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At least 163 records · Page 9Linked to original sources
PubMed2006

ATR microspectroscopy with multivariate analysis segregates grades of exfoliative cervical cytology.

Although cervical cancer screening in the UK has led to reductions in the incidence of invasive disease, this programme remains flawed. We set out to examine the potential of infrared (IR) microspectroscopy to allow the profiling of cellular biochemical constituents associated with disease progression. Attenuated total reflection-Fourier Transform IR (ATR) microspectroscopy was employed to interrogate spectral differences between samples of exfoliative cervical cytology collected into liquid based cytology (LBC). These were histologically characterised as normal (n = 5), low-grade (n = 5), high-grade (n = 5) or severe dyskaryosis (? carcinoma) (n = 5). Examination of resultant spectra was coupled with principal component analysis (PCA) and subsequent linear discriminant analysis (LDA). The interrogation of LBC samples using ATR microspectroscopy with PCA-LDA facilitated the discrimination of different categories of exfoliative cytology and allowed the identification of potential biomarkers of abnormality; these occurred prominently in the IR spectral region 1200 cm(-1) - 950 cm(-1) consisting of carbohydrates, phosphate, and glycogen. Shifts in the centroids of amide I (approximately 1650 cm(-1)) and II (approximately 1530 cm(-1)) absorbance bands, indicating conformational changes to the secondary structure of intracellular proteins and associated with increasing disease progression, were also noted. This work demonstrates the potential of ATR microspectroscopy coupled with multivariate analysis to be an objective alternative to routine cytology.

Female↗
PubMed2005

ATR-FTIR spectroscopy: a chemometric approach for studying the lipid organisation of the stratum corneum.

The barrier function of skin resides in the lipid components of the stratum corneum, particularly their spatial organisation. FTIR spectroscopy has already been used as a relevant tool to study this lipid organisation: IR vibration band shifts have been attributed to the variations in lipid organisation induced by temperature. Our study included a stratum corneum model, composed of the three main lipids: palmitic acid as an example of fatty acids, cholesterol and ceramide III as an example of ceramide. Different films with various ratios of these lipids were studied. In our analytical strategy, the interest of using a chemometric analysis of global data obtained from ATR-FTIR spectra to highlight the main interactions involved in the molecular organisation of lipids has been demonstrated. Two kinds of interaction between the three main lipids have been shown: a non polar interaction between the long hydrocarbon chains and a polar interaction as the hydrogen bonding between polar functional groups. By varying the lipid ratio, we have shown first that the relative importance of each interaction was modified, second, that the induced modification of organisation can be detected by chemometric analysis of the ATR-FTIR spectra. The role of each kind of lipid in the organisation has been discussed. In conclusion, associating the ATR-FTIR with chemometric treatment is a promising tool: firstly, to understand the consequence of lipid relative compositions on the structural organisation of the stratum corneum, secondly, to show the relationship between lipid organisation and percutaneous penetration data. Indeed, this methodology will be transposed to in vivo studies with IR measurements through a probe.

Animals↗
PubMedDate not supplied

Regulation of DNA replication by ATR: signaling in response to DNA intermediates.

The nuclear protein kinase ATR controls S-phase progression in response to DNA damage and replication fork stalling, including damage caused by ultraviolet irradiation, hyperoxia, and replication inhibitors like aphidicolin and hydroxyurea. ATR activation and substrate specificity require the presence of adapter and mediator molecules, ultimately resulting in the downstream inhibition of the S-phase kinases that function to initiate DNA replication at origins of replication. The data reviewed strongly support the hypothesis that ATR is activated in response to persistent RPA-bound single-stranded DNA, a common intermediate of unstressed and damaged DNA replication and metabolism.

Animals↗
PubMedDate not supplied

An overview of three new disorders associated with genetic instability: LIG4 syndrome, RS-SCID and ATR-Seckel syndrome.

