The nature of the prompt X-ray and radio emission from SN 2002ap

We report on the combined X-ray and radio observations of the type Ic SN 2002ap, using XMM-Newton TOO observation of M 74 and the Giant Metrewave Radio Telescope ( GMRT). We account for the presence of a nearby source in the pre-supernova Chandra field of view in our measurements of the X-ray flux (0.3-10 KeV) 5.2 days after the explosion. The X-ray spectrum is well fitted by a power law spectrum with photon index alpha = 2.6. Our results suggest that the prompt X-ray emission originates from inverse Compton scattering of photospheric thermal emission by energetic electrons. Radio observations with the GMRT at 610 MHz (8 days after the explosion) and 1420 MHz (70 days after the explosion) are combined with the high frequency VLA observations of SN 2002ap reported by Berger et al. ( 2002), and the early radiospheric properties of SN 2002ap are compared with similar data from two other supernovae. Finally, the GMRT radio map reveals four other X-ray sources in the field of view of M 74 with radio counterparts.

Stabilizing a pulsed field emission from an array of carbon nanotubes

In this paper, we propose a new design configuration for a carbon nanotube (CNT) array based pulsed field emission device to stabilize the field emission current. In the new design, we consider a pointed height distribution of the carbon nanotube array under a diode configuration with two side gates maintained at a negative potential to obtain a highly intense beam of electrons localized at the center of the array. The randomly oriented CNTs are assumed to be grown on a metallic substrate in the form of a thin film. A model of field emission from an array of CNTs under diode configuration was proposed and validated by experiments. Despite high output, the current in such a thin film device often decays drastically. The present paper is focused on understanding this problem. The random orientation of the CNTs and the electromechanical interaction are modeled to explain the self-assembly. The degraded state of the CNTs and the electromechanical force are employed to update the orientation of the CNTs. Pulsed field emission current at the device scale is finally obtained by using the Fowler-Nordheim equation by considering a dynamic electric field across the cathode and the anode and integration of current densities over the computational cell surfaces on the anode side. Furthermore we compare the subsequent performance of the pointed array with the conventionally used random and uniform arrays and show that the proposed design outperforms the conventional designs by several orders of magnitude. Based on the developed model, numerical simulations aimed at understanding the effects of various geometric parameters and their statistical features on the device current history are reported.

Ferrocene-Conjugated L-Tryptophan Copper(II) Complexes of Phenanthroline Bases Showing DNA Photocleavage Activity and Cytotoxicity

Ferrocene-conjugated L-tryptophan (L-Trp) reduced Schiff base (Fc-TrpH) copper(II) complexes [Cu(Fc-Trp)(L)](ClO(4)) of phenanthroline bases (L), viz. 2,2'-bipyridine (bpy in 1), 1,10-phenanthroline (phen in 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq in 3), and dipyrido[3,2-a:2',3'-c]phenazine (dppz in 4), were prepared and characterized and their photocytotoxicity studied. Cationic reduced Schiff base (Ph-TrpH) complexes [Cu(Ph-Trp)(L)(H(2)O)] (ClO(4)) (L = phen in 5; dppz in 6) having the ferrocenyl moiety replaced by a phenyl group and the Zn(II) analogue (7) of complex 4 were prepared and used as control species. The crystal structures of 1 and 5 with respective square-planar CuN(3)O and square-pyramidal CuN(3)O(2) coordination geometry show significantly different core structures. Complexes 1-4 exhibit a Cu(II)-Cu(I) redox couple near -0.1 V and the Fc(+)-Fc couple at similar to 0.5 V vs SCE in DMF-0.1 M [Bu(4)(n)N] (ClO(4)) (Fc = ferrocenyl moiety). The complexes display a copper(II)-based d-d band near 600 nm and a Fc-centered band at similar to 450 nm in DMF-Tris-HCl buffer. The complexes are efficient binders to calf thymus DNA. They are synthetic chemical nucleases in the presence of thiol or H(2)O(2), forming hydroxyl radicals. The photoactive complexes are cleavers of pUC19 DNA in visible light, forming hydroxyl radicals. Complexes 2-6 show photocytotoxicity in HeLa cancer cells, giving IC(50) values of 4.7, 10.2, 1.3, 4.8, and 4.3 mu M, respectively, in visible light with the appearance of apoptotic bodies. The complexes also show photocytotoxicity in MCF-7 cancer cells. Nuclear chromatin cleavage has been observed with acridine orange/ethidium bromide (AO/EB) dual staining with complex 4 in visible light. The complexes induce caspase-independent apoptosis in the HeLa cells.

