Four-level systems and a universal quantum gate

We discuss the possibility of implementing a universal quantum XOR gate by using two coupled quantum dots subject to external magnetic fields that are parallel and slightly different. We consider this system in two different field configurations. In the first case, parallel external fields with the intensity difference at each spin being proportional to the time-dependent interaction between the spins. A general exact solution describing this system is presented and analyzed to adjust field parameters. Then we consider parallel fields with intensity difference at each spin being constant and the interaction between the spins switching on and off adiabatically. In both cases we adjust characteristics of the external fields (their intensities and duration) in order to have the parallel pulse adequate for constructing the XOR gate. In order to provide a complete theoretical description of all the cases, we derive relations between the spin interaction, the inter-dot distance, and the external field. (C) 2008 WILEYNCH Verlag GmbH & Co. KGaA. Weinheim.

Taxonomic and Phylogenetic Relationships Between Species of the Genus Culex (Diptera: Culicidae) From Brazil Inferred From the Cytochrome c Oxidase I Mitochondrial Gene

Species of the genus Culex Linnaeus have been incriminated as the main vectors of lymphatic filariases and are important vectors of arboviruses, including West Nile virus. Sequences corresponding to a fragment of 478 bp of the cytochrome c oxidase subunit I gene, which includes part of the barcode region, of 37 individuals of 17 species of genus Culex were generated to establish relationships among five subgenera, Culex, Phenacomyia, Melanoconion, Microculex, and Carrollia, and one species of the genus Lutzia that occurs in Brazil. Bayesian methods were employed for the phylogenetic analyses. Results of sequence comparisons showed that individuals identified as Culex dolosus, Culex mollis, and Culex imitator possess high intraspecific divergence (3.1, 2.3, and 3.5%, respectively) when using the Kimura two parameters model. These differences were associated either with distinct morphological characteristics of the male genitalia or larval and pupal stages, suggesting that these may represent species complexes. The Bayesian topology suggested that the genus and subgenus Culex are paraphyletic relative to Lutzia and Phenacomyia, respectively. The cytochrome c oxidase subunit I sequences may be a useful tool to both estimate phylogenetic relationships and identify morphologically similar species of the genus Culex.

Cytochrome-b variation in Apis mellifera samples and its association with COI-COII patterns

Five Mbo I (Mbo-A, Mbo-M, Mbo-C(1), Mbo-C(2) and Mbo-C(3)) and Hinf I (Hinf-1 to Hinf-5) patterns were observed in Apis mellifera samples after restriction of a 485 bp fragment of the mitochondrial cytochrome-b (cyt-b) gene. Associating the cyt-b Restriction fragment length polymorphism (RFLP) pattern of each sample to its respective previously established COI-COII (Dra I sites) pattern, five restriction patterns (Mbo-C(1), Mbo-C(2), Mbo-C(3), Hinf-1 and Hinf-4) were observed in samples of maternal origin associated to the evolutionary branch C. No deletions or insertions were observed and the nucleotide substitution rate was estimated at 5.4%. Higher nucleotide diversity was observed among the branch C-haplotypes when compared with A and M lineages. Further studies are needed to confirm if the cyt-b + COI-COII haplotypes help to assign certain phylogeographic patterns to the branch C and to clarify phylogenetic relationships among A. mellifera subspecies.

A new genotype of Trypanosoma cruzi associated with bats evidenced by phylogenetic analyses using SSU rDNA, cytochrome b and Histone H2B genes and genotyping based on ITS1 rDNA

We characterized 15 Trypanosoma cruzi isolates from bats captured in the Amazon, Central and Southeast Brazilian regions. Phylogenetic relationships among T. cruzi lineages using SSU rDNA, cytochrome b, and Histone H2B genes positioned all Amazonian isolates into T. cruzi I (TCI). However, bat isolates from the other regions, which had been genotyped as T. cruzi II (TC II) by the traditional genotyping method based on mini-exon gene employed in this study, Were not nested within any of the previously defined TCII sublineages, constituting a new genotype designated as TCbat. Phylogenetic analyses demonstrated that TCbat indeed belongs to T. cruzi and not to other closely related bat trypanosomes of the subgenus Schizotrypanum, and that although separated by large genetic distances TO-tat is closest to lineage TCI. A genotyping method targeting ITS1 rDNA distinguished TCbat from established T. cruzi lineages, and from other Schizotrypanum species. In experimentally infected mice, TCbat lacked virulence and yielded loss parasitaemias. Isolates of TCbat presented distinctive morphological features and behaviour in triatomines. To date, TCbat genotype wall found only in bats from anthropic environments of Central and Southeast Brazil. Our findings indicate that the complexity of T. cruzi is larger than currently known, and confirmed bats as important reservoirs and potential source of T. cruzi infections to humans.

