Kinetic spectra of light-adaptation dark-adaptation and M-intermediate of BR-D96N

BR-D96N is a kind of genetically site-specific mutants of bacteriorhodopsin (BR) with obvious photochromic effect. Compared to the wild type BR, the lifetime of M state of BR-D96N is prolonged to several minutes so that the photochromic kinetics and the intermediates formation can be studied by the conventional spectra analysis. In the experiment, the absorption spectra of the sample at different time after light illumination are measured with spectrophotometer. By fitting and analyzing the variation of the spectra, we suppose that there are three main states in the, photochromic process, i.e., B state (light-adapted state), M state and D state (dark-adapted state). The absorption spectra of the B state, M state and D state are extracted from the experimental data based on this three-state model and the spectra at various time are fitted with the least-square method. So, the variations of population percentages of the M state, B state and D state are obtained and the M state and B state lifetimes are estimated. In another way, from the measurement of the absorption dynamics at 407 and 568 nm, the M state and B state lifetimes are also obtained by two exponential data fitting, which give coincident results with those of the spectra analysis. (C) 2003 Elsevier Science B.V. All rights reserved.

Degradation mechanism of polystyrene sulfonic acid membrane and application of its composite membranes in fuel cells

The lifetime behavior of a H-2/O-2 proton exchange membrane (PEM) fuel cell with polystyrene sulfonic acid (PSSA) membrane have been investigated in order to give an insight into the degradation mechanism of the PSSA membrane. The distribution of sulfur concentration in the cross section of the PSSA membrane was measured by energy dispersive analysis of X-ray, and the chemical composition of the PSSA membrane was characterized by infrared spectroscopy before and after the lifetime experiment. The degradation mechanism of the PSSA membrane is postulated as: the oxygen reduction at the cathode proceeds through some peroxide intermediates during the fuel cell operation, and these intermediates have strong oxidative ability and may chemically attack the tertiary hydrogen at the a carbon of the PSSA; the degradation of the PSSA membrane mainly takes place at the cathode side of the cell, and the loss of the aromatic rings and the SO3- groups simultaneously occurs from the PSSA membrane. A new kind of the PSSA-Nafion composite membrane, where the Nafion membrane is bonded with the PSSA membrane and located at the cathode of the cell, was designed to prevent oxidation degradation of the PSSA membrane in fuel cells. The performances of fuel cells with PSSA-Nafion101 and PSSA-recast Nafion composite membranes are demonstrated to be stable after 835 h and 240 h, respectively.

Synthesis and characterization of monodisperse oligo(fluorene-co-bithiophene)s

A series of monodisperse oligo(9,9-di-n-octylfluorene-co-bithiophene)s (OFbTs) with molecular lengths of up to 19.5 nm and molecular weights up to 7025 g mol(-1) has been synthesized by a divergent/convergent approach involving Stille coupling reactions. Stille coupling is quite efficient in preparing this class of oligomers, and even the molecule with nine fluorene units and eight bithiophene units (F9Th16) can be synthesized in a yield as high as 70%. Because of easy functionalization of the thiophene ring at its alpha position, no additional protecting group allowing activation for further reaction is necessary. However, the synthetic routes must be optimized to eliminate contamination of the targeting compounds with the homocoupling product of the organotin reagents. Synthesis of the longest oligomer F13Th24 in a relative large quantity is limited by its low yield due to the pronounced ligand-exchange side reactions of the starting materials and reaction intermediates. All oligomers longer than F4Th6 are nematic mesomorphs and exhibit enhanced glass transition temperature and clearing point with increasing molecular length, as revealed by differential scanning calorimetry and polarizing optical microscopy.

Chemistry and synthesis of 3(2H)-furanones and 4,5-dihydro analogues: mechanistic investigations and stereochemical control

The subject matter of this thesis relates to the chemistry of the five-membered oxygen heterocycles – 3(2H)-furanones and their 4, 5-dihydro analogues. Chapter one of the thesis is a review of the relevant chemistry of the compounds: their synthesis and key transformations. In chapter two, new research on 3(2H)-furanones is outlined in two parts. The first describes an investigation into the cyclisation of α'-trialkylsilyloxyenone adducts with arenesulfenyl and selenenyl chlorides into the corresponding sulfur and selenium substituted 3(2H)-furanones without the involvement of a Lewis acid catalyst. The study, largely involving in situ NMR techniques, identified key features associated with the formation and reaction of the chlorosulfide and chloroselenide intermediates, including operation of the Thorpe-Ingold effect. The knowledge gained in this study was applied (the second part) to the synthesis of vinyl substituted furanone systems from α'-trialkylsilyloxydienones where choice of the reaction conditions and electrophilic reagent was a key feature. An important difference in the behaviour of arenesulfenyl and selenenyl halides towards conjugated dienes emerged from this work. This phase of the research concluded with a new synthesis of geiparvarin, a natural product possessing anti-tumour properties.