Around 15-20 hereditary disorders associated with impaired DNA damage response mechanisms have been previously described. The range of clinical features associated with these disorders attests to the significant role that these pathways play during development. Recently, three new such disorders have been reported extending the importance of the damage response pathways to human health. LIG4 syndrome is conferred by hypomorphic mutations in DNA ligase IV, an essential component of DNA non-homologous end-joining (NHEJ), and is associated with pancytopaenia, developmental and growth delay and dysmorphic facial features. Radiosensitive severe combined immunodeficiency (RS-SCID) is caused by mutations in Artemis, a protein that plays a subsidiary role in non-homologous end-joining although it is not an essential component. RS-SCID is characterised by severe combined immunodeficiency but patients have no overt developmental abnormalities. ATR-Seckel syndrome is caused by mutations in ataxia telangiectasia and Rad3 related protein (ATR), a component of a DNA damage signalling pathway. ATR-Seckel syndrome patients have dramatic microcephaly and marked growth and developmental delay. The clinical features of these patients are considered in the light of the function of the defective protein.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2006

Integrity and stability studies of precipitated rhBMP-2 microparticles with a focus on ATR-FTIR measurements.

A major obstacle in the development of protein drug formulations is the need to maintain the native, active protein structure both during the formulation process and upon long time storage. Controlled precipitation was evaluated for its potential to supply stable microparticulate formulations of bone-regenerating recombinant human Bone Morphogenetic Protein-2 (rhBMP-2). Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) did provide insight into the protein formulation and stability. Temperature dependent ATR-FTIR measurements and DSC measurements allow for the study of changes in the protein structure during melting. To address the question of isomerization, peptide mapping was performed, and protein aggregation was monitored by size exclusion chromatography (SEC). It could be demonstrated by ATR-FTIR that controlled precipitation did not harm the protein and the process is fully reversible. DSC measurements further confirmed these findings. No changes in the transition temperature and process were observed after precipitation and redissolution. Upon storage, isomerization and aggregation could be detected, but to a lower extent in the precipitated formulation as compared to a solution reference. Thus, controlled precipitation of rhBMP-2 is fully reversible and has the potential as alternative formulation tool for the generation of a microparticulate drug delivery system.

Bone Morphogenetic Protein 2↗
PubMed2006

Regulation of Claspin degradation by the ubiquitin-proteosome pathway during the cell cycle and in response to ATR-dependent checkpoint activation.

Claspin is involved in ATR-dependent activation of Chk1 during DNA replication and in response to DNA damage. We show that degradation of Claspin by the ubiquitin-proteosome pathway is regulated during the cell cycle. Claspin is stabilized in S-phase but is abruptly degraded in mitosis and is absent from early G(1) cells in which the phosphorylation of Chk1 by ATR is abrogated. In response to hydroxyurea, UV or aphidicolin, Claspin is phosphorylated in the Chk1-binding domain and its protein levels are increased in an ATR-dependent manner. Thus, the Chk1 pathway is regulated through both phosphorylation of Claspin and its controlled degradation.

Adaptor Proteins, Signal Transducing↗
PubMed2005

ATR-FTIR investigation on the complexation of myo-inositol hexaphosphate with aluminum hydroxide.

The adsorption isotherm of and the pH effect on the adsorption of myo-inositol hexaphosphate (myo-IP6) on amorphous aluminum hydroxide was investigated. It was found that the adsorption isotherm of myo-IP6 on aluminum hydroxide could be well fitted with the Freundlich isotherm. The amount of myo-IP6 adsorbed remained almost constant in the range of pH 4.0 to 7.0, but it decreased considerably as the initial pH was over 7. The adsorption of myo-IP6 resulted in an increase in the pH level due to the release of OH(-) ions, which suggested that the adsorption of myo-IP6 on aluminum hydroxide was caused by a ligand exchange reaction. ATR-FTIR analysis of myo-IP6 in solution and adsorbed on aluminum hydroxide at different pH were performed. The ATR-FTIR investigation indicated that myo-IP6 was adsorbed onto aluminum hydroxide by forming inner-sphere complexes and adsorption facilitated the deprotonation of phosphate groups. The asymmetric vibration of the PO bond in AlPO(-)(3) appearing at a lower frequency than that in the terminal HPO(-)(3) indicated that Al bound to the O atom not as strongly as the H atom did. The ATR-FTIR investigation and theoretical calculation (with the Gaussian 03 program) revealed that three of the six phosphate groups in myo-IP6 molecules were bound to aluminum hydroxide while the other three remained free when myo-IP6 was adsorbed on aluminum hydroxide.

Aluminum Hydroxide↗
PubMed2006

ATR regulates hexavalent chromium-induced S-phase checkpoint through phosphorylation of SMC1.

Hexavalent chromium (Cr[VI]) is an industrial waste product known to cause nasal and lung cancer in exposed workers. Intracellularly, Cr[VI] undergoes a series of enzymatic reductions resulting in the formation of reactive chromate intermediates and oxygen free radicals. These metabolites react with DNA to cause numerous types of genomic lesions, but the cellular response to these genotoxic insults is poorly understood. Recently, we demonstrated that in response to DNA damage induced by Cr[VI], an ataxia-telangiectasia mutated (ATM) and structural maintenance of chromosomal protein 1 (SMC1)-dependent S-phase checkpoint is activated. Interestingly, this checkpoint response was only ATM-dependent in cells exposed to low doses of Cr[VI], we demonstrate that the ATM and Rad3 related kinase, ATR, is required to activate the S-phase checkpoint. In response to all doses of Cr[VI], ATR is activated and phosphorylates SMC1 to facilitate the checkpoint. Further, chromatin binding ability of Rad17 is required for this process. Taken together, these results indicate that the Rad17-ATR-SMC1 pathway is essential for Cr[VI]-induced S-phase checkpoint activation.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2006

Selective detection of the structural changes upon photoreactions of several redox cofactors in photosystem II by means of light-induced ATR-FTIR difference spectroscopy.

Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was applied for the first time to detect the structural changes upon photoreactions of redox cofactors in photosystem II (PSII). The PSII-enriched membranes from spinach were adsorbed on the surface of a silicon prism, and FTIR measurements of various redox cofactors were performed for the same sample but under different conditions by exchanging buffers in a flow cell. Light-induced FTIR difference spectra upon redox reactions of the oxygen-evolving Mn cluster, the primary quinone electron acceptor QA, the redox-active tyrosine YD, the primary electron acceptor pheophytin, and the primary electron donor chlorophyll P680 were successively recorded in buffers including different redox reagents and inhibitors. All of these cofactors remained active in the PSII membranes on the silicon surface, and the resultant spectra were basically identical to those previously recorded by the conventional transmission method. These ATR-FTIR measurements enable accurate comparison between reactions of different active sites in a single PSII sample. The present results demonstrated that the ATR-FTIR spectroscopy is a useful technique for investigation of the reaction mechanism of PSII.

Buffers↗
PubMed2002

ATR regulates fragile site stability.

Conditions that partially inhibit DNA replication induce expression of common fragile sites. These sites form gaps and breaks on metaphase chromosomes and are deleted and rearranged in many tumors. Yet, the mechanism of fragile site expression has been elusive. We demonstrate that the replication checkpoint kinase ATR, but not ATM, is critical for maintenance of fragile site stability. ATR deficiency results in fragile site expression with and without addition of replication inhibitors. Thus, we propose that fragile sites are unreplicated chromosomal regions resulting from stalled forks that escape the ATR replication checkpoint. These findings have important implications for understanding both the mechanism of fragile site instability and the consequences of stalled replication in mammalian cells.

2-Aminopurine↗
PubMed2000

Investigation of drug release from suspension using FTIR-ATR technique: part I. Determination of effective diffusion coefficient of drugs.

Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy was used to study directly the release of drug particles (ketoconazole) in a liquid medium (paraffinum liquidum). In the case of the release experiment, the formulation is placed on the ATR crystal and the acceptor membrane on the top of the ointment. The decrease of the drug content in the sediment near the interface ATR crystal-formulation in the course of the release process was quantified by monitoring the changes of the IR spectrum in relevant spectral ranges using multivariate analysis. A mathematical model based on Fick's second law with appropriate initial and boundary conditions was applied in order to determine the diffusion coefficient of the drug in the liquid medium. Knowing this value, it is possible to calculate the effective diffusion coefficient of the drug in heterogeneous semisolid formulation (Vaseline) as a function of the volume fraction of the solid phase.

Antifungal Agents↗
PubMed2004

BCR/ABL translocates to the nucleus and disrupts an ATR-dependent intra-S phase checkpoint.

Chronic myelogeneous leukemia (CML) is a two-stage disease associated with expression of the BCR/ABL tyrosine kinase protein. However, whether BCR/ABL expression directly causes blast crisis, and if so by what mechanism, is unknown. We have found that BCR/ABL translocates from the cytoplasm to the nucleus after genotoxic stress. Furthermore, BCR/ABL increases DNA double-strand damage after etoposide treatment and leads to a defect in an intra-S phase checkpoint, causing a radioresistant DNA synthesis (RDS) phenotype. In the nucleus, BCR/ABL associates with the ataxia-telangiectasia and rad 3-related protein (ATR) and disrupts ATR-dependent signal transduction. Overexpression of ATR in a BCR/ABL-expressing cell line corrects the DNA damage phenotype. These results demonstrate a nuclear role for BCR/ABL in altering the cellular response to DNA damage.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2004

Polarized ATR-FTIR spectroscopy of the membrane-embedded domains of the particulate methane monooxygenase.

The particulate methane monooxygenase (pMMO) of Methylococcus capsulatus (Bath) is an integral membrane protein that catalyzes the conversion of methane to methanol. To gain some insight into the structure-reactivity pattern of this protein, we have applied attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy to investigate the secondary structure of the pMMO. The results showed that ca. 60% of the amino acid residues were structured as alpha-helices. About 80% of the peptide residues were estimated to be protected from the amide (1)H/(2)H exchange during a 21 h exposure to (2)H(2)O. In addition, a significant portion of the protein was shown to be sequestered within the bilayer membrane, protected from trypsin proteolysis. The ATR-FTIR difference spectrum between the intact and the proteolyzed pMMO-enriched membranes revealed absorption peaks only in the spectral regions characteristic for unordered and beta-structures. These observations were corroborated by amino acid sequence analysis of the pMMO subunits using the program TransMembrane topology with a Hidden Markov Model: 15 putative transmembrane alpha-helices were predicted. Finally, an attempt was also made to model the three-dimensional folding of the protein subunits from the sequence using the Protein Fold Recognition Server based on the 3D Position Specific Scoring Matrix Method. The C-terminal solvent-exposed sequence (N255-M414) of the pMMO 45 kDa subunit was shown to match the beta-sheet structure of the multidomain cupredoxins. We conclude on the basis of this ATR-FTIR study that pMMO is an alpha-helical bundle with ca. 15 transmembrane alpha-helices embedded in the bilayer membrane, together with a water-exposed domain comprised mostly of beta-sheet structures similar to the cupredoxins.

Amides↗
PubMed2003

Catalyzed oxidation of arsenic(III) by hydrogen peroxide on the surface of ferrihydrite: an in situ ATR FTIR study.

Knowledge of arsenic redox kinetics is crucial for understanding the impact and fate of As in the environment and for optimizing As removal from drinking water. Rapid oxidation of As(III) adsorbed to ferrihydrite (FH) in the presence of hydrogen peroxide (H2O2) might be expected for two reasons. First, the adsorbed As(III) is assumed to be oxidized more readily than the undissociated species in solution. Second, catalyzed decomposition of H2O2 on the FH surface might also lead to As(III) oxidation. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy was used to monitor the oxidation of adsorbed As(III) on the FH surface in situ. No As(III) oxidation within minutes to hours was observed prior to H2O2 addition. Initial pseudo-first-order oxidation rate coefficients for adsorbed As(III), determined at H2O2 concentrations between 8.4 microM and 8.4 mM and pH values from 4 to 8, increased with the H2O2 concentration according to the equation log k(ox) (min(-1)) = 0.17 + 0.50 log [H2O] (mol/L), n = 21, r2 = 0.87. Only a weak pH dependence of log k(ox) was observed (approximately 0.04 logarithm unit increase per pH unit). ATR-FTIR experiments with As(III) adsorbed onto amorphous aluminum hydroxide showed that Fe was necessary to induce As(III) oxidation by catalytic H2O2 decomposition. Supplementary As(III) oxidation experiments in FH suspensions qualitatively confirmed the findings from the in situ ATR-FTIR experiments. Our results indicate that the catalyzed oxidation of As(III) by H2O2 on the surface of iron (hydr)oxides might be a relevant reaction pathway in environmental systems such as surface waters, as well as in engineered systems for As removal from water.

Arsenic↗
PubMed2005

In situ ATR-IR spectroscopic and reaction kinetics studies of water-gas shift and methanol reforming on Pt/Al2O3 catalysts in vapor and liquid phases.

Reaction kinetics measurements of the water-gas shift reaction were carried out at 373 K on Pt/Al2O3 in vapor phase to investigate the effects of CO, H2, and H2O partial pressures. Results of in situ ATR-IR studies conducted in vapor phase under similar conditions suggest that the Pt surface coverage by adsorbed CO is high (approximately 90% of the saturation coverage), leading to a negligible effect of the CO pressures on the rate of reaction. The negative reaction order with respect to the H2 pressure is caused by the increased coverage of adsorbed H atoms, and the fractional positive order with respect to the water pressure is consistent with non-equilibrated H2O dissociation on Pt. Results of in situ ATR-IR studies carried out at 373 K show that the presence of liquid water leads to a slight decrease in the Pt surface coverage by adsorbed CO (approximately 80% of the saturation coverage) when the CO partial pressure is the same as in the vapor-phase studies. The rate of the WGS reaction in the presence of liquid water is comparable to the rate under complete vaporization conditions when other factors (such as CO partial pressure) are held constant. Reaction kinetics measurements of methanol reforming were carried out at 423 K over a total pressure range of 1.36-5.84 bar. In situ ATR-IR studies were conducted at 423 K to determine the Pt surface coverage by adsorbed CO in completely vaporized methanol feeds and in aqueous methanol solutions. The decomposition of methanol is found to be slower during the reforming of methanol in liquid phase than in vapor phase, which leads to a lower rate of hydrogen production in liquid phase (0.08 min(-1) at 4.88 bar) than in vapor phase (0.23 min(-1) at 4.46 bar). The lower reaction order with respect to methanol concentration observed for vapor-phase versus liquid-phase methanol reforming (0.2 versus 0.8, respectively) is due to the higher extent of CO poisoning on Pt for reforming in vapor phase than in liquid phase, based on the higher coverage by adsorbed CO observed in completely vaporized methanol feeds (55-60% of the saturation coverage) than in aqueous methanol feed solutions (29-40% of the saturation coverage).

Aluminum Oxide↗
PubMed2005

Unraveling the surface reactions during liquid-phase oxidation of benzyl alcohol on Pd/Al2O3: an in situ ATR-IR study.

The palladium-catalyzed liquid-phase reaction of benzyl alcohol to benzaldehyde was investigated in the presence and absence of oxygen by attenuated total reflection infrared (ATR-IR) spectroscopy. The 5 wt % Pd/Al2O3 catalyst was fixed in a flow-through ATR-IR cell serving as a continuous-flow reactor. The reaction conditions (cyclohexane solvent, 323 K, 1 bar) were set in the range commonly applied in the heterogeneous catalytic aerobic oxidation of alcohols. The in situ ATR-IR study of the solid-liquid interface revealed a complex reaction network, including dehydrogenation of benzyl alcohol to benzaldehyde, decarbonylation of benzaldehyde, oxidation of hydrogen and CO on Pd, and formation of benzoic acid catalyzed by both Pd and Al2O3. Continuous formation of CO and its oxidative removal by air resulted in significant steady-state CO coverage of Pd during oxidation of benzyl alcohol. Unexpectedly, benzoic acid formed already in the early stage of the reaction and adsorbed strongly (irreversibly) on the basic sites of Al2O3 and thus remained undetectable in the effluent. This observation questions the reliability of product distributions conventionally determined from the liquid phase. The occurrence of the hydrogenolysis of the C-O bond of benzyl alcohol and formation of toluene indicates that Pd was present in a reduced state (Pd0) even in the presence of oxygen, in agreement with the dehydrogenation mechanism of alcohol oxidation.

Journal Article↗
PubMed2005

Adsorption kinetics, orientation, and self-assembling of N-acetyl-L-cysteine on gold: a combined ATR-IR, PM-IRRAS, and QCM study.

The adsorption of N-acetyl-L-cysteine from ethanol solution on gold has been studied by in situ attenuated total reflection infrared (ATR-IR) spectroscopy, polarization modulation infrared reflection absorption spectroscopy, and a quartz crystal microbalance. After an initial fast adsorption, in situ ATR-IR revealed two considerably slower processes, besides further adsorption. The appearance of carboxylate bands and the partial disappearance of the carboxylic acid bands demonstrated that part of the molecules on the surface underwent deprotonation. In addition, the C=O stretching vibration of the carboxylic acid group shifted to lower and the amide II band to higher wavenumbers, indicating hydrogen-bonding interactions within the adsorbate layer. Based on the initial ATR-IR spectrum, which did not reveal deprotonation, the orientation of the molecule within the adsorbate layer was determined. For this, density functional theory was used to calculate the transition dipole moment vectors of the vibrational modes of N-acetyl-l-cysteine. The projections of the latter onto the z-axis of the fixed surface coordinate system were used to determine relative band intensities for different orientations of the molecule. The analysis revealed that the amide group is tilted with respect to and points away from the surface, whereas the carboxylic acid is in proximity to the surface, which is also supported by a shift of the C-O-H bending mode. This position of the acid group favors its deprotonation assisted by the gold surface and easily enables intermolecular interactions. Periodic acid stimuli revealed reversible protonation/deprotonation of part of the adsorbed molecules. However, only non-hydrogen-bonded carboxylic acid groups showed a response toward the acid stimuli.

Acetylcysteine↗
PubMed2005

Distinct modes of ATR activation after replication stress and DNA double-strand breaks in Caenorhabditis elegans.

ATM and ATR are key components of the DNA damage checkpoint. ATR primarily responds to UV damage and replication stress, yet may also function with ATM in the checkpoint response to DNA double-strand breaks (DSBs), although this is less clear. Here, we show that atl-1 (Caenorhabditis elegans ATR) and rad-5/clk-2 prevent mitotic catastrophe, function in the S-phase checkpoint and also cooperate with atm-1 in the checkpoint response to DSBs after ionizing radiation (IR) to induce cell cycle arrest or apoptosis via the cep-1(p53)/egl-1 pathway. ATL-1 is recruited to stalled replication forks by RPA-1 and functions upstream of rad-5/clk-2 in the S-phase checkpoint. In contrast, mre-11 and atm-1 are dispensable for ATL-1 recruitment to stalled replication forks. However, mre-11 is required for RPA-1 association and ATL-1 recruitment to DSBs. Thus, DNA processing controlled by mre-11 is important for ATL-1 activation at DSBs but not following replication fork stalling. We propose that atl-1 and rad-5/clk-2 respond to single-stranded DNA generated by replication stress and function with atm-1 following DSB resection.

Animals↗