The role of His-134, -147, and -150 residues in subunit assembly, cofactor binding, and catalysis of sheep liver cytosolic serine hydroxymethyltransferase

In an attempt to unravel the role of conserved histidine residues in the structure-function of sheep liver cytosolic serine hydroxymethyltransferase (SHMT), three site-specific mutants (H134N, H147N, and H150N) were constructed and expressed, H134N and H147N SHMTs had K-m values for L-serine, L-allo-threonine and beta-phenylserine similar to that of wild type enzyme, although the k(cat) values were markedly decreased, H134N SHMT was obtained in a dimeric form with only 6% of bound pyridoxal 5'-phosphate (PLP) compared with the wild type enzyme, Increasing concentrations of PLP (up to 500 mu M) enhanced the enzyme activity without changing its oligomeric structure, indicating that His-134 may be involved in dimer-dimer interactions, H147N SHMT was obtained in a tetrameric form but with very little PLP (3%) bound to it, suggesting that this residue was probably involved in cofactor binding, Unlike the wild type enzyme, the cofactor could be easily removed by dialysis from H147N SHMT, and the apoenzyme thus formed was present predominantly in the dimeric form, indicating that PLP binding is at the dimer-dimer interface, H150N SHMT was obtained in a tetrameric form with bound PLP, However, the mutant had very little enzyme activity (<2%). The k(cat)/K-m values for L-serine, L-allo-threonine and beta-phenylserine were 80-, 56-, and SS-fold less compared with wild type enzyme, Unlike the wild type enzyme, it failed to form the characteristic quinonoid intermediate and was unable to carry out the exchange of 2-S proton from glycine in the presence of H-4-folate. However, it could form an external aldimine with serine and glycine, The wild type and the mutant enzyme had similar K-d values for serine and glycine, These results suggest that His-150 may be the base that abstracts the alpha-proton of the substrate, leading to formation of the quinonoid intermediate in the reaction catalyzed by SHMT.

Differentiation of neural stem cells in fragile X syndrome

Multipotent stem cells can self-renew and give rise to multiple cell types. One type of mammalian multipotent stem cells are neural stem cells (NSC)s, which can generate neurons, astrocytes and oligodendrocytes. NSCs are likely involved in learning and memory, but their exact role in cognitive function in the developing and adult brain is unclear. We have studied properties of NSCs in fragile X syndrome (FXS), which is the most common form of inherited mental retardation. FXS is caused by the lack of functional fragile X mental retardation protein (FMRP). FMRP is involved in the regulation of postsynaptic protein synthesis in a group I metabotropic glutamate receptor 5 (mGluR5)-dependent manner. In the absence of functional FMRP, the formation of functional synapses is impaired in the forebrain which results in alterations in synaptic plasticity. In our studies, we found that FMRP-deficient NSCs generated more neurons and less glia than control NSCs. The newborn neurons derived from FMRP-deficient NSCs showed an abnormally immature morphology. Furthermore, FMRP-deficient NSCs exhibited aberrant oscillatory Ca2+ responses to glutamate, which were specifically abolished by an antagonist of the mGluR5 receptor. The data suggested alterations in glutamatergic differentiation of FMRP-deficient NSCs and were further supported by an accumulation of cells committed to glutamatergic lineage in the subventricular zone of the embryonic Fmr1-knockout (Fmr1-KO) neocortex. Postnatally, the aberrant cells likely contributed to abnormal formation of the neocortex. The findings suggested a defect in the differentiation of distinct glutamatergic mGluR5 responsive cells in the absence of functional FMRP. Furthermore, we found that in the early postnatal Fmr1-KO mouse brain, the expression of mRNA for regulator of G-protein signalling-4 (RGS4) was decreased which was in line with disturbed G-protein signalling in NSCs lacking FMRP. Brain derived neurotrophic factor (BDNF) promotes neuronal differentiation of NSCs as the absence of FMRP was shown to do. This led us to study the effect of impaired BDNF/TrkB receptor signaling on NSCs by overexpression of TrkB.T1 receptor isoform. We showed that changes in the relative expression levels of the full-length and truncated TrkB isoforms influenced the replication capacity of NSCs. After the differentiation, the overexpression of TrkB.T1 increased neuronal turnover. To summarize, FMRP and TrkB signaling are involved in normal differentiation of NSCs in the developing brain. Since NSCs might have potential for therapeutic interventions in a variety of neurological disorders, our findings may be useful in the design of pharmacological interventions in neurological disorders of learning and memory.

