding site. This paper presents a systematic investigation into the effect of TF binding dependencies on the predicted regulatory function of this “bio-logic”. Four extreme scenarios, commonly used to classify enzyme activation and inhibition patterns, for the binding of two TFs were explored: independent (the TFs bind without affecting each other’s affinities), competitive (the TFs compete for the same binding site), ordered (the TFs bind in a compulsory order), and joint binding (the TFs either bind as a preformed complex, or binding of one is virtually impossible in the absence of the other). The conclusions are: 1) the laws of combinatorial logic hold only for systems with independently binding TFs; 2) systems formed according to the other scenarios can mimic the functions of their Boolean logical counterparts, but cannot be combined or decomposed in the same way; and 3) the continuously scaled output of systems consisting of competitively binding activators and repressors can be more robustly controlled than that of single TF or (quasi-) logical multi-TF systems. Keywords: Transcription regulation, Genetic regulatory networks, Enzyme kinetics, Combinatorial logic, Non-Boolean continuous logic, Modelling.Peer reviewe

Generic Schemes for Single Molecule Kinetics 2: Information Content of the Poisson Indicator

Recently, we described a pathway analysis technique (paper 1) for analyzing generic schemes for single-molecule kinetics based upon the first-passage time distribution. Here, we employ this method to derive expressions for the Poisson indicator, a measure of stochastic variation (essentially equivalent to the Fano factor and Mandel's Q parameter), for various renewal (memoryless) enzymatic reactions. We examine its dependence on substrate concentration, without assuming all steps follow Poissonian kinetics. Based upon fitting to the functional forms of the first two waiting time moments, we show that, to second order, the non-Poissonian kinetics are generally underdetermined but can be specified in certain scenarios. For an enzymatic reaction with an arbitrary intermediate topology, we identify a generic minimum of the Poisson indicator as a function of substrate concentration, which can be used to tune substrate concentration to the stochastic fluctuations and estimate the largest number of underlying consecutive links in a turnover cycle. We identify a local maximum of the Poisson indicator (with respect to substrate concentration) for a renewal process as a signature of competitive binding, either between a substrate and an inhibitor or between multiple substrates. Our analysis explores the rich connections between Poisson indicator measurements and microscopic kinetic mechanisms

The effect of experimental hyperoxia on erythrocytes’ oxygen-transport function

The aim of this study was to investigate the effect of hyperoxia, calcium ions and pH value on the composition of major phospholipids in human erythrocyte membranes and erythrocytes’ oxygen-transport function. To create a model of hyperoxia, we saturated the incubated mixture with oxygen by constant passing of oxygen–air mixture through the incubation medium. To assess the effect of elevated calcium ion concentrations, CaCl2 was added to the incubation medium. An incubation medium with different pH was used to study the effect of various pH values. Lipids were extracted from erythrocytes and chromatographic separation was carried out in a thin layer of silica gel deposited on a glass plate. The thiobarbituric acid (TBA)-active products and the content of diene conjugates (DC) in erythrocytes were determined. The oxygen-binding capacity of haemoglobin was evaluated using Raman spectroscopy. The obtained results indicated that hyperoxia causes deep changes both in the composition and character of bilayer lipids of erythrocyte membranes, which affects the functional characteristics of erythrocytes, primarily the oxygen-transport properties of erythrocyte haemoglobin. It should be noted that a combination of Ca2+ ions and change in the pH value intensify the processes associated with disruption of phospholipids’ composition. The findings indicate that the lipid phase is one of the key elements in the functioning of erythrocytes in norm as well as during development of various pathological processes

Systems approaches to modelling pathways and networks.

Peer reviewedPreprin

Constrained Allocation Flux Balance Analysis

New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an "ensemble averaging" procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws.Comment: 21 pages, 6 figures (main) + 33 pages, various figures and tables (supporting); for the supplementary MatLab code, see http://tinyurl.com/h763es

Propriedades físicas das misturas e dos lipídios estruturados obtidos a partir de banha e óleo de soja por interesterificação enzimática

The main goal of the present research was to evaluate the physical properties of blends of lard and soybean oil modified by enzymatic interesterification catalyzed by two different commercial (microbial) lipases, viz. from Candida cylindracea (AY30TM) and from Mucor circinelloides (M10TM). Pure lard exhibited a softening point of ca. 31.8 °C before interesterification, and this value shifted towards 29.1 °C after interesterification by AY30 lipase and towards 28.8 °C after interesterification by M10 lipase The interesterified lard exhibited lower consistency after reaction with both lipases, and this decrease was more pronounced for the reaction catalyzed by M10 lipase. This result was most likely due to the sn-1,3-specificity of M10 lipase. Pure lard displayed a lower SFC after interesterification, and M10 lipase proved to be more effective than AY30 lipase. The non-interesterified lard had a SFC of 31.3% at 10 °C, which was reduced to 23.8 and 19.9% after interesterification with AY30 lipase and M10 lipase, respectively. The lard and soybean oil blends were affected by the enzymatic interesterification and dilution with soybean oil.O objetivo deste trabalho foi avaliar as propriedades físicas das misturas entre banha e óleo de soja modificadas pela interesterificação enzimática catalisada por duas diferentes lipases comerciais, a AY30TM proveniente do microorganismo Candida cylindracea e a M10TM proveniente do microorganismo Mucor circinelloides. A banha apresentou ponto de amolecimento de 31,8 °C antes da interesterificação e este valor foi reduzido a 29,1 e 28,8 °C após a interesterificação com as lipases AY30TM e M10TM, respectivamente. A consistência da banha diminuiu após a interesterificação enzimática com ambas as lipases, e a redução foi maior quando o catalisador utilizado foi a lipase M10TM. Este resultado se deve à especificidade das posições sn-1,3 da lipase M10TM. A banha apresentou menor conteúdo de gordura sólida após a interesterificação, e essa redução foi mais efetiva quando a reação foi catalisada pela lipase M10TM. A banha não interesterificada apresentou conteúdo de gordura sólida de 31,3% a 10 °C, que foi reduzido a 23,8 e 19,9% após a interesterificação com as lipases AY30 e M10, respectivamente. A banha e suas misturas binárias com o óleo de soja foram afetadas pela interesterificação enzimática e pela diluição com o óleo de soja.(CNPq) National Council for Scientific and Technological DevelopmentCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)Fundação Fernando Pesso

Characterization of Substrate Preference for Slc1p and Cst26p in Saccharomyces cerevisiae Using Lipidomic Approaches and an LPAAT Activity Assay

10.1371/journal.pone.0011956PLoS ONE58