Biomimetic modeling of the nitrogen-centered radical postulated to occur during the inhibition of ribonucleotide reductases by 2'-azido-2'-deoxynucleotides

Ribonucleotide reductases (RNR) are essential enzymes that catalyze the reduction of ribonucleotides to 2'-deoxyribonucleotides, which is a critical step that produces precursors for DNA replication and repair. The inactivation of RNR, logically, would discontinue producing the precursors of the DNA of viral or cancer cells, which then would consequently end the cycle of DNA replication. Among different compounds that were found to be inhibitors of RNR, 2'-azido-2'-deoxynucleotide diphosphates (N3NDPs) have been investigated in depth as potent inhibitors of RNR. Decades of investigation has suggested that the inactivation of RNR by N3NDPs is a result of the formation of a nitrogen-centered radical (N·) that is covalently attached to the nucleotide at C3' and cysteine molecule C225 [3'-C(R-S-N·-C-OH)]. Biomimetic simulation reactions for the generation of the nitrogen-centered radicals similar to the one observed during the inactivation of the RNR by azionuclotides was investigated. The study included several modes: (i) theoretical calculation that showed the feasibility of the ring closure reaction between thiyl radicals and azido group; (ii) synthesis of the model azido nucleosides with a linker attached to C3' or C5' having a thiol or vicinal dithiol functionality; (iii) generation of the thiyl radical under both physiological and radiolysis conditions whose role is important in the initiation on RNR cascades; and (iv) analysis of the nitrogen-centered radical species formed during interaction between the thiyl radical and azido group by electron paramagnetic resonance spectroscopy (EPR). Characterization of the aminyl radical species formed during one electron attachment to the azido group of 2'-azido-2'-deoxyuridine and its stereospecifically labelled 1'-, 2'-, 3'-, 4'- or 5,6-[2H 2]-analogues was also examined. This dissertation gave insight toward understanding the mechanism of the formation of the nitrogen-centered radical during the inactivation of RNRs by azidonucleotides as well as the mechanism of action of RNRs that might provide key information necessary for the development of the next generation of antiviral and anticancer drugs.

Charge compensation and Ce3+ formation in trivalent doping of the CeO2(110) surface: The key role of dopant ionic radius

In this paper, we use density functional theory corrected for on-site Coulomb interactions (DFT + U) and hybrid DFT (HSE06 functional) to study the defects formed when the ceria (110) surface is doped with a series of trivalent dopants, namely, Al3+, Sc3+, Y3+, and In 3+. Using the hybrid DFT HSE06 exchange-correlation functional as a benchmark, we show that doping the (110) surface with a single trivalent ion leads to formation of a localized MCe / + O O • (M = the 3+ dopant), O- hole state, confirming the description found with DFT + U. We use DFT + U to investigate the energetics of dopant compensation through formation of the 2MCe ′ +VO ̈ defect, that is, compensation of two dopants with an oxygen vacancy. In conjunction with earlier work on La-doped CeO2, we find that the stability of the compensating anion vacancy depends on the dopant ionic radius. For Al3+, which has the smallest ionic radius, and Sc3+ and In3+, with intermediate ionic radii, formation of a compensating oxygen vacancy is stable. On the other hand, the Y3+ dopant, with an ionic radius close to that of Ce4+, shows a positive anion vacancy formation energy, as does La3+, which is larger than Ce4+ (J. Phys.: Condens. Matter 2010, 20, 135004). When considering the resulting electronic structure, in Al3+ doping, oxygen hole compensation is found. However, Sc 3+, In3+, and Y3+ show the formation of a reduced Ce3+ cation and an uncompensated oxygen hole, similar to La3+. These results suggest that the ionic radius of trivalent dopants strongly influences the final defect formed when doping ceria with 3+ cations. In light of these findings, experimental investigations of these systems will be welcome.

Morpho-Anatomical Analysis of the Rhizome in Species of Scleria Berg. (Cyperaceae) from Serra do Cipó (MG)

Aspects related to the nature of stem thickening in monocotyledons have been the subject of many studies. Primary thickening has been attributed to the Primary Thickening Meristem (PTM). According to most authors, it gives rise, besides the adventitious roots, to the vascular tissues and part of the cortex. In other words, it has centripetal and centrifugal activity. For some authors, however, it gives rise only to the vascular system, and for others, only to part of the cortex. However, this work demonstrated that PTM corresponds to the pericycle in the meristematic phase or to the pericycle associated with the endodermis, also with meristematic activity. It was observed that the pericycle was responsible for the formation of the vascular system of the rhizome and of the adventitious roots; the endodermis gave rise to cell layers with radial disposition which comprised the inner portion of the stem cortex, and which corresponded to the region known as the derivatives of the meristematic endodermis (DME). A continuity was also demonstrated between the tissues of the stem and root in species of Scleria Berg. (Cyperaceae).

