The ester hydrolytic and synthetic activities of X-prolyl dipeptidyl peptidase from Streptococcus thermophilus : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Biochemistry at Massey University, New Zealand

X-prolyl dipeptidyl peptidase (EC 3.4.14.11), or PepX, is a dipeptidase found in most dairy lactic acid bacteria that hydrolyses N-terminal dipeptides from larger peptides where proline is the residue penultimate to the scissile bond. It has recently been found that PepX will also catalyse the hydrolysis of some chromogenic esters and synthesise esters via an acyltransferase mechanism that uses ethanol as the acceptor molecule and tributyrin as the donor molecule. In this study, the pepX gene from Streptococcus thermophilus strain B2513 was cloned and sequenced. This sequence was found to differ in several positions from the recently published pepX sequence of S.thermophilus strain ACA-DC4. None of the observed substitutions occurred in the catalytic domain of the enzyme, all being localised to the C-terminal β-sheet domain. An activity assay using a chromogenic peptide substrate with tributyrin as an was used to prove that PepX binds peptide substrates and acylglycerides at the same binding site, implying that the same catalytic machinery carries out both peptide hydrolysis and activities involving acylglycerides. PepX was found to form esters only from the acylglyceride tributyrin, and was not active on any of the larger triglycerides tested. The chemical mechanism for this ester formation is proposed to involve the direct transfer of an acyl group from the donor to an acceptor, rather than acyl hydrolysis followed by the separate transfer of a carboxylic acid product onto an acceptor, as the enzyme does not form esters when provided with butyric acid and ethanol. PepX was found to be incapable of hydrolysing milkfat and tributyrin in aqueous solution. This contrasts with the ability of PepX to hydrolyse the synthetic ester p-nitrophenyl butyrate, which probably is a reflection of the lability of the ester bond in this substrate. The results of this study show that PepX is a peptidase that has a secondary acyltransferase activity, with no hydrolase activity on natural acylglyceride substrates

Tilting Modules in Truncated Categories

We begin the study of a tilting theory in certain truncated categories of modules $\mathcal G(\Gamma)$ for the current Lie algebra associated to a finite-dimensional complex simple Lie algebra, where $\Gamma = P^+ \times J$, $J$ is an interval in $\mathbb Z$, and $P^+$ is the set of dominant integral weights of the simple Lie algebra. We use this to put a tilting theory on the category $\mathcal G(\Gamma')$ where $\Gamma' = P' \times J$, where $P'\subseteq P^+$ is saturated. Under certain natural conditions on $\Gamma'$, we note that $\mathcal G(\Gamma')$ admits full tilting modules.Comment: v7: rearrangement of Sections 2, 3 and 7, reference [5] updated, misprints correcte

The validity of quasi steady-state approximations in discrete stochastic simulations

In biochemical networks, reactions often occur on disparate timescales and can be characterized as either "fast" or "slow." The quasi-steady state approximation (QSSA) utilizes timescale separation to project models of biochemical networks onto lower-dimensional slow manifolds. As a result, fast elementary reactions are not modeled explicitly, and their effect is captured by non-elementary reaction rate functions (e.g. Hill functions). The accuracy of the QSSA applied to deterministic systems depends on how well timescales are separated. Recently, it has been proposed to use the non-elementary rate functions obtained via the deterministic QSSA to define propensity functions in stochastic simulations of biochemical networks. In this approach, termed the stochastic QSSA, fast reactions that are part of non-elementary reactions are not simulated, greatly reducing computation time. However, it is unclear when the stochastic QSSA provides an accurate approximation of the original stochastic simulation. We show that, unlike the deterministic QSSA, the validity of the stochastic QSSA does not follow from timescale separation alone, but also depends on the sensitivity of the non-elementary reaction rate functions to changes in the slow species. The stochastic QSSA becomes more accurate when this sensitivity is small. Different types of QSSAs result in non-elementary functions with different sensitivities, and the total QSSA results in less sensitive functions than the standard or the pre-factor QSSA. We prove that, as a result, the stochastic QSSA becomes more accurate when non-elementary reaction functions are obtained using the total QSSA. Our work provides a novel condition for the validity of the QSSA in stochastic simulations of biochemical reaction networks with disparate timescales.Comment: 21 pages, 4 figure

On a Democratic Future: Nietzsche, Derrida, and Democracy to Come

In this paper I analyse and critically assess Jacques Derrida’s political reading of Nietzsche. Derrida’s reading of Nietzsche’s multiple styles and their ramifications for how we read philosophical texts is well known. But Derrida also maintained that Nietzsche’s addresses to an unknown future readership evidenced a democratic aspect to Nietzsche’s work. Derrida’s is a heretofore unexamined interpretation, and in this paper I aim to show that his emphasis on the democratic style of Nietzsche’s writing raises different questions about the kind of political values that support Nietzsche’s critique of modernity. I argue that Derrida’s reading merits discussion, particularly in virtue of its intriguing account of what it means to experience the future democratically. However, I think Derrida’s reading has its own exegetical and philosophical problems. In sections one and two I explain why Derrida thought that Nietzsche’s hopes for the future of Europe constitute a democratic comportment; in section three I show how this reading of Nietzsche can be defended against a philosophical objection to its plausibility; and in section four I suggest exegetical reasons for questioning Derrida’s interpretation. I will end by drawing on Nietzsche’s work to raise an objection to the political quietism of democracy to come

Investigating visual and auditory scene feedback to early visual foveal and peripheral cortex using fMRI

No abstract available