Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner

Sequence specific interaction between DNA and protein molecules has been a subject of active investigation for decades now. Here, we have chosen single promoter containing bacteriophage Delta D-III T7 DNA and Escherichia coli RNA polymerase and followed their recognition at the air-water interface by using the surface plasmon resonance (SPR) technique, where the movement of one of the reacting species is restricted by way of arraying them on an immobilized support. For the Langmuir monolayer studies, we used a RNA polymerase with a histidine tag attached to one of its subunits, thus making it an xcellent substrate for Ni(II) ions, while the SPR Studies were done using biotin-labeled DNA immobilized on a streptavidin-coated chip. Detailed analysis of the thermodynamic parameters as a function of concentration and temperature revealed that the interaction of RNA polymerase with T7 DNA is largely entropy driven (83 (+/- 12) kcal mol(-1)) with a positive enthalpy of 13.6 (+/- 3.6) kcal mol(-1), The free energy of reaction determined by SPR and Langmuir-Blodgett technique was -11 (+/- 2) and -15.6 kcal mol(-1), respectively. The ability of these methods to retain the specificity of the recognition process was also established.

Molecular Marriage through Partner Preferences in Covalent Cage Formation and Cage-to-Cage Transformation

Unprecedented self-sorting of three-dimensional purely organic cages driven by dynamic covalent bonds is described. Four different cages were first synthesized by condensation of two triamines and two dialdehydes separately. When a mixture of all the components was allowed to react, only two cages were formed, which suggests a high-fidelity self-recognition. The issue of the preference of one triamine for a particular dialdehyde was further probed by transforming a non-preferred combination to either of the two preferred combinations by reacting it with the appropriate triamine or dialdehyde.

Interplay of vector-like top partner multiplets in a realistic mixing set-up

The ATLAS and CMS collaborations at the LHC have performed analyses on the existing data sets, studying the case of one vector-like fermion or multiplet coupling to the standard model Yukawa sector. In the near future, with more data available, these experimental collaborations will start to investigate more realistic cases. The presence of more than one extra vector-like multiplet is indeed a common situation in many extensions of the standard model. The interplay of these vector-like multiplet between precision electroweak bounds, flavour and collider phenomenology is a important question in view of establishing bounds or for the discovery of physics beyond the standard model. In this work we study the phenomenological consequences of the presence of two vector-like multiplets. We analyse the constraints on such scenarios from tree-level data and oblique corrections for the case of mixing to each of the SM generations. In the present work, we limit to scenarios with two top-like partners and no mixing in the down-sector.

Thermodynamic properties of Pb2PtO4 and PbPt2O4 and phase equilibria in the system Pb–Pt–O

The compounds Pb2PtO4 and PbPt2O4 were synthesized from an intimate mixture of yellow PbO and Pt metal powders by heating under pure oxygen gas at 973 K for periods up to 600 ks with intermediate grinding and recompacting. Both compounds were found to decompose on heating in pure oxygen to PbO and Pt, apparently in conflict with the requirements for equilibrium phase relations in the ternary system Pb–Pt–O. The oxygen chemical potential corresponding to the three-phase mixtures, Pb2PtO4 + PbO + Pt and PbPt2O4 + PbO + Pt were measured as a function of temperature using solid-state electrochemical cells incorporating yttria-stabilized zirconia as the solid electrolyte and pure oxygen gas at 0.1 MPa pressure as the reference electrode. The standard Gibbs free energies of formation of the ternary oxides were derived from the measurements. Analysis of the results indicated that the equilibrium involving three condensed phases Pb2PtO4 + PbO + Pt is metastable. Under equilibrium conditions, Pb2PtO4 should have decomposed to a mixture of PbO and PbPt2O4. Measurement of the oxygen potential corresponding to this equilibrium decomposition as a function of temperature indicated that decomposition temperature in pure oxygen is 1014(±2) K. This was further confirmed by direct determination of phase relations in the ternary Pb–Pt–O by equilibrating several compositions at 1023 K for periods up to 850 ks and phase identification of quenched samples using X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). Only one ternary oxide PbPt2O4 was stable at 1023 K under equilibrium conditions. Alloys and intermetallic compounds along the Pb–Pt binary were in equilibrium with PbO.

A cooperative game of a pair of learning automata

A cooperative game played in a sequential manner by a pair of learning automata is investigated in this paper. The automata operate in an unknown random environment which gives a common pay-off to the automata. Necessary and sufficient conditions on the functions in the reinforcement scheme are given for absolute monotonicity which enables the expected pay-off to be monotonically increasing in any arbitrary environment. As each participating automaton operates with no information regarding the other partner, the results of the paper are relevant to decentralized control.

