Three-dimensional structure of heat shock protein 90 from Plasmodium falciparum: molecular modelling approach to rational drug design against malaria

We have recently implicated heat shock protein 90 from Plasmodium falciparum (PfHsp90) as a potential drug target against malaria. Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory effects on development of malarial parasite in human erythrocytes. To gain better understanding of the vital role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length structure of yeast Hsp90. Sequence similarity found between PfHsp90 and yeast Hsp90 allowed us to model the core structure with high confidence. The superimposition of the predicted structure with that of the template yeast Hsp90 structure reveals an RMSD of 3.31 angstrom. The N-terminal and middle domains showed the least RMSD (1.76 angstrom) while the more divergent C-terminus showed a greater RMSD (2.84 angstrom) with respect to the template. The structure shows overall conservation of domains involved in nucleotide binding, ATPase activity, co-chaperone binding as well as inter-subunit interactions. Important co-chaperones known to modulate Hsp90 function in other eukaryotes are conserved in malarial parasite as well. An acidic stretch of amino acids found in the linker region, which is uniquely extended in PfHsp90 could not be modeled in this structure suggesting a flexible conformation. Our results provide a basis to compare the overall structure and functional pathways dependent on PfHsp90 in malarial parasite. Further analysis of differences found between human and parasite Hsp90 may make it possible to design inhibitors targeted specifically against malaria.

Shock acceleration in the solar corona

In this thesis acceleration of energetic particles at collisionless shock waves in space plasmas is studied using numerical simulations, with an emphasis on physical conditions applicable to the solar corona. The thesis consists of four research articles and an introductory part that summarises the main findings reached in the articles and discusses them with respect to theory of diffusive shock acceleration and observations. This thesis gives a brief review of observational properties of solar energetic particles and discusses a few open questions that are currently under active research. For example, in a few large gradual solar energetic particle events the heavy ion abundance ratios and average charge states show characteristics at high energies that are typically associated with flare-accelerated particles, i.e. impulsive events. The role of flare-accelerated particles in these and other gradual events has been discussed a lot in the scientific community, and it has been questioned if and how the observed features can be explained in terms of diffusive shock acceleration at shock waves driven by coronal mass ejections. The most extreme solar energetic particle events are the so-called ground level enhancements where particle receive so high energies that they can penetrate all the way through Earth's atmosphere and increase radiation levels at the surface. It is not known what conditions are required for acceleration into GeV/nuc energies, and the presence of both very fast coronal mass ejections and X-class solar flares makes it difficult to determine what is the role of these two accelerators in ground level enhancements. The theory of diffusive shock acceleration is reviewed and its predictions discussed with respect to the observed particle characteristics. We discuss how shock waves can be modeled and describe in detail the numerical model developed by the author. The main part of this thesis consists of the four scientific articles that are based on results of the numerical shock acceleration model developed by the author. The novel feature of this model is that it can handle complex magnetic geometries which are found, for example, near active regions in the solar corona. We show that, according to our simulations, diffusive shock acceleration can explain the observed variations in abundance ratios and average charge states, provided that suitable seed particles and magnetic geometry are available for the acceleration process in the solar corona. We also derive an injection threshold for diffusive shock acceleration that agrees with our simulation results very well, and which is valid under weakly turbulent conditions. Finally, we show that diffusive shock acceleration can produce GeV/nuc energies under suitable coronal conditions, which include the presence of energetic seed particles, a favourable magnetic geometry, and an enhanced level of ambient turbulence.

Heat-shock protein 70-2 (HSP70-2) expression in bladder urothelial carcinoma is associated with tumour progression and promotes migration and invasion