Operationalising and measuring flow in video games

This paper explores the obstacles associated with designing video game levels for the purpose of objectively measuring flow. We sought to create three video game levels capable of inducing a flow state, an overload state (low-flow), and a boredom state (low-flow). A pilot study, in which participants self-reported levels of flow after playing all three game levels, was undertaken. Unexpected results point to the challenges of operationalising flow in video game research, obstacles in experimental design for invoking flow and low-flow, concerns about flow as a construct for measuring video game enjoyment, the applicability of self-report flow scales, and the experience of flow in video game play despite substantial challenge-skill differences.

Boson-fermion duality in SU(m vertical bar n) supersymmetric Haldane-Shastry spin chain

By using the Y(gl(m|n)) super Yangian symmetry of the SU(m|n) supersymmetric Haldane-Shastry spin chain, we show that the partition function of this model satisfies a duality relation under the exchange of bosonic and fermionic spin degrees of freedom. As a byproduct of this study of the duality relation, we find a novel combinatorial formula for the super Schur polynomials associated with some irreducible representations of the Y(gl(m|n)) Yangian algebra. Finally, we reveal an intimate connection between the global SU(m|n) symmetry of a spin chain and the boson-fermion duality relation. (C) 2007 Elsevier B.V. All rights reserved.

Structure determination and biochemical studies on Bacillus stearothermophilus E53Q serine hydroxymethyltransferase and its complexes provide insights on function and enzyme memory

Serine hydroxymethyltransferase (SHMT) belongs to the alpha-family of pyridoxal 5'-phosphate-dependent enzymes and catalyzes the reversible conversion of L-Ser and etrahydrofolate to Gly and 5,10-methylene tetrahydrofolate. 5,10-Methylene tetrahydrofolate serves as a source of one-carbon fragment in many biological processes. SHMT also catalyzes the tetrahydrofolate-independent conversion of L-allo-Thr to Gly and acetaldehyde. The crystal structure of Bacillus stearothermophilus SHMT (bsSHMT) suggested that E53 interacts with the substrate, L-Ser and etrahydrofolate. To elucidate the role of E53, it was mutated to Q and structural and biochemical studies were carried out with the mutant enzyme. The internal aldimine structure of E53QbsSHMT was similar to that of the except for significant changes at Q53, Y60 and Y61. The wild-type enzyme, carboxyl of Gly and side chain of L-Ser were in two conformations in the respective external aldimine structures. The mutant enzyme was completely inactive for tetrahydrofolate-depen dent cleavage of L-Ser, whereas there was a 1.5-fold increase in the rate of tetrahydrofolate-independent reaction with L-allo-Thr. The results obtained from these studies suggest that E53 plays an essential role in tetrahydrofolate/5-formyl tetrahydrofolate binding and in the proper positioning of C beta of L-Ser for direct attack by N5 of tetrahydrofolate. Most interestingly, the structure of the complex obtained by cocrystallization of E53QbsSHMT with Gly and 5-formyl tetrahydrofolate revealed the gem-diamine form of pyridoxal 5'-phosphate bound to Gly and active site Lys. However, density for 5-formyl tetrahydrofolate was not observed. Gly carboxylate was in a single conformation, whereas pyridoxal 5'-phosphate had two distinct conformations. The differences between the structures of this complex and Gly external aldimine suggest that the changes induced by initial binding of 5-formyl tetrahydrofolate are retained even though 5-formyl tetrahydrofolate is absent in the final structure. Spectral studies carried out with this mutant enzyme also suggest that 5-formyl tetrahydrofolate binds to the E53QbsSHMT-Gly complex forming a quinonoid intermediate and falls off within 4 h of dialysis, leaving behind the mutant enzyme in the gemdiamine form. This is the first report to provide direct evidence for enzyme memory based on the crystal structure of enzyme complexes.