Impact of metal on the DNA photocleavage activity and cytotoxicity of ferrocenyl terpyridine 3d metal complexes

Ferrocenyl terpyridine 3d metal complexes and their analogues, viz. [M(Fc-tpy)(2)](ClO(4))(2) (1-4), [Zn(Ph-tpy)(2)](ClO(4))(2) (5) and [Zn(Fc-dpa)(2)]X(2) (X = ClO(4), 6; PF6, 6a), where M = Fe(II) in 1, Co(II) in 2, Cu(II) in 3 and Zn(II) in 4, Fc-tpy is 4'-ferrocenyl-2,2': 6', 2 `'-terpyridine, Ph-tpy is 4'-phenyl-2,2': 6', 2 `'-terpyridine and Fc-dpa is ferrocenyl-N,N-dipicolylmethanamine, are prepared and their DNA binding and photocleavage activity in visible light studied. Complexes 2, 4, 5 and 6a that are structurally characterized by X-ray crystallography show distorted octahedral geometry with the terpyridyl ligands binding to the metal in a meridional fashion, with Fc-dpa in 6a showing a facial binding mode. The Fc-tpy complexes display a charge transfer band in the visible region. The ferrocenyl (Fc) complexes show a quasi-reversible Fc(+)-Fc redox couple within 0.48 to 0.66 V vs. SCE in DMF-0.1 M TBAP. The DNA binding constants of the complexes are similar to 10(4) M(-1). Thermal denaturation and viscometric data suggest DNA surface binding through electrostatic interaction by the positively charged complexes. Barring the Cu(II) complex 3, the complexes do not show any chemical nuclease activity in the presence of glutathione. Complexes 1-4 exhibit significant plasmid DNA photocleavage activity in visible light via a photoredox pathway. Complex 5, without the Fc moiety, does not show any DNA photocleavage activity. The Zn(II) complex 4 shows a significant PDT effect in HeLa cancer cells giving an IC(50) value of 7.5 mu M in visible light, while being less toxic in the dark (IC(50) = 49 mu M).

Gyrator realisation

A new gyrator realisation is presented, which is a simplified version of a circuit published previously. Experimental results are included.

Prebreakdown Current and Sparking Potential in a Nonuniform Electric Field with a Crossed Magnetic Field

Prebreakdown currents in a coaxial cylindrical geometry in nitrogen have been measured with and without a crossed magnetic field. The range of parameters used in the investigation are 2.6 ÿ p ÿ 14.5 torr, 50 ÿ (E/p) ÿ 420 V cm-1 torr-1, and 43.0 ÿ H/p ÿ 1185 Oe torr-1 (p is the pressure, E is the electric field, and H is the magnetic field). The initial photoelectric current is obtained by allowing photons produced in an auxiliary glow discharge to strike the cathode. Ions and electrons produced in the auxiliary discharge are prevented from reaching the main gap by suitable shielding. By modifying the Rice equation for back diffusion, the measured ionization current multiplication without a crossed magnetic field is compared with the multiplication predicted by the Townsend growth equation for nonuniform electric fields. It is observed that over the range of 50 Ã�¿ (E/P)max Ã�¿ 250 [(E/P)max is the value of E/p at the central electrode of the coaxial system] measured and calculated multiplication of current agree with each other. With a crossed magnetic field the prebreakdown currents have been measured and compared with the theoretically calculated currents using the equivalent pressure concept. Agreement between the calculated and measured currents is not satisfactory, and this has been attributed more to the uncertainty in the collision frequency data available than nonuniformity of the electric field. Sparking potentials have been measured with and without a crossed magnetic field.

A new pentameric structure of rotavirus NSP4 revealed by molecular replacement

The region spanning residues 95-146 of the rotavirus nonstructural protein NSP4 from the asymptomatic human strain ST3 has been purified and crystallized and diffraction data have been collected to a resolution of 2.6 angstrom. Several attempts to solve the structure by the molecular-replacement method using the available tetrameric structures of this domain were unsuccessful despite a sequence identity of 73% to the already known structures. A more systematic approach with a dimer as the search model led to an unexpected pentameric structure using the program Phaser. The various steps involved in arriving at this molecular-replacement solution, which unravelled a case of subtle variation between different oligomeric states unknown at the time of solving the structure, are presented in this paper.