Purpose: Testis specific heat-shock protein 70-2 (HSP70-2), a member of HSP70 chaperone family, is essential for the growth of spermatocytes and cancer cells. We investigated the association of HSP70-2 expression with clinical behaviour and progression of urothelial carcinoma of bladder. Experimental design: We assessed the HSP70-2 expression by RT-PCR and HSP70-2 protein expression by immunofluorescence, flow cytometry, immunohistochemistry and Western blotting in urothelial carcinoma patient specimens and HTB-1, UMUC-3, HTB-9, HTB-2 and normal human urothelial cell lines. Further, to investigate the role of HSP70-2 in bladder tumour development, HSP70-2 was silenced in the high-grade invasive HTB-1 and UMUC-3 cells. The malignant properties of urothelial carcinoma cells were examined using colony formation, migration assay, invasion assay in vitro and tumour growth in vivo. Results: Our RT-PCR analysis and immunohistochemistry analysis revealed that HSP70-2 was expressed in both moderate to well-differentiated and high-grade invasive urothelial carcinoma cell lines studied and not in normal human urothelial cells. In consistence with these results, HSP70-2 expression was also observed in superficially invasive (70%) and muscle-invasive (90%) patient's tumours. Furthermore, HSP70-2 knockdown significantly suppressed cellular motility and invasion ability. An in vivo xenograft study showed that inhibition of HSP70-2 significantly suppressed tumour growth. Conclusions: In conclusion, our data suggest that the HSP70-2 expression is associated with early spread and progression of urothelial carcinoma of bladder cancer and that HSP70-2 can be the potential therapeutic target for bladder urothelial carcinoma. (C) 2009 Elsevier Ltd. All rights reserved.

Electron temperature distribution across a shock wave in a partially ionized gas

The electron temperature structure in a weakly ionized plasma is studied allowing the degree of ionization to vary across the shock wave. The values of the electron temperature and the downstream equilibrium temperature obtained with variable ionization are less than those for frozen ionization. The electron temperature rises sharply behind the shock for variable ionization while a gradual increase is predicted by frozen ionization.

Approximate solutions for the structure of shock waves

Approximate solutions of the B-G-K model equation are obtained for the structure of a plane shock, using various moment methods and a least squares technique. Comparison with available exact solution shows that while none of the methods is uniformly satisfactory, some of them can provide accurate values for the density slope shock thickness delta n . A detailed error analysis provides explanations for this result. An asymptotic analysis of delta n for largeMach numbers shows that it scales with theMaxwell mean free path on the hot side of the shock, and that their ratio is relatively insensitive to the viscosity law for the gas.

Propagation of an isothermal shock in stellar envelopes

We have studied in this paper the propagation of an isothermal shock in the radiative envelopes of the Bosman-Crespin model for a hot star and Boury’s model for a giant star. A spherically symmetric disturbance is supposed to be originated at or outside the surface of the convective core. We have used Whitham’s rule to study the variation in the shock strength and the shock velocity after modifying it for inclusion of pressure, energy and flux of radiation. We find the shock increases in strength as it propagates through the envelopes of decreasing density, pressure and temperature. The velocity of the shock decreases for very weak initial shock strengths, for intermediate initial shock strength it first decreases and then increases, while for large initial shock strength, it always increases. This aspect of the problem throws some light on the stability of the models under consideration.

Propagation of a spherical shock in an inhomogeneous self-gravitating or nongravitating system

The propagation of a shock wave of finite strength due to an explosion into inhomogeneous nongravitating and self-gravitating systems has been considered, using similarity principles, supposing that the density varies as an inverse power of distance from the centre of explosion. A large number of systems, characterised by different density exponents and different adiabatic coefficients of the gas have been considered for different shock strengths. The numerical integration from the shock inward has been continued to the surface of singularity where density tends to infinity and which acts like a piston in the self-gravitating case and to the surface where the velocity gradient tends to infinity in the nongravitating case. The effect of variation of shock strength, density exponent and adiabatic coefficient on the location of these singularities and on the distribution of flow parameters behind the shock has been studied. The initial energy of the system and the manner of release of the explosion energy influence strongly the flow behind the shock. The results have been graphically depicted.

Strong shock with radiation near the surface of a star

The propagation of a shock wave, originating in a stellar interior, is considered when it approaches the surface of the star and assumes a self-similar character, "forgetting" its initial conditions. The flow behind the shock is assumed to be spatially isothermal rather than adiabatic to simulate the conditions of large radiative transfer near the stellar surface. The adiabatic and isothermal flows behind such a shock are compared. The exact shock-propagation laws, obtained by solving the equations in similarity variables, for different values of the parameter δ in the undisturbed density law, ρ0 ∝ xδ, and γ, the ratio of specific heats, are compared with the approximate values calculated by Whitham's characteristic rule and the two show a generally good agreement.

