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At least 289 records · Page 16Linked to original sources
PubMed2005

[ATR-X syndrome: a new mutation in the XNP/ATRX gene near the helicase domain].

The alpha-thalassemia/mental retardation syndrome, X linked, also named ATR-X syndrome is a X-linked mental retardation syndrome. Mutations have been found in the ATRX gene in about one half of the patients. We report a typical clinical case. The clinical evidence leads us to continue the analysis of the gene despite a negative first screening. Indeed a new mutation was found, just behind the helicase domain, bringing up the interest of an effective collaboration between physicians and biologists.

DNA Helicases↗
PubMed2004

Evidence for heterodimers of 2,4,5-trichlorophenol on planar lipid layers. A FTIR-ATR investigation.

Trichlorophenols are weak acids of high hydrophobicity and are able to transport protons across the mitochondrial membrane. Thus the proton motive force is dissipated and the ATP production decreased. In situ Fourier Transform Infrared-Attenuated Total Reflection (FTIR-ATR) experiments with 2,4,5-trichlorophenol (TCP) adsorbed to model membranes resulted in good evidence for the formation of the TCP-heterodimer. Two surfaces were examined: a dipalmitoyl phosphatidic acid (DPPA) monolayer and a planar DPPA/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. TCP was adsorbed from 1 to 3 mM solutions at pH 6.0 to the lipid layers leading to surface layers at the water/lipid interface. Difference spectra showed an effect on DPPA acyl chains even when it was covered with POPC. Time-resolved measurements revealed two distinct adsorption processes, which were assigned to TCP and its deprotonated anion (phenoxide), respectively. For DPPA/POPC bilayers, the adsorption of TCP was faster than that of its phenoxide, whereas adsorption of both species to DPPA monolayers proceeded with similar velocity. In both cases, phenoxide formation at the membrane was found to be delayed with respect to phenol adsorption. Phenoxide and phenol were retained after replacing the TCP solution with buffer. For the retained species, we estimated a phenol/phenoxide molar ratio of 1 at pH 6.0 (pKa=6.94 for TCP), demonstrating strong evidence for heterodimer formation.

Adsorption↗
PubMed2005

Soil identification and chemometrics for direct determination of nitrate in soils using FTIR-ATR mid-infrared spectroscopy.

The use of mid-infrared attenuated total reflectance (ATR) spectroscopy enables direct measurement of nitrate concentration in soil pastes, but strong interfering absorbance bands due to water and soil constituents limit the accuracy of straightforward determination. Accurate subtraction of the water spectrum improves the correlation between nitrate concentration and its nu3 vibration band around 1350 cm(-1). However, this correlation is soil-dependent, due mostly to varying contents of carbonate, whose absorbance band overlaps the nitrate band. In the present work, a two-stage method is developed: First, the soil type is identified by comparing the "fingerprint" region of the spectrum (800-1200 cm(-1)) to a reference spectral library. In the second stage, nitrate concentration is estimated using the spectrum interval that includes the nitrate band, together with the soil type previously identified. Three methods are compared for estimating nitrate concentration: integration of the nitrate absorbance band, cross-correlation with a reference spectrum, and principal component analysis (PCA) followed by a neural network. When using simple band integration, the use of soil specific calibration curves leads to determination errors ranging from 5.5 to 24 mg[N]/kg[dry soil] for the mineral soils tested. The cross-correlation technique leads to similar results. The combination of soil identification with PCA and neural network modeling improves the predictions, especially for soils containing calcium carbonate. Typical prediction errors for light non-calcareous soils are about 4 mg[N]/kg[dry soil], whereas for soils containing calcium carbonate they range from 6 to 20 mg[N]/kg[dry soil], which is less than four percent of the concentration range investigated.

Aluminum Silicates↗
PubMed2006

ATR-FTIR investigation of the role of phenolic groups in the interaction of some NOM model compounds with aluminum hydroxide.

The role of phenolic groups in the interaction of natural organic matter (NOM) with metal hydroxides was investigated with ATR-FTIR spectroscopy and adsorption tests by employing a series of dihydroxybenzoic acids (DHBAs) as the NOM surrogates and aluminum hydroxide as the adsorbent. All DHBAs examined in this study were found to be adsorbed on aluminum hydroