Protein interactions in hydrophobic charge induction chromatography (HCIC)

A quantitative understanding of how proteins interact with hydrophobic charge induction chromatographic resins is provided. Selectivity on this mode of chromatography for monoclonal antibodies as compared to other model proteins is probed by means of a linear retention vs pH plot. The pH-dependent adsorption behavior on this mode of chromatography for a hydrophobic, charged solute is described by taking into account the equilibrium between a hydrophobic, charged solute and an ionizable, heterocyclic ligand. By analogy, an equation that is seen to adequately describe macromolecular retention under linear conditions over a range of pH is developed. A preparative, nonlinear isotherm that can capture both pH and salt concentration dependency for proteins is proposed by using an exponentially modified Langmuir isotherm model. This model is seen to successfully simulate adsorption isotherms for a variety of proteins over a range of pHs and mobile phase salt concentrations. Finally, the widely differing retention characteristics of two monoclonal antibodies are used to derive two different strategies for improving separations on this mode of chromatography. A better understanding of protein binding to this class of resins is seen as an important step to future exploitation of this mode of chromatography for industrial scale purification of proteins.     

Learning in mammalian sensory cortex

The improvement of perceptual capabilities with training can offer important insight into the physiological basis of learning in the cerebral cortex. The rapid time course and ease with which some perceptual capabilities can improve suggest that learning is an integral part of normal perception. Electrophysiological and neuroimaging studies of sensory systems in the cortex suggest that the changes underlying perceptual learning can occur in a variety of areas and are likely to involve multiple mechanisms. In particular, recent psychological and physiological studies suggest that perceptual learning might often involve the task-specific suppression of signals that interfere with performance.     

Chemical mechanism and substrate specificity of RhlI, an acylhomoserine lactone synthase from Pseudomonas aeruginosa

The enzyme RhlI catalyzes the formation of N-butyrylhomoserine lactone from S-adenosylmethionine and N-butyrylacyl carrier protein. N-Butyrylhomoserine lactone serves as a quorum-sensing signal molecule in Pseudomonas aeruginosa, and is implicated in the regulation of many processes involved in bacterial virulence and infectivity. The P. aeruginosa genome contains three genes encoding acyl carrier proteins. We have cloned all three genes, expressed the acyl carrier proteins, and characterized each as a substrate for RhlI. A continuous, spectrophotometric assay was developed to facilitate kinetic and mechanistic studies of RhlI. Acp1, which has not been characterized previously, was a good substrate for RhlI, with a K(m) of 7 microM; the reaction proceeded with a k(cat) value of 0.35 s(-1). AcpP, which supports fatty acid biosynthesis, was also a good substrate in the RhlI reaction, where k(cat) was 0.46 s(-1), and the K(m) for AcpP was 6 microM. The third acyl carrier protein, Acp3, was a poor substrate for RhlI, with a K(m) of 280 microM; k(cat) was 0.03 s(-1). Taken together with microarray data from the literature which show that expression of the gene encoding Acp1 is under the control of the quorum-sensing system, our data suggest that Acp1 is likely to be the substrate for RhlI in vivo. Isotope labeling studies were conducted to investigate the chemical mechanism of the RhlI-catalyzed lactonization reaction. Solvent deuterons were not incorporated into product, which implicates a direct attack mechanism in which the carboxylate oxygen of the presumptive N-butyryl-SAM intermediate attacks the methylene carbon adjacent to the sulfonium ion. Alternative mechanisms, in which N-butyrylvinylglycine is formed via elimination of methylthioadenosine, were ruled out on the basis of the observation that RhlI failed to convert authentic N-butyrylvinylglycine to N-butyryl-L-homoserine lactone.     

Antibodies (IgG) to lipopolysaccharide of Vibrio cholerae O1 mediate protection through inhibition of intestinal adherence and colonisation in a mouse model

An antiserum raised against purified lipopolysaccharide (LPS) of a Vibrio cholerae O1 strain (Co366) induced passive protection against challenge with the parent as well as other O1 organisms but not against O139 or non-O1/non-O139 organisms. A considerable level of protection against O1 strains was also observed with the IgG fraction of the antiserum which inhibited intestinal adherence and colonisation. The monovalent Fab(IgG) fragment, on the other hand, showed only a low level of protection. Interestingly, purified LPS failed to inhibit intestinal colonisation by the parent strain (Co366), thereby suggesting that the cell surface LPS moieties of vibrios may not be directly involved in the colonisation process. It may be concluded that the anti-LPS antibodies induce passive protection through microagglutination and/or immobilisation of vibrios which do not allow the organisms to adhere to and colonise the intestine.     

Generating Boolean networks with a prescribed attractor structure

MOTIVATION: Dynamical modeling of gene regulation via network models constitutes a key problem for genomics. The long-run characteristics of a dynamical system are critical and their determination is a primary aspect of system analysis. In the other direction, system synthesis involves constructing a network possessing a given set of properties. This constitutes the inverse problem. Generally, the inverse problem is ill-posed, meaning there will be many networks, or perhaps none, possessing the desired properties. Relative to long-run behavior, we may wish to construct networks possessing a desirable steady-state distribution. This paper addresses the long-run inverse problem pertaining to Boolean networks (BNs). RESULTS: The long-run behavior of a BN is characterized by its attractors. The rest of the state transition diagram is partitioned into level sets, the j-th level set being composed of all states that transition to one of the attractor states in exactly j transitions. We present two algorithms for the attractor inverse problem. The attractors are specified, and the sizes of the predictor sets and the number of levels are constrained. Algorithm complexity and performance are analyzed. The algorithmic solutions have immediate application. Under the assumption that sampling is from the steady state, a basic criterion for checking the validity of a designed network is that there should be concordance between the attractor states of the model and the data states. This criterion can be used to test a design algorithm: randomly select a set of states to be used as data states; generate a BN possessing the selected states as attractors, perhaps with some added requirements such as constraints on the number of predictors and the level structure; apply the design algorithm; and check the concordance between the attractor states of the designed network and the data states. AVAILABILITY: The software and supplementary material is available at http://gsp.tamu.edu/Publications/BNs/bn.htm     

Cortical maps: where theory meets experiments

Primary visual cortex (V1) has remarkably systematic functional maps. One commonly used class of computational models proposes that such maps are generated by a mechanism that projects the multiple dimensions of neuronal responses smoothly onto the two dimensions of cortex. In this issue of Neuron, Mriganka Sur and colleagues find a close match between such model predictions and measurements from ferret V1.     

pH Transitions in ion-exchange systems: role in the development of a cation-exchange process for a recombinant protein

Unexpected transient changes in effluent pH can occur during ion-exchange chromatography. Such changes can occur even if a column that is equilibrated with a buffer receives another solution in the same buffer and of the same pH but of a different salt concentration. An attempt is made to understand the basis for this phenomenon and apply it to the process purification of a recombinant protein on a strong cation-exchange resin. Incomplete column equilibration was eliminated as a possible cause of these effects. Various buffering species and various salt ions were studied at different solution concentrations to investigate pH transitions on strong cation-exchange resins. A further comparison was made between cation-exchange resins with different backbone chemistries. On the basis of these studies, a mechanism is proposed for these phenomena based on competitive equilibria between ions from the buffer salts and H(+)/OH(-) ions. In addition to the equilibria between these ions and the functional groups on the resins, charged groups on the resin backbone were also found to contribute to transient pH changes. The results from this study were applied to the cation-exchange step for a recombinant protein that was sensitive to pH excursions to help maintain activity of the protein during the purification process.     

Selenium and signal transduction: roads to cell death and anti-tumour activity

Accumulated evidence from prospective studies, intervention trials and studies on animal models of cancer have suggested a strong inverse correlation between selenium intake and cancer incidence. Several putative mechanisms have been suggested to mediate the chemopreventive activities of selenium: of these, the inhibition of cellular proliferation and the induction of apoptosis are particularly attractive. The mitogen activated protein kinase (MAPK) pathways are known to be important regulators of cell death and our recent work has focused on the involvement of these pathways in selenium-induced apoptosis in primary cultures of oral cancers and corresponding normal mucosa derived from biopsy material. Using this system, the oral carcinoma cells were found to have enhanced sensitivity to apoptosis when treated with certain selenium compounds compared to normal oral mucosa. Induction of Fas ligand was associated with selenium-induced apoptosis. Signal transduction studies suggests that selenium induces several changes in the MAPK signalling pathways but functional intervention/inhibitor studies indicate that activation of the JNK pathway seems to be most important.