Adsopption isotherms-A critique

The possibility or the impossibility of separating the particle and the electrode interactions is discussed in a wider context of the effects due to any two interaction potentials on the equation of state. The involved nature of the pressure dependence on two individually definable forces is illustrated through the Percus Yevick results for the adhesive hard spheres. An alternative form of the adsorption isotherm is given to bring home the intimate relationship between the actual equation of state and the free energy of adsorption. Thermodynamic consequences of congruence with respect to E (or q) as reflected through the linear plots of q (or E) vs. θ are well known. Mathematical consequences of simultaneous congruence have been pointed out recently. In this paper, the physical nature of congruence hypothesis is revealed. In passing "the pseudo-congruence" is also discussed. It is emphasised that the problem is no less ambiguous with regard to modelling the particle/particle interaction. The ad hoc nature of our dependence of the available equations of state is emphasised through a discussion on the HFL theory. Finally, a heuristic method for modelling ΔG mathematically-incorporating its behaviour at saturation coverages-is advanced. The more interesting aspects of this approach, which generalises almost all isotherms hitherto known, are sketched.

Crystal structure and conformation of the cyclic dipeptide cyclo-(L-histidyl-L-aspartyl) trihydrate

The crystal structure of cyclo-(L-histidyl-L-aspartyl) trihydrate has been determined by x-ray diffraction techniques, and refined to a final R index of 0.056 for 1601 reflections. The molecule is in a folded conformation, with the imidazole ring facing the diketopiperazine ring. However, since the diketopiperazine ring is essentially planar, the interaction between the two rings is not as intimate as in those cyclic dipeptides in which the diketopiperazine ring is in a boat conformation with the side chain occupying an axial, or flagpole, site. Planarity of the diketopiperazine ring may be dictated by steric interactions between the imidazole ring and the aspartyl side chain. The molecule is a zwitterion, a proton having been transferred from the carboxyl group of the aspartyl side chain to the imidazole ring.

Characterization of circumstellar carbonaceous dust analogues produced by pyrolysis of acetylene in a porous graphite reactor

Carbon particles synthesized by acetylene pyrolysis in a porous graphite reactor have been investigated. The intimate chemical and physical structures of the particles were probed by proton nuclear magnetic resonance spectroscopy, infrared Fourier transform spectroscopy and X-ray diffraction. The analysis points towards a chemical structure composed of soluble low-mass aromatics surrounding small insoluble larger aromatic islands bridged by aliphatic groups. The diffraction profile indicates that the particles are mostly amorphous with small crystalline domains of not, vert, similar6.5 Å composed of a few stacked graphene layers. The properties of these particles are compared with these obtained with other types of production methods such as laser pyrolysis and combustion flames. The results are briefly discussed in the context of the evolution of infrared interstellar emitters. Possible uses of the reactor are proposed.

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.

Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality

It is well known that protein crystallizability can be influenced by site-directed mutagenesis of residues on the molecular surface of proteins, indicating that the intermolecular interactions in crystal-packing regions may play a crucial role in the structural regularity at atomic resolution of protein crystals. Here, a systematic examination was made of the improvement in the diffraction resolution of protein crystals on introducing a single mutation of a crystal-packing residue in order to provide more favourable packing interactions, using diphthine synthase from Pyrococcus horikoshii OT3 as a model system. All of a total of 21 designed mutants at 13 different crystal-packing residues yielded almost isomorphous crystals from the same crystallization conditions as those used for the wild-type crystals, which diffracted X-rays to 2.1 angstrom resolution. Of the 21 mutants, eight provided crystals with an improved resolution of 1.8 angstrom or better. Thus, it has been clarified that crystal quality can be improved by introducing a suitable single mutation of a crystal-packing residue. In the improved crystals, more intimate crystal-packing interactions than those in the wild-type crystal are observed. Notably, the mutants K49R and T146R yielded crystals with outstandingly improved resolutions of 1.5 and 1.6 angstrom, respectively, in which a large-scale rearrangement of packing interactions was unexpectedly observed despite the retention of the same isomorphous crystal form. In contrast, the mutants that provided results that were in good agreement with the designed putative structures tended to achieve only moderate improvements in resolution of up to 1.75 angstrom. These results suggest a difficulty in the rational prediction of highly effective mutations in crystal engineering.

Influence of drying on the liquid limit behaviour of a marine clay

The possible mechanisms of particle aggregation and reduction in liquid limit of the Cochin marine clay on drying are investigated. Mineralogical analysis showed the absence of halloysite in the marine specimen. Experimental results also ruled out the possibility of cementitious material being responsible for particle aggregation and reduction in clay plasticity on drying. The presence of calcium and magnesium as the predominant exchangeable ions and of a high pore salt concentration facilitates strong interparticle attraction and small particle separations; the latter leads to development of significant capillary stresses that permits an intimate contact of particles and growth of strong van der Waals' and Coulombic bonds.