Insights on the Milky Way bulge formation from the correlations between kinematics and metallicity

Context. Two main scenarios for the formation of the Galactic bulge are invoked, the first one through gravitational collapse or hierarchical merging of subclumps, the second through secular evolution of the Galactic disc. Aims. We aim to constrain the formation of the Galactic bulge through studies of the correlation between kinematics and metallicities in Baade's Window (l = 1 degrees, b = -4 degrees) and two other fields along the bulge minor axis (l = 0 degrees, b = -6 degrees and b = -12 degrees). Methods. We combine the radial velocity and the [Fe/H] measurements obtained with FLAMES/GIRAFFE at the VLT with a spectral resolution of R = 20 000, plus for the Baade's Window field the OGLE-II proper motions, and compare these with published N-body simulations of the Galactic bulge. Results. We confirm the presence of two distinct populations in Baade's Window found in Hill et al. (2010, A&A, submitted): the metal-rich population presents bar-like kinematics while the metal-poor population shows kinematics corresponding to an old spheroid or a thick disc. In this context the metallicity gradient along the bulge minor axis observed by Zoccali et al. (2008, A&A, 486, 177), visible also in the kinematics, can be related to a varying mix of these two populations as one moves away from the Galactic plane, alleviating the apparent contradiction between the kinematic evidence of a bar and the existence of a metallicity gradient. Conclusions. We show evidence that the two main scenarios for the bulge formation co-exist within the Milky Way bulge.

Study of the influence of indium segregation on the optical properties of InGaAs/GaAs quantum wells via split-operator method

In the case of quantum wells, the indium segregation leads to complex potential profiles that are hardly considered in the majority of the theoretical models. The authors demonstrated that the split-operator method is useful tool for obtaining the electronic properties in these cases. Particularly, they studied the influence of the indium surface segregation in optical properties of InGaAs/GaAs quantum wells. Photoluminescence measurements were carried out for a set of InGaAs/GaAs quantum wells and compared to the results obtained theoretically via split-operator method, showing a good agreement.

Formation of atomic carbon chains from graphene nanoribbons

The formation of one-dimensional carbon chains from graphene nanoribbons is investigated using ab initio molecular dynamics. We show under what conditions it is possible to obtain a linear atomic chain via pulling of the graphene nanoribbons. The presence of dimers composed of two-coordinated carbon atoms at the edge of the ribbons is necessary for the formation of the linear chains, otherwise there is simply the full rupture of the structure. The presence of Stone-Wales defects close to these dimers may lead to the formation of longer chains. The local atomic configuration of the suspended atoms indicates the formation of single and triple bonds, which is a characteristic of polyynes.

Obtaining and stability verification of superconducting phases of the Nb-Al and Nb-Sn systems by mechanical alloying and low-temperature heat treatments

The development of Nb(3)Al and Nb(3)Sn superconductors is of great interest for the applied superconductivity area. These intermetallics composites are obtained normally by heat treatment reactions at high temperature. Processes that allow formation of the superconducting phases at lower temperatures (<1000 degrees C), particularly for Nb(3)Al, are of great interest. The present work studies phase formation and stability of Nb(3)Al and Nb(3)Sn superconducting phases using mechanical alloying (high energy ball milling). Our main objective was to form composites near stoichiometry, which could be transformed into the superconducting phases using low-temperature heat treatments. High purity Nb-Sn and Nb-Al powders were mixed to generate the required superconducting phases (Nb-25at.%Sn and Nb-25at.%Al) in an argon atmosphere glove-box. After milling in a Fritsch mill, the samples were compressed in a hydraulic uniaxial press and encapsulated in evacuated quartz tubes for heat treatment. The compressed and heat treated samples were characterized using X-ray diffractometry. Microstructure and chemical analysis were accomplished using scanning electron microscopy and energy dispersive spectrometry. Nb(3)Al XRD peaks were observed after the sintering at 800 degrees C for the sample milled for 30 h. Nb(3)Sn XRD peaks could be observed even before the heat treatment. (C) 2009 Elsevier B.V. All rights reserved.

Deterministic mathematical model for the prediction of the as-cast macrostructure

A multiphase deterministic mathematical model was implemented to predict the formation of the grain macrostructure during unidirectional solidification. The model consists of macroscopic equations of energy, mass, and species conservation coupled with dendritic growth models. A grain nucleation model based on a Gaussian distribution of nucleation undercoolings was also adopted. At some solidification conditions, the cooling curves calculated with the model showed oscillations (""wiggles""), which prevented the correct prediction of the average grain size along the structure. Numerous simulations were carried out at nucleation conditions where the oscillations are absent, enabling an assessment of the effect of the heat transfer coefficient on the average grain size and columnar-to-equiaxed transition.

Photoinduced Degradation of the Herbicide Clomazone Model Reactions for Natural and Technical Systems

The photodegradation of the herbicide clomazone in the presence of S(2)O(8)(2-) or of humic substances of different origin was investigated. A value of (9.4 +/- 0.4) x 10(8) m(-1) s(-1) was measured for the bimolecular rate constant for the reaction of sulfate radicals with clomazone in flash-photolysis experiments. Steady state photolysis of peroxydisulfate, leading to the formation of the sulfate radicals, in the presence of clomazone was shown to be an efficient photodegradation method of the herbicide. This is a relevant result regarding the in situ chemical oxidation procedures involving peroxydisulfate as the oxidant. The main reaction products are 2-chlorobenzylalcohol and 2-chlorobenzaldehyde. The degradation kinetics of clomazone was also studied under steady state conditions induced by photolysis of Aldrich humic acid or a vermicompost extract (VCE). The results indicate that singlet oxygen is the main species responsible for clomazone degradation. The quantum yield of O(2)(a(1)Delta(g)) generation (lambda = 400 nm) for the VCE in D(2)O, Phi(Delta) = (1.3 +/- 0.1) x 10(-3), was determined by measuring the O(2)(a(1)Delta(g)) phosphorescence at 1270 nm. The value of the overall quenching constant of O(2)(a(1)Delta(g)) by clomazone was found to be (5.7 +/- 0.3) x 10(7) m(-1) s(-1) in D(2)O. The bimolecular rate constant for the reaction of clomazone with singlet oxygen was k(r) = (5.4 +/- 0.1) x 10(7) m(-1) s(-1), which means that the quenching process is mainly reactive.

An ESR and NMR study of the gamma radiolysis of a bisphenol-A based polycarbonate and a phthalic acid ester

A study of the gamma-radiolysis of the commercial polymers U-polymer, UP (Unitake) and polycarbonate, PC, (Aldrich) has been undertaken using ESR spectroscopy. The G-value of radical formation at 77 K has been found to be 0.31 +/- 0.01 for UP and 0.5 +/- 0.02 for PC. By using thermal annealing and spectral subtraction, the paramagnetic species formed on irradiation has been assigned. The effect of radiation on the chemical structure of UP and PC has been investigated at ambient temperature and at 423 K. The NMR results show that a new phenol type chain end is formed in the polymers on exposure to gamma-radiation. The G-value of formation of the new phenol ends was estimated to be 0.7 for PC (423 K) and 0.4 for UP (300 K). (C) 1998 John Wiley & Sons, Ltd.

Chemical synthesis and folding pathways of large cyclic polypeptide: Studies of the cystine knot polypeptide kalata B1

Kalata B1 is a member of a new family of polypeptides, isolated from. plants, which have a cystine knot structure embedded within an amide-cyclized backbone. This family of molecules are the largest known cyclic peptides, and thus, the mechanism of synthesis and folding is of great interest. To provide information about both these phenomena, we have synthesized kalata B1 using two distinct strategies. In the first, oxidation of the cysteine residues of a linear precursor peptide to form the correct disulfide bonds results in folding of the three-dimensional structure and preorganization of the termini in close proximity for subsequent cyclization. The second approach involved cyclization prior to oxidation. In the first method, the correctly folded peptide was produced only in the presence of partially hydrophobic solvent conditions. These conditions are presumably required to stabilize the surface-exposed hydrophobic residues. However,; in the synthesis,involving cyclization prior to oxidation, the cyclic reduced peptide folded to a significant degree in the absence of hydrophobic solvents and even more efficiently in the presence of hydrophobic solvents. Cyclization clearly has a major effect on the folding pathway and facilitates formation of the correctly disulfide-bonded form in aqueous solution; In addition to facilitating folding to a compact stable structure cyclization has an important effect on biological activity as assessed by hemolytic activity.