Excited-state absorption spectroscopy in oxidized Cytochrome c

This work reports on the excited-state absorption spectrum of oxidized Cytochrome c (Fe(3+)) dissolved in water, measured with the Z-scan technique with femtosecond laser pulses. The excited-state absorption cross-sections between 460 and 560 nm were determined with the aid of a three-energy-level model. Reverse saturable absorption was observed below 520 nm, while a saturable absorption process occurs in the Q-band, located around 530 nm. Above 560 nm, a competition between saturable absorption and two-photon absorption was inferred. These results show that Cytochrome c presents distinct nonlinear behaviors, which may be useful to study electron transfer chemistry in proteins by one- and two-photon absorption. In addition, owing to these nonlinear optical features, this molecule may be employed in applications involving photodynamics therapy and saturable absorbers. (C) 2009 Elsevier B.V. All rights reserved.

P-T-Fluid evolution and graphite deposition during retrograde metamorphism in Ribeira Fold Belt, SE Brazil: Oxygen fugacity, fluid inclusions and C-O-H isotopic evidence

Combined fluid inclusion (FI) microthermometry, Raman spectroscopy, X-ray diffraction, C-O-H isotopes and oxygen fugacities of granulites from central Ribeira Fold Belt, SE Brazil, provided the following results: i) Magnetite-Hematite fO(2) estimates range from 10(-11.5) bar (QFM + 1) to 10(-18.3) bar (QFM - 1) for the temperature range of 896 degrees C-656 degrees C, implying fO(2) decrease from metamorphic peak temperatures to retrograde conditions; ii) 5 main types of fluid inclusions were observed: a) CO(2) and CO(2)-N(2) (0-11 mol%) high to medium density (1.01-0.59 g/cm(3)) FI; b) CO(2) and CO(2)-N(2) (0-36 mol%) low density (0.19-0.29 g/cm(3)) FI; c) CO(2) (94-95 mol%)-N(2) (3 mol%)-CH(4) (2-3 mol%)-H(2)O (water phi(v) (25 degrees C) = 0.1) FI; d) low-salinity H(2)O-CO(2) FI; and e) late low-salinity H(2)O FI; iii) Raman analyses evidence two graphite types in khondalites: an early highly ordered graphite (T similar to 450 degrees C) overgrown by a disordered kind (T similar to 330 degrees C); iv) delta(18)O quartz results of 10.3-10.7 parts per thousand, imply high-temperature CO(2) delta(18)O values of 14.4-14.8 parts per thousand, suggesting the involvement of a metamorphic fluid, whereas lower temperature biotite delta(18)O and delta D results of 7.5-8.5 parts per thousand and -54 to -67 parts per thousand respectively imply H(2)O delta(18)O values of 10-11 parts per thousand and delta D(H2O) of -23 to -36 parts per thousand suggesting delta(18)O depletion and increasing fluid/rock ratio from metamorphic peak to retrograde conditions. Isotopic results are compatible with low-temperature H(2)O influx and fO(2) decrease that promoted graphite deposition in retrograde granulites, simultaneous with low density CO(2), CO(2)-N(2) and CO(2)-N(2)-CH(4)-H(2)O fluid inclusions at T = 450-330 degrees C. Graphite delta(13)C results of -10.9 to -11.4 parts per thousand imply CO(2) delta(13)C values of -0.8 to -1.3 parts per thousand suggesting decarbonation of Cambrian marine carbonates with small admixture of lighter biogenic or mantle derived fluids. Based on these results, it is suggested that metamorphic fluids from the central segment of Ribeira Fold Belt evolved to CO(2)-N(2) fluids during granulitic metamorphism at high fO(2), followed by rapid pressure drop at T similar to 400-450 degrees C during late exhumation that caused fO(2) reduction induced by temperature decrease and water influx, turning carbonic fluids into CO(2)-H(2)O (depleting biotite delta(18)O and delta D values), and progressively into H(2)O. When fO(2) decreased substantially by mixture of carbonic and aqueous fluids, graphite deposited forming khondalites. (C) 2010 Elsevier Ltd. All rights reserved.

Superoxide radical protects liposome-contained cytochrome c against oxidative damage promoted by peroxynitrite and free radicals

The effects of nitrosative species on cyt c structure and peroxidase activity were investigated here in the presence of O(2)(center dot-) and anionic and zwitterionic vesicles. Nitrosative species were generated by 3-morpholinesydnonymine (SIN1) decomposition, using cyt c heme iron and/or molecular oxygen as electron acceptor. Far-and near-UV CD spectra of SIN1-treated cyt c revealed respectively a slight decrease of a-helix content (from 39 to 34%) and changes in the tryptophan structure accompanied by increased fluorescence. The Soret CD spectra displayed a significant decrease of the positive signal at 403 nm. EPR spectra revealed the presence of a low-spin cyt c form (S = 1/2) with g(1) = 2.736, g(2) = 2.465, and g(3) = 2.058 after incubation with SIN1. These data suggest that the concomitant presence of NO(center dot) and O(2)(center dot-) generated from dissolved oxygen, in a system containing cyt c and liposomes, promotes chemical and conformational modi. cations in cyt c, resulting in a hypothetical bis-histidine hexacoordinated heme iron. We also show that, paradoxically, O(2)(center dot-) prevents not only membrane lipoperoxidation by peroxide-derived radicals but also oxidation of cyt c itself due to the ability of O(2)(center dot-) to reduce heme iron. Finally, lipoperoxidation measurements showed that, although it is a more efficient peroxidase, SIN1-treated cyt c is not more effective than native cyt c in promoting damage to anionic liposomes in the presence of tert-ButylOOH, probably due to loss of affinity with negatively charged lipids. (C) 2009 Elsevier Inc. All rights reserved.

pH-Sensitive Binding of Cytochrome c to the Inner Mitochondrial Membrane. Implications for the Participation of the Protein in Cell Respiration and Apoptosis

Cytochrome c exhibits two positively charged sites: site A containing lysine residues with high pK(a) values and site L containing ionizable groups with pK(aobs),values around 7.0. This protein feature implies that cytochrome c can participate in the fusion of mitochondria and have its detachment from the inner membrane regulated by cell acidosis and alkalosis. In this study, We demonstrated that both horse and tuna cytochrome c exhibited two types of binding to inner mitochondrial membranes that contributed to respiration: a high-affinity and low-efficiency pi-I-independent binding (microscopic dissociation constant K(sapp2), similar to 10 nM) and a low-affinity and high-efficiency pH-dependent binding that for horse cytochrome c had a pK(a) of similar to 6.7. For tuna cytochrome c (Lys22 and His33 replaced with Asn and Trp, respectively), the effect of pH on K(sapp1), was less striking than for the horse heme protein, and both tuna and horse cytochrome c had closed K(sapp1) values at pH 7.2 and 6.2, respectively. Recombinant mutated cytochrome c H26N and H33N also restored the respiration of the cytochrome c-depleted mitoplast in a pH-dependent manner. Consistently, the detachment of cytochrome c from nondepleted mitoplasts was favored by alkalinization, suggesting that site Lionization influences the participation of cytochrome c in the respiratory chain and apoptosis.

Nitric oxide sensing by cytochrome c bonded to a conducting polymer modified glassy carbon electrode

A nitric oxide biosensor based on cytochrome c (an heme protein) covalently immobilized to poly(5-amino-1-naphthol) by using cyanuric chloride as a bridge was developed. The immobilization was studied by cyclic voltammetry and quartz crystal microbalance. The nitric oxide detection as a function of poly(5-amino-1-naphthol) amount was recorded, and the best result was obtained with the electrode prepared by 70 cycles. The sensitivity and detection limit were 0.015 mu A cm(-2)/mu mol L(-1) and 2.85 mu mol L(-1), respectively. (C) 2009 Elsevier B.V. All rights reserved.

Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4

Cytochrome P450 (CYP450) is a class of enzymes where the substrate identification is particularly important to know. It would help medicinal chemists to design drugs with lower side effects due to drug-drug interactions and to extensive genetic polymorphism. Herein, we discuss the application of the 2D and 3D-similarity searches in identifying reference Structures with higher capacity to retrieve Substrates of three important CYP enzymes (CYP2C9, CYP2D6, and CYP3A4). On the basis of the complementarities of multiple reference structures selected by different similarity search methods, we proposed the fusion of their individual Tanimoto scores into a consensus Tanimoto score (T(consensus)). Using this new score, true positive rates of 63% (CYP2C9) and 81% (CYP2D6) were achieved with false positive rates of 4% for the CYP2C9-CYP2D6 data Set. Extended similarity searches were carried out oil a validation data set, and the results showed that by using the T(consensus) score, not only the area of a ROC graph increased, but also more substrates were recovered at the beginning of a ranked list.