Quantitative DRIFTS investigation of possible reaction mechanisms for the water-gas shift reaction on high-activity Pt- and Au-based catalysts

The present work emphasizes the importance of including a full quantitative analysis when in situ operando methods are used to investigate reaction mechanisms and reaction intermediates. The fact that some surface species exchange at a similar rate to the reaction product during isotopic transients is a necessary but not sufficient criterion for participation as a key reaction intermediate. This is exemplified here in the case of highly active low-temperature water-gas shift (WGS) catalysts based on gold and platinum. Operando DRIFTS data, isotopic exchanges, and DRIFTS calibration curves relating the concentration of formate species to the corresponding DRIFTS band intensity were combined to obtain a quantitative measure of the specific rate of formate decomposition. Despite displaying a rapid isotopic exchange rate (sometimes as fast as that of the reaction product CO2), the concentration of formates seen by DRIFTS was found to account for at most only 10% of the CO2 produced under the experimental conditions reported herein. These new results obtained on Au/CeZrO4 and Pt/CeO2 preparations (which are among the most active low-temperature WGS catalysts reported to date), led to the same conclusions regarding the minor role of IR-observable formates as those obtained in the case of less active Au/Ce(La)O-2 and Pt/ZrO2 catalysts. (c) 2007 Elsevier Inc. All rights reserved.

Phosphorylated polyols, pyrophosphates, and derivatives thereof having biological activity

The present invention provides phosphorylated and pyrophosphate derivatives of polyols, and structural derivatives of these compounds, and provides pharmaceutical compositions comprising the same. The compounds and compositions disclosed herein have various biological activities, including for example, as allosteric effectors of hemoglobin and/or as kinase inhibitors. The present invention further provides methods for therapy in human or mammalian patients, and methods for synthesis of biologically active compounds and their intermediates.

Bronsted Acid Catalyzed Morita-Baylis-Hillman Reaction: A New Mechanistic View for Thioureas Revealed by ESI-MS(/MS) Monitoring and DFT Calculations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Photodegradation of sulfamethoxazole in various aqueous media: Persistence, toxicity and photoproducts assessment

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Evaluation of macrophage activity and antibody production in genetically selected mice infected with Leptospira serovar pomona

The aim of the present study was to evaluate the role of macrophage activity and antibody production in experimental infection with Leptospira Pomona in mice genetically selected for high (H) or low (L) humoral immune response. To evaluate macrophage activity, reactive oxygen and nitrogen intermediates were determined. Also, the production of tumor necrosis factor (TNF-alpha) and the recovery of Leptospira-specific antibodies in the kidneys and liver were assessed; histological lesions were analyzed using the hematoxylin-eosin technique, and Leptospira antigens in tissues were determined by immunohistochemistry. Results showed that recovery of microorganisms from the analyzed organs was lower in LIV-A mice. However, HIV-A animals showed total restraint since the 14th day after infection, whereas LIV-A mice still had bacteria in the liver at the 21st post-infection day. Immune response against Pomona serovar in those lineages was characterized as high production of antibodies, mainly in late periods of the infectious process. The production of reactive oxygen and nitrogen intermediates also contributed to the elimination of Leptospira Pomona in all two lineages; H2O2 production was an important factor in HIV-A mice, as well as NO production in the LIV-A animals, mainly at the latest post-inoculation periods. The same occurred regarding TNF-alpha production. Severe renal lesions were observed at periods in which larger numbers of leptospires were isolated using the culture technique. Tissue alterations persisted in LIV-A mice, even at periods in which leptospires were not recovered. Immunohistochemistry showed to be more sensitive than culturing. However, both techniques were appropriate for the agent identification in the studied lineages. Results suggest that such lineages could represent an important model to investigate pathogenesis and immune response against the varied serovars of leptospires.