A one point shock capturing kinetic scheme for hyperbolic conservation laws

We have presented a new low dissipative kinetic scheme based on a modified Courant Splitting of the molecular velocity through a parameter φ. Conditions for the split fluxes derived based on equilibrium determine φ for a one point shock. It turns out that φ is a function of the Left and Right states to the shock and that these states should satisfy the Rankine-Hugoniot Jump condition. Hence φ is utilized in regions where the gradients are sufficiently high, and is switched to unity in smooth regions. Numerical results confirm a discrete shock structure with a single interior point when the shock is aligned with the grid.

Simultaneous measurement of aerodynamic and heat transfer data for large angle blunt cones in hypersonic shock tunnel

Aerodynamic forces and fore-body convective surface heat transfer rates over a 60 degrees apex-angle blunt cone have been simultaneously measured at a nominal Mach number of 5.75 in the hypersonic shock tunnel HST2. An aluminum model incorporating a three-component accelerometer-based balance system for measuring the aerodynamic forces and an array of platinum thin-film gauges deposited on thermally insulating backing material flush mounted on the model surface is used for convective surface heat transfer measurement in the investigations. The measured value of the drag coefficient varies by about +/-6% from the theoretically estimated value based on the modified Newtonian theory, while the axi-symmetric Navier-Stokes computations overpredict the drag coefficient by about 9%. The normalized values of measured heat transfer rates at 0 degrees angle of attack are about 11% higher than the theoretically estimated values. The aerodynamic and the heat transfer data presented here are very valuable for the validation of CFD codes used for the numerical computation of How fields around hypersonic vehicles.

A note on the equivalence of shock manifold equations

The shock manifold equation is a first order nonlinear partial differential equation, which describes the kinematics of a shockfront in an ideal gas with constant specific heats. However, it was found that there was more than one of these shock manifold equations, and the shock surface could be embedded in a one parameter family of surfaces, obtained as a solution of any of these shock manifold equations. Associated with each shock manifold equation is a set of characteristic curves called lsquoshock raysrsquo. This paper investigates the nature of various associated shock ray equations.

On methods of calculating successive positions of a shock front

In this paper we have discussed limits of the validity of Whitham's characteristic rule for finding successive positions of a shock in one space dimension. We start with an example for which the exact solution is known and show that the characteristic rule gives correct result only if the state behind the shock is uniform. Then we take the gas dynamic equations in two cases: one of a shock propagating through a stratified layer and other down a nonuniform tube and derive exact equations for the evolution of the shock amplitude along a shock path. These exact results are then compared with the results obtained by the characteristic rule. The characteristic rule not only incorrectly accounts for the deviation of the state behind the shock from a uniform state but also gives a coefficient in the equation which differ significantly from the exact coefficients for a wide range of values of the shock strength.

Uniformly valid analytical solution to the problem of a decaying shock wave

An explicit representation of an analytical solution to the problem of decay of a plane shock wave of arbitrary strength is proposed. The solution satisfies the basic equations exactly. The approximation lies in the (approximate) satisfaction of two of the Rankine-Hugoniot conditions. The error incurred is shown to be very small even for strong shocks. This solution analyses the interaction of a shock of arbitrary strength with a centred simple wave overtaking it, and describes a complete history of decay with a remarkable accuracy even for strong shocks. For a weak shock, the limiting law of motion obtained from the solution is shown to be in complete agreement with the Friedrichs theory. The propagation law of the non-uniform shock wave is determined, and the equations for shock and particle paths in the (x, t)-plane are obtained. The analytic solution presented here is uniformly valid for the entire flow field behind the decaying shock wave.

Ion-acoustic solutions and shock waves in multicomponent plasmas

The present investigation of ion-acoustic waves is based on the study of the nonlinearity of plasma waves in a dispersive medium. Here the authors study ion-acoustic solitary waves in a warm ion plasma with non-isothermal electrons and then the results for solitary waves in a plasma with isothermal electrons are obtained. Incorporating the previous results obtained from the solitary wave solutions, the authors generalize the effect of negative ions on ion-acoustic waves in plasmas consisting of either a warm or cold ion species. A reflection phenomenon of ions in these waves is also studied. These results can be generalized, but the discussion is limited to a particular model of the plasma.