Regulation by the exogenous polyamine spermidine of Na,K-ATPase activity from the gills of the euryhaline swimming crab Callinectes danae (Brachyura, Portunidae)

Euryhaline crustaceans rarely hyporegulates and employ the driving force of the Na,K-ATPase, located at the basal surface of the gill epithelium, to maintain their hemolymph osmolality within a range compatible with cell function during hyper-regulation. Since polyamine levels increase during the adaptation of crustaceans to hyperosmotic media, we investigate the effect of exogenous polyamines on Na,K-ATPase activity in the posterior gills of Callinectes danae, a euryhaline swimming crab. Polyamine inhibition was dependent on cation concentration, charge and size in the following order: spermine > spermidine > putrescine. Spermidine affected K-0.5 values for Na+ with minor alterations in K-0.5 values for K+ and N-H-4(+), causing a decrease in maximal velocities under saturating Na+, K+ and NH4+ concentrations. Phosphorylation measurements in the presence of 20 mu M ATP revealed that the Na,K-ATPase possesses a high affinity site for this substrate. In the presence of 10 mM Na+, both spermidine and spermine inhibited formation of the phosphoenzyme; however, in the presence of 100 mM Na+, the addition of these polyamines allowed accumulation of the phosphoenzyme. The polyamines inhibited pumping activity, both by competing with Na+ at the Na+-binding site, and by inhibiting enzyme dephosphorylation. These findings suggest that polyamine-induced inhibition of Na,K-ATPase activity may be physiologically relevant during migration to fully marine environments. (c) 2008 Elsevier Inc. All rights reserved.

H-1 NMR spectroscopic studies of the stability of an oxazolidine condensation product

Condensation of (-)-norephedrine with excess formaldehyde under mild conditions leads to formation of the 2:1 condensation product N,N'-methylenebis(4-methyl-5-phenyl)oxazolidine compared with the reaction with 1 mol of formaldehyde, which leads to 4-methyl-5-phenyloxazolidine. H-1 and C-13 NMR spectroscopy was used to monitor the stability of this compound and its decomposition products. The 2:1 condensation product is found to be stable in CDC1(3) but breaks down rapidly in CD3OD to yield a 50:50 mixture of 4-methyl-5-phenyloxazolidine and 3-hydroxymethyl-4-methyl-5-phenyloxazolidine. Upon addition of D2O to this equimolar mixture, the latter compound decomposes to norephedrine and formaldehyde, whereas the former compound is stable. (C) 1997 by John Wiley & Sons, Ltd.

An investigation of the microstructure/electrical conductivity relationship in In2O3-substituted LSGM

The effect of controlled In3+ substitution on to the B-site in the perovskite oxygen ion conductor La0.9Sr0.1Ga0.8Mg0.2O2.85 (LSGM) has been examined with a view to exploring the influence on oxygen ion conductivity. In combination with the electrical conductivity study, detailed microstructural analysis was used to verify the location of the substituting cation and to determine the nature of secondary phase formation. The indium species clearly substituted for Ga3+ on the B-site of the lattice and the electrical conductivity showed a gradual decrease as the In+3 content increased. The interpretation of this data was complicated by the formation of the secondary phases LaInO3 and LaSrGaO4. (C) 2001 Elsevier Science Ltd. All rights reserved.

Visualising the activity of the cystine-glutamate antiporter in glial cells using antibodies to aminoadipic acid, a selectively transported substrate

The cystine-glutamate antiporter is a transport system that facilitates the uptake of cystine, concomitant with the release of glutamate. The cystine accumulated by this transporter is generally considered for use in the formation of the cysteine-containing antioxidant glutathione, which is abundant in many glial cells. This study used the simple strategy of generating an antibody to aminoadipic acid, a selective substrate for the cystine-glutamate antiporter. Stereospecific accumulation of aminoadipic acid into specific cell types in rat brain slice preparations was detected immunocytochemically. Strong accumulation was detected in astroglial cells in all brain regions studied including those in white matter tracts. Strong accumulation into radial glial cells, including the retinal Muller cells and the Bergmann glial cells was also observed. Glial accumulation was observed not only in cells within the blood brain barrier, but also outside such; anterior pituitary folliculostellate cell and intermediate lobe pituitary glial cells exhibited strong accumulation of aminoadipic acid. Interestingly, some glial cells such as the posterior pituitary glial cells (pituicytes) exhibited very little if any accumulation of aminoadipic acid. Within the brain labelling was not uniform. Particularly strong labelling was noted in some regions, such as the glial cells surrounding the CA1 pyramidal cells. By contrast, neurons never exhibited uptake of aminoadipic acid. Because cystine uptake is associated with glutamate release, it is suggested that this antiporter might contribute to release of glutamate from glial cells under some pathophysiological conditions. (C) 2001 Wiley-Liss, Inc.