Eliminating exposure to aqueous solvents is necessary for the early detection and ultrastructural elemental analysis of sites of calcium and phosphorus enrichment in mineralizing UMR106-01 osteoblastic cultures

The mechanism underlying the mineralization of bone is well studied and yet it remains controversial. Inherent difficulties of imaging mineralized tissues and the aqueous solubility of calcium and phosphate, the 2 ions which combine to form bone mineral crystals, limit current analyses of labile diffusible, amorphous, and crystalline intermediates by electron microscopy. To improve the retention of calcium and phosphorus, we developed a pseudo nonaqueous processing approach and used it to characterize biomineralization foci, extracellular sites of hydroxyapatite deposition in osteoblastic cell cultures. Since mineralization of UMR106-01 osteoblasts is temporally synchronized and begins 78 h after plating, we used these cultures to evaluate the effectiveness of our method when applied to cells just prior to the formation of the first mineral crystals. Our approach combines for the first time 3 well-established methods with a fourth one, i.e. dry ultrathin sectioning. Dry ultrathin sectioning with an oscillating diamond knife was used to produce electron spectroscopic images of mineralized biomineralization foci which were high-pressure frozen and freeze substituted. For comparison, cultures were also treated with conventional processing and wet sectioning. The results show that only the use of pseudo nonaqueous processing was able to detect extracellular sites of early calcium and phosphorus enrichment at 76 h, several hours prior to detection of mineral crystals within biomineralization foci.

Characterization of antibodies specific for canine TLR4, 5 and 9 by ELISA, Western blotting and immunohistochemistry

Toll-like receptors recognize pathogen-associated molecular patterns of microbial origin, and ligand recognition results in the production of different immune mediators such as pro-inflammatory cytokines, interferon, reactive oxygen and nitrogen intermediates, and upregulation of costimmulatory molecules. As these receptors have a critical role in linking pathogen recognition to induction of inflammation and innate as well as adaptive immunity, there is tremendous interest in understanding how the tissue and cell-type expression of TLRs is regulated and its influence on the local innate immune response. While TLRs are well studied in humans and rodents, to date little is known about them in dogs. The purpose of this study was to develop canine specific antibodies against TLR2, 4, 5 and 9 that were used to measure relative expression of these TLRs in healthy and reactive canine mesenteric lymph nodes. All 8 rabbit sera (2 each for TLR2, 4, 5 and 9) were strongly positive in ELISA against the respective 2 peptides per TLR used for immunization. The purified antibodies selected specifically detected a protein band with an apparent size of approximately 70 kDa in lysates of canine PBMCs by Western blotting. Immunostaining was observed with purified antibodies against TLR4, 5 and 9, whereas for canine TLR2, staining was only observed with the unpurified antibodies. In the mesenteric lymph node of healthy dogs, the overall staining pattern was very similar for TLR4 and 5 with positive cells predominantly found in the internodular areas and lower part of the cortex. Compared to the TLR4 and 5, more cells stained positive for TLR9 especially in the lymphoid nodules. The reactive lymph nodes contained more TLR4 and 9 positive cells. Moreover, a shift of TLR-9 positive cells from the lymphoid follicles to the deep cortex and medullary cords was observed. Whereas TLR9 co-localized with CD79-positive areas, TLR4 and 5 antibodies stained cells primarily in the CD3-positive areas. All three TLR antibodies stained cells within the area that co-localized with lysozyme-positive cells. In conclusion, this study demonstrates that the antibodies generated against canine TLR 4, 5 and 9 identify the expression of these TLRs in formalin-fixed canine lymph nodes and demonstrate increased expression in reactive canine mesenteric lymph nodes.

Binding specificities and potential roles of isoforms of eukaryotic initiation factor 4E in Leishmania

The 5' cap structure of trypanosomatid mRNAs, denoted cap 4, is a complex structure that contains unusual modifications on the first four nucleotides. We examined the four eukaryotic initiation factor 4E (eIF4E) homologues found in the Leishmania genome database. These proteins, denoted LeishIF4E-1 to LeishIF4E-4, are located in the cytoplasm. They show only a limited degree of sequence homology with known eIF4E isoforms and among themselves. However, computerized structure prediction suggests that the cap-binding pocket is conserved in each of the homologues, as confirmed by binding assays to m(7)GTP, cap 4, and its intermediates. LeishIF4E-1 and LeishIF4E-4 each bind m(7)GTP and cap 4 comparably well, and only these two proteins could interact with the mammalian eIF4E binding protein 4EBP1, though with different efficiencies. 4EBP1 is a translation repressor that competes with eIF4G for the same residues on eIF4E; thus, LeishIF4E-1 and LeishIF4E-4 are reasonable candidates for serving as translation factors. LeishIF4E-1 is more abundant in amastigotes and also contains a typical 3' untranslated region element that is found in amastigote-specific genes. LeishIF4E-2 bound mainly to cap 4 and comigrated with polysomal fractions on sucrose gradients. Since the consensus eIF4E is usually found in 48S complexes, LeishIF4E-2 could possibly be associated with the stabilization of trypanosomatid polysomes. LeishIF4E-3 bound mainly m(7)GTP, excluding its involvement in the translation of cap 4-protected mRNAs. It comigrates with 80S complexes which are resistant to micrococcal nuclease, but its function is yet unknown. None of the isoforms can functionally complement the Saccharomyces cerevisiae eIF4E, indicating that despite their structural conservation, they are considerably diverged.

Spectral bounds and basis results for non-self-adjoint pencils, with an application to Hagen-Poiseuille flow

We obtain eigenvalue enclosures and basisness results for eigen- and associated functions of a non-self-adjoint unbounded linear operator pencil A−λBA−λB in which BB is uniformly positive and the essential spectrum of the pencil is empty. Both Riesz basisness and Bari basisness results are obtained. The results are applied to a system of singular differential equations arising in the study of Hagen–Poiseuille flow with non-axisymmetric disturbances.

Definition of amide protection factors for early kinetic intermediates in protein folding

Hydrogen–deuterium exchange experiments have been used previously to investigate the structures of well defined states of a given protein. These include the native state, the unfolded state, and any intermediates that can be stably populated at equilibrium. More recently, the hydrogen–deuterium exchange technique has been applied in kinetic labeling experiments to probe the structures of transiently formed intermediates on the kinetic folding pathway of a given protein. From these equilibrium and nonequilibrium studies, protection factors are usually obtained. These protection factors are defined as the ratio of the rate of exchange of a given backbone amide when it is in a fully solvent-exposed state (usually obtained from model peptides) to the rate of exchange of that amide in some state of the protein or in some intermediate on the folding pathway of the protein. This definition is straightforward for the case of equilibrium studies; however, it is less clear-cut for the case of transient kinetic intermediates. To clarify the concept for the case of burst-phase intermediates, we have introduced and mathematically defined two different types of protection factors: one is Pstruc, which is more related to the structure of the intermediate, and the other is Papp, which is more related to the stability of the intermediate. Kinetic hydrogen–deuterium exchange data from disulfide-intact ribonuclease A and from cytochrome c are discussed to explain the use and implications of these two definitions.

Uracil-DNA glycosylase–DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects

Enzymatic transformations of macromolecular substrates such as DNA repair enzyme/DNA transformations are commonly interpreted primarily by active-site functional-group chemistry that ignores their extensive interfaces. Yet human uracil–DNA glycosylase (UDG), an archetypical enzyme that initiates DNA base-excision repair, efficiently excises the damaged base uracil resulting from cytosine deamination even when active-site functional groups are deleted by mutagenesis. The 1.8-Å resolution substrate analogue and 2.0-Å resolution cleaved product cocrystal structures of UDG bound to double-stranded DNA suggest enzyme–DNA substrate-binding energy from the macromolecular interface is funneled into catalytic power at the active site. The architecturally stabilized closing of UDG enforces distortions of the uracil and deoxyribose in the flipped-out nucleotide substrate that are relieved by glycosylic bond cleavage in the product complex. This experimentally defined substrate stereochemistry implies the enzyme alters the orientation of three orthogonal electron orbitals to favor electron transpositions for glycosylic bond cleavage. By revealing the coupling of this anomeric effect to a delocalization of the glycosylic bond electrons into the uracil aromatic system, this structurally implicated mechanism resolves apparent paradoxes concerning the transpositions of electrons among orthogonal orbitals and the retention of catalytic efficiency despite mutational removal of active-site functional groups. These UDG/DNA structures and their implied dissociative excision chemistry suggest biology favors a chemistry for base-excision repair initiation that optimizes pathway coordination by product binding to avoid the release of cytotoxic and mutagenic intermediates. Similar excision chemistry may apply to other biological reaction pathways requiring the coordination of complex multistep chemical transformations.