Synthesis, Reactivity Studies, Structural Aspects, and Solution Behavior of Half Sandwich Ruthenium(II) N,N `,N `'-Triarylguanidinate Complexes

[(eta(6)-C(10)H(14))RuCl(mu-Cl)](2) (eta(6)-C(10)H(14) = eta(6)-p-cymene) was subjected to a bridge-splitting reaction with N,N',N `'-triarylguanidines, (ArNH)(2)C=NAr, in toluene at ambient temperature to afford [(eta(6)-C(10)H(14))RuCl{kappa(2)(N,N')((ArN)(2)C-N(H)Ar)}] (Ar = C(6)H(4)Me-4 (1), C(6)H(4)(OMe)-2 (2), C(6)H(4)Me-2 (3), and C(6)H(3)Me(2)-2,4 (4)) in high yield with a view aimed at understanding the influence of substituent(s) on the aryl rings of the guanidine upon the solid-state structure, solution behavior, and reactivity pattern of the products. Complexes 1-3 upon reaction with NaN(3) in ethanol at ambient temperature afforded [(eta(6)-C(10)H(14))RuN(3){kappa(2)(N,N')((ArN)(2)C-N(H)Ar)}] (Ar = C(6)H(4)Me-4 (5), C(6)H(4)(OMe)-2 (6), and C(6)H(4)Me-2 (7)) in high yield. [3 + 2] cycloaddition reaction of 5-7 with RO(O)C-C C-C(O)OR (R = Et (DEAD) and Me (DMAD)) (diethylacetylenedicarboxylate, DEAD; dimethylacetylenedicarboxylate, DMAD) in CH(2)Cl(2) at ambient temperature afforded [(eta(6)-C(10)H(14))Ru{N(3)C(2)(C(O)OR)(2)}{kappa(2)(N,N')((ArN)(2) C-N(H)Ar)}center dot xH(2)O (x = 1, R = Et, Ar = C(6)H(4)Me-4 (8 center dot H(2)O); x = 0, R = Me, Ar = C(6)H(4)(OMe)-2 (9), and C(6)H(4)Me-2 (10)) in moderate yield. The molecular structures of 1-6, 8 center dot H(2)O, and 10 were determined by single crystal X-ray diffraction data. The ruthenium atom in the aforementioned complexes revealed pseudo octahedral ``three legged piano stool'' geometry. The guanidinate ligand in 2, 3, and 6 revealed syn-syn conformation and that in 4, and 10 revealed syn-anti conformation, and the conformational difference was rationalized on the basis of subtle differences in the stereochemistry of the coordinated nitrogen atoms caused by the aryl moiety in 3 and 4 or steric overload caused by the substituents around the ruthenium atom in 10. The bonding pattern of the CN(3) unit of the guanidinate ligand in the new complexes was explained by invoking n-pi conjugation involving the interaction of the NHAr/N(coord)Ar lone pair with C=N pi* orbital of the imine unit. Complexes 1, 2, 5, 6, 8 center dot H(2)O, and 9 were shown to exist as a single isomer in solution as revealed by NMR data, and this was ascribed to a fast C-N(H)Ar bond rotation caused by a less bulky aryl moiety in these complexes. In contrast, 3 and 10 were shown to exist as a mixture of three and five isomers in about 1:1:1 and 1.0:1.2:2:7:3.5:6.9 ratios, respectively in solution as revealed by a VT (1)H NMR, (1)H-(1)H COSY in conjunction with DEPT-90 (13)C NMR data measured at 233 K in the case of 3. The multiple number of isomers in solution was ascribed to the restricted C-N(H)(o-tolyl) bond rotation caused by the bulky o-tolyl substituent in 3 or the aforementioned restricted C-NH(o-tolyl) bond rotation as well as the restricted ruthenium-arene(centroid) bond rotation caused by the substituents around the ruthenium atom in 10.

Structure of DNA-functionalized dendrimer nanoparticles

Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated (corresponding to neutral pH) poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single strand DNAs (ssDNAs). The four ssDNA strands that are attached via an alkythiolate [-S(CH(2))(6)-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers are observed to undergo a rapid conformational change during the 25 ns long simulation period. From the RMSD values of ssDNAs, we find relative stability in the case of purine rich (having more adenine and guanine) ssDNA strands than pyrimidine rich (thymine and cytosine) ssDNA strands. The degree of wrapping of ssDNA strands on the dendrimer molecule was found to be influenced by the charge ratio of DNA and the dendrimer. As the G4 dendrimer contains relatively more positive charge than G3 dendrimer, we observe extensive wrapping of ssDNAs on the G4 dendrimer than G3 dendrimer. This might indicate that DNA functionalized G3 dendrimer is more suitable to construct higher order nanostructures. The linker molecule was also found to undergo drastic conformational change during the simulation. During nanosecond long simulation some portion of the linker molecule was found to be lying nearly flat on the surface of the dendrimer molecule. The ssDNA strands along with the linkers are seen to penetrate the surface of the dendrimer molecule and approach closer to the center of the dendrimer indicating the soft sphere nature of the dendrimer molecule. The effective radius of DNA-functionalized dendrimer nanoparticles was found to be independent of base composition of ssDNAs and was observed to be around 19.5 angstrom and 22.4 angstrom when we used G3 and G4 PAMAM dendrimers as the core of the nanoparticle respectively. The observed effective radius of DNA-functionalized dendrimer molecules apparently indicates the significant shrinkage in the structure that has taken place in dendrimer, linker and DNA strands. As a whole our results describe the characteristic features of DNA-functionalized dendrimer nanoparticles and can be used as strong inputs to design effectively the DNA-dendrimer nanoparticle self-assembly for their active biological applications.