Role and function of nonmuscle alpha-actinin-1 and -4 in regulating distinct subcategories of actin stress fibers in mammalian cells

Actin stress fibers are dynamic structures in the cytoskeleton, which respond to mechanical stimuli and affect cell motility, adhesion and invasion of cancer cells. In nonmuscle cells, stress fibers have been subcategorized to three distinct stress fiber types: dorsal and ventral stress fibers and transverse arcs. These stress fibers are dissimilar in their subcellular localization, connection to substratum as well as in their dynamics and assembly mechanisms. Still uncharacterized is how they differ in their function and molecular composition. Here, I have studied involvement of nonmuscle alpha-actinin-1 and -4 in regulating distinct stress fibers as well as their localization and function in human U2OS osteosarcoma cells. Except for the correlation of upregulation of alpha-actinin-4 in invasive cancer types very little is known about whether these two actinins are redundant or have specific roles. The availability of highly specific alpha-actinin-1 antibody generated in the lab, revealed localization of alpha-actinin-1 along all three categories of stress fibers while alphaactinin-4 was detected at cell edge, distal ends of stress fibers as well as perinuclear regions. Strikingly, by utilizing RNAi-mediated gene silencing of alpha-actinin-1 resulted in specific loss of dorsal stress fibers and relocalization of alpha-actinin-4 to remaining transverse arcs and ventral stress fibers. Unexpectedly, aberrant migration was not detected in cells lacking alpha-actinin-1 even though focal adhesions were significantly smaller and fewer. Whereas, silencing of alpha-actinin-4 noticeably affected overall cell migration. In summary, as part of my master thesis study I have been able to demonstrate distinct localization and functional patterns for both alpha-actinin-1 and -4. I have identified alpha-actinin-1 to be a selective dorsal stress fiber crosslinking protein as well as to be required for focal adhesion maturation, while alpha-actinin-4 was demonstrated to be fundamental for cell migration.

Asymtotic solution of the Frieman and Book equation for the pair-correlation function

Using Thomé's procedure, the asymptotic solutions of the Frieman and Book equation for the two-particle correlation in a plasma have been obtained in a complete form. The solution is interpreted in terms of the Lorentz distance. The exact expressions for the internal energy and pressure are evaluated and they are found to be a generalization of the result obtained earlier by others.

Circular elastic inclusions in cylindrical shells

The problem of a circular elastic inclusion in a cylindrical shell subjected to internal pressure or thermal loading is studied. The two shallow-shell equations governing the behaviour of a cylindrical shell are transformed into a single differential equation involving a curvature parameter and a complex potential function in a non-dimensional form. In the shell region, the solution is represented by Hankel functions of first kind, whereas in the inclusion region it is represented by Bessel functions of first kind. Boundary conditions at the shell-inclusion junction are expressed in a simple form involving in-plane strains and change in curvature. The effect of such inclusion parameters as extensional rigidity, bending rigidity, and thermal expansion coefficients on the stress concentrations has been determined. The results are presented in non-dimensional form for ready use.

Solution concepts in continuous-kernel multicriteria games

This paper considers nonzero-sum multicriteria games with continuous kernels. Solution concepts based on the notions of Pareto optimality, equilibrium, and security are extended to these games. Separate necessary and sufficient conditions and existence results are presented for equilibrium, Pareto-optimal response, and Pareto-optimal security strategies of the players.

Determination of rational strategies for players in two-target games

This paper addresses some of the basic issues involved in the determination of rational strategies for players in two-target games. We show that unlike single-target games where the task of role assignment and selection of strategies is conceptually straightforward, in two-target games, many factors like the preference ordering of outcomes by players, the relative configuration of the target sets and secured outcome regions, the uncertainty about the parameters of the game, etc., also influence the rational selection of strategies by players. The importance of these issues is illustrated through appropriate examples.

Form, Content, and Magnetism in Iron Oxide Nanocrystals

Monodisperse iron oxide nanocrystals with spherical and cubic morphologies, of comparable dimensions, have been prepared by the thermal decomposition of FeOOH. The lattice spacings of both forms agree with that of magnetite, Fe(3)O(4). The two, however, exhibit very different blocking temperatures. Nanocrystals of cubic morphology are superparamagnetic above 190 K while the spherical nanocrystals at a lower temperature, 142 K. The higher blocking temperatures in particles of cubic morphology are shown to be a consequence of exchange bias fields. We show that in the present iron oxide nanocrystals the exchange bias fields originate from the presence of trace amounts of wustite, FeO. A Reitveld refinement analysis of the X-ray diffraction patterns shows that nanocrystals of cubic morphology have a higher FeO content. The higher FeO content is responsible for the larger exchange bias fields that in turn lead to a higher blocking temperature for nanocrystals with cubic morphology.