Analysis,Insights and Generalization of a Fast Decentralized Relay Selection Mechanism

Relay selection for cooperative communications has attracted considerable research interest recently. While several criteria have been proposed for selecting one or more relays and analyzed, mechanisms that perform the selection in a distributed manner have received relatively less attention. In this paper, we analyze a splitting algorithm for selecting the single best relay amongst a known number of active nodes in a cooperative network. We develop new and exact asymptotic analysis for computing the average number of slots required to resolve the best relay. We then propose and analyze a new algorithm that addresses the general problem of selecting the best Q >= 1 relays. Regardless of the number of relays, the algorithm selects the best two relays within 4.406 slots and the best three within 6.491 slots, on average. Our analysis also brings out an intimate relationship between multiple access selection and multiple access control algorithms.

Chaperone expression profiles correlate with distinct physiological states of Plasmodium falciparum in malaria patients

Background: Molecular chaperones have been shown to be important in the growth of the malaria parasite Plasmodium falciparum and inhibition of chaperone function by pharmacological agents has been shown to abrogate parasite growth. A recent study has demonstrated that clinical isolates of the parasite have distinct physiological states, one of which resembles environmental stress response showing up-regulation of specific molecular chaperones. Methods: Chaperone networks operational in the distinct physiological clusters in clinical malaria parasites were constructed using cytoscape by utilizing their clinical expression profiles. Results: Molecular chaperones show distinct profiles in the previously defined physiologically distinct states. Further, expression profiles of the chaperones from different cellular compartments correlate with specific patient clusters. While cluster 1 parasites, representing a starvation response, show up-regulation of organellar chaperones, cluster 2 parasites, which resemble active growth based on glycolysis, show up-regulation of cytoplasmic chaperones. Interestingly, cytoplasmic Hsp90 and its co-chaperones, previously implicated as drug targets in malaria, cluster in the same group. Detailed analysis of chaperone expression in the patient cluster 2 reveals up-regulation of the entire Hsp90-dependent pro-survival circuitries. In addition, cluster 2 also shows up-regulation of Plasmodium export element (PEXEL)-containing Hsp40s thought to have regulatory and host remodeling roles in the infected erythrocyte. Conclusion: In all, this study demonstrates an intimate involvement of parasite-encoded chaperones, PfHsp90 in particular, in defining pathogenesis of malaria.

Over-expression and purification strategies for recombinant multi-protein oligomers: A case study of Mycobacterium tuberculosis sigma/anti-sigma factor protein complexes

The function of a protein in a cell often involves coordinated interactions with one or several regulatory partners. It is thus imperative to characterize a protein both in isolation as well as in the context of its complex with an interacting partner. High resolution structural information determined by X-ray crystallography and Nuclear Magnetic Resonance offer the best route to characterize protein complexes. These techniques, however, require highly purified and homogenous protein samples at high concentration. This requirement often presents a major hurdle for structural studies. Here we present a strategy based on co-expression and co-purification to obtain recombinant multi-protein complexes in the quantity and concentration range that can enable hitherto intractable structural projects. The feasibility of this strategy was examined using the sigma factor/anti-sigma factor protein complexes from Mycobacterium tuberculosis. The approach was successful across a wide range of sigma factors and their cognate interacting partners. It thus appears likely that the analysis of these complexes based on variations in expression constructs and procedures for the purification and characterization of these recombinant protein samples would be widely applicable for other multi-protein systems. (C) 2010 Elsevier Inc. All rights reserved.

A real transformation for modal analysis of flexible damped spacecraft

Modal approach is widely used for the analysis of dynamics of flexible structures. However, space analysts yet lack an intimate modal analysis of current spacecraft which are rich with flexibility and possess both structural and discrete damping. Mathematical modeling of such spacecraft incapacitates the existing real transformation procedure, for it cannot include discrete damping, demands uncomputable inversion of a modal matrix inaccessible due to its overwhelming size and does not permit truncation. On the other hand, complex transformation techniques entail more computational time and cannot handle structural damping. This paper presents a real transformation strategy which averts inversion of the associated real transformation matrix, allows truncation and accommodates both forms of damping simultaneously. This is accomplished by establishing a key relation between the real transformation matrix and its adjoint. The relation permits truncation of the matrices and leads to uncoupled pairs of coupled first order equations which contain a number of adjoint eigenvectors. Finally these pairs are solved to obtain a literal modal response of forced gyroscopic damped flexibile systems at arbitrary initial conditions.