Chain Length Effects on Helix-Hairpin Distribution in Short Peptides with Aib-(D)Ala and Aib-Aib Segments

The Aib-(D)Ala dipeptide segment has a tendency to form both type-I'/III' and type-I/III beta-turns. The occurrence of prime turns facilitates the formation of beta-hairpin conformations, while type-I/III turns can nucleate helix formation. The octapeptide Boc-Leu-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-OMe (1) has been previously shown to form a beta-hairpin in the crystalline state and in solution. The effects of sequence truncation have been examined using the model peptides Boc-Phe-Val-Aib-Xxx-Leu-Phe-NHMe (2, 6), Boc-Val-Aib-Xxx-Leu-NHMe (3, 7), and Boc-Aib-Xxx-NHMe (4, 8), where Xxx = (D)Ala, Aib. For peptides with central Aib-Aib segments, Boc-Phe-Val-Aib-Aib-Leu-Phe-NHMe (6), Boc-Val-Aib-Aib-Leu-NHMe (7), and Boc-Aib-Aib-NHMe (8) helical conformations have been established by NMR studies in both hydrogen bonding (CD(3)OH) and non-hydrogen bonding (CDCl(3)) solvents. In contrast, the corresponding hexapeptide Boc-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-NHMe (2) favors helical conformations in CDCl(3) and beta-hairpin conformations in CD(3)OH. The beta-turn conformations (type-I'/III) stabilized by intramolecular 4 -> 1 hydrogen bonds are observed for the peptide Boc-Aib-(D)Ala-NHMe (4) and Boc-Aib-Aib-NIiMe (8) in crystals. The tetrapeptide Boc-Val-Aib-Aib-Leu-NHMe (7) adopts an incipient 3(10)-helical conformation stabilized by three 4 -> 1 hydrogen bonds. The peptide Boc-Val-Aib-(D)Ala-Leu-NHMe (3) adopts a novel et-turn conformation, stabilized by three intramolecular hydrogen bonds (two 4 -> 1 and one 5 -> 1). The Aib-L(D)Ala segment adopts a type-I' beta-turn conformation. The observation of an NOE between Val (1) NH <-> HNCH(3) (5) in CD(3)OH suggests, that the solid state conformation is maintained in methanol solutions. (C) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 744-756, 2011.

Ferrocene-Conjugated Oxidovanadium(IV) Complexes as Potent Near-IR Light Photocytotoxic Agents

Ferrocene-conjugated oxidovanadium(IV) complexes [VO(Fc-tpy)(B)](ClO4)(2) (1-4) and [VO(Ph-tpy)(dppz)](ClO4)(2) (5) as a control [Fc = (eta(5)-C5H4)Fe-II(eta(5)-C5H5), Fc-tpy = 4'-ferrocenyl-2,2':6',2 `'-terpyridine, Ph-tpy = 4'-phenyl-2,2':6',2 `'-terpyridine, B = heterocyclic base: 2,2'-bipyridine (bpy in 1), 1,10-phenanthroline (phen in 2), dipyridoquinoxaline (dpq in 3), dipyridophenazine (dppz in 4)] were prepared and their DNA binding, DNA photocleavage activity and photocytotoxicity studied. The crystal structure of [VO(Fc-tpy)(bpy)](PF6)(2)center dot 3Me(2)CO shows a vanadyl group in six-coordinate (VON5)-O-IV coordination geometry, in which Fc-tpy and bpy display tridentate meridional and bidentate N-donor axial-equatorial binding modes, respectively. The one-electron paramagnetic complexes exhibit a charge-transfer band near 590 nm in DMF. The V-IV/V-III redox couple in 1-4 appears near -0.7 V, whereas the Fc moiety shows a response near 0.6 V vs. SCE in DMF/0.1 M TBAP. The complexes are good binders to calf thymus DNA with K-b values of 10(4)-10(6) M-1. DNA melting and viscometric data suggest groove and/or partial intercalative DNA binding of the complexes. Complexes 3-5 display DNA photocleavage activity in nearIR light of 785 nm. Complex 4 shows significant photocytotoxicity in visible light (400-700 nm) in HeLa cells with low dark toxicity.