Filtered density function for large eddy simulation of turbulent reacting flows

A methodology termed the “filtered density function” (FDF) is developed and implemented for large eddy simulation (LES) of chemically reacting turbulent flows. In this methodology, the effects of the unresolved scalar fluctuations are taken into account by considering the probability density function (PDF) of subgrid scale (SGS) scalar quantities. A transport equation is derived for the FDF in which the effect of chemical reactions appears in a closed form. The influences of scalar mixing and convection within the subgrid are modeled. The FDF transport equation is solved numerically via a Lagrangian Monte Carlo scheme in which the solutions of the equivalent stochastic differential equations (SDEs) are obtained. These solutions preserve the Itô-Gikhman nature of the SDEs. The consistency of the FDF approach, the convergence of its Monte Carlo solution and the performance of the closures employed in the FDF transport equation are assessed by comparisons with results obtained by direct numerical simulation (DNS) and by conventional LES procedures in which the first two SGS scalar moments are obtained by a finite difference method (LES-FD). These comparative assessments are conducted by implementations of all three schemes (FDF, DNS and LES-FD) in a temporally developing mixing layer and a spatially developing planar jet under both non-reacting and reacting conditions. In non-reacting flows, the Monte Carlo solution of the FDF yields results similar to those via LES-FD. The advantage of the FDF is demonstrated by its use in reacting flows. In the absence of a closure for the SGS scalar fluctuations, the LES-FD results are significantly different from those based on DNS. The FDF results show a much closer agreement with filtered DNS results. © 1998 American Institute of Physics.

Thermodynamics of ideal gas in doubly special relativity

We study thermodynamics of an ideal gas in doubly special relativity. A new type of special functions (which we call ``incomplete modified Bessel functions'') emerge. We obtain a series solution for the partition function and derive thermodynamic quantities. We observe that doubly special relativity thermodynamics is nonperturbative in the special relativity and massless limits. A stiffer equation of state is found.

Dynamical behavior in the nonlinear rheology of surfactant solutions

Several surfactant molecules self-assemble in solution to form long, flexible wormlike micelles which get entangled with each other, leading to viscoelastic gel phases. We discuss our recent work on the rheology of such a gel formed in the dilute aqueous solutions of a surfactant CTAT. In the linear rheology regime, the storage modulus G′(ω) and loss modulus G″(ω) have been measured over a wide frequency range. In the nonlinear regime, the shear stress σ shows a plateau as a function of the shear rate math above a certain cutoff shear rate mathc. Under controlled shear rate conditions in the plateau regime, the shear stress and the first normal stress difference show oscillatory time-dependence. The analysis of the measured time series of shear stress and normal stress has been done using several methods incorporating state space reconstruction by embedding of time delay vectors. The analysis shows the existence of a finite correlation dimension and a positive Lyapunov exponent, unambiguously implying that the dynamics of the observed mechanical instability can be described by that of a dynamical system with a strange attractor of dimension varying from 2.4 to 2.9.

Case for multiple views of function in design based on a common definition

Functions are important in designing. However, several issues hinder progress with the understanding and usage of functions: lack of a clear and overarching definition of function, lack of overall justifications for the inevitability of the multiple views of function, and scarcity of systematic attempts to relate these views with one another. To help resolve these, the objectives of this research are to propose a common definition of function that underlies the multiple views in literature and to identify and validate the views of function that are logically justified to be present in designing. Function is defined as a change intended by designers between two scenarios: before and after the introduction of the design. A framework is proposed that comprises the above definition of function and an empirically validated model of designing, extended generate, evaluate, modify, and select of state-change, and an action, part, phenomenon, input, organ, and effect model of causality (Known as GEMS of SAPPhIRE), comprising the views of activity, outcome, requirement-solution-information, and system-environment. The framework is used to identify the logically possible views of function in the context of designing and is validated by comparing these with the views of function in the literature. Describing the different views of function using the proposed framework should enable comparisons and determine relationships among the various views, leading to better understanding and usage of functions in designing.