Photoactivated DNA cleavage and anticancer activity of pyrenyl-terpyridine lanthanide complexes

Lanthanide(III) complexes Ln(R-tpy)(acac)(NO3)(2)] (Ln = La(III) in 1, 2; Gd(III) in 4, 5) and Ln(py-tpy)(sacac)(NO3)(2)] (Ln = La(III), Gd(III), 6), where R-tpy is 4'-phenyl-2,2':6',2 `'-terpyridine (ph-tpy in 1, 4), 4'-(1-pyrenyl)-2,2':6',2 `'-terpyridine (py-tpy in 2, 3, 5 and 6), acac is acetylacetonate and sacac is 4-hydroxy-6-{4-(beta-D-glucopyranoside)oxy]phenyl}hex-3,5-dien-2-on ate, were prepared to study their DNA photocleavage activity and photocytotoxicity. Complexes La(ph-tpy)(acac)(E-tOH)(NO3)(2)] (1a) and Gd(ph-tpy)(acac)(NO3)(2)] (4) were characterized by X-ray crystallography. The 1:1 electrolytic complexes bind to calf thymus DNA. The py-tpy complexes cleave pUC19 DNA and exhibit remarkable photocytotoxicity in HeLa cells in UV-A light of 365 nm with apoptotic cell death (IC50: similar to 40 nM in light, >200 mu M in dark). Confocal microscopy using HeLa cells reveal primarily cytosolic localization of the complexes. (C) 2012 Elsevier Masson SAS. All rights reserved.

Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase

Salmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. It also efficiently degrades beta-chloro-D-alanine (beta CDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, beta CDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 angstrom. The polypeptide fold of StDCyD consisting of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and beta CDA show the product, pyruvate, bound at a site 4.0-6.0 angstrom away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at C alpha proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for C alpha proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed.

A Raman study of the interaction of electron-donor and -acceptor molecules with chemically doped graphene

Effect of interaction of tetracyanoethylene (TCNE) and tetrathia fulvalene (TTF) with boron- and nitrogen-doped graphene has been investigated by Raman spectroscopy. The G- and 2D bands of boron- and nitrogen-doped graphenes in the Raman spectra show significantly different changes on interaction with electron-donor and -acceptor molecules. Thus, tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF) have different effects on the Raman spectra of boron- and nitrogen-doped graphenes. The changes in the Raman spectra brought about by electron-donor and -acceptor molecules can be understood in general terms on the basis of molecular charge transfer. (c) 2012 Elsevier B.V. All rights reserved.

Stochastic Simulations Suggest that HIV-1 Survives Close to Its Error Threshold

The use of mutagenic drugs to drive HIV-1 past its error threshold presents a novel intervention strategy, as suggested by the quasispecies theory, that may be less susceptible to failure via viral mutation-induced emergence of drug resistance than current strategies. The error threshold of HIV-1, mu(c), however, is not known. Application of the quasispecies theory to determine mu(c) poses significant challenges: Whereas the quasispecies theory considers the asexual reproduction of an infinitely large population of haploid individuals, HIV-1 is diploid, undergoes recombination, and is estimated to have a small effective population size in vivo. We performed population genetics-based stochastic simulations of the within-host evolution of HIV-1 and estimated the structure of the HIV-1 quasispecies and mu(c). We found that with small mutation rates, the quasispecies was dominated by genomes with few mutations. Upon increasing the mutation rate, a sharp error catastrophe occurred where the quasispecies became delocalized in sequence space. Using parameter values that quantitatively captured data of viral diversification in HIV-1 patients, we estimated mu(c) to be 7 x 10(-5) -1 x 10(-4) substitutions/site/replication, similar to 2-6 fold higher than the natural mutation rate of HIV-1, suggesting that HIV-1 survives close to its error threshold and may be readily susceptible to mutagenic drugs. The latter estimate was weakly dependent on the within-host effective population size of HIV-1. With large population sizes and in the absence of recombination, our simulations converged to the quasispecies theory, bridging the gap between quasispecies theory and population genetics-based approaches to describing HIV-1 evolution. Further, mu(c) increased with the recombination rate, rendering HIV-1 less susceptible to error catastrophe, thus elucidating an added benefit of recombination to HIV-1. Our estimate of mu(c) may serve as a quantitative guideline for the use of mutagenic drugs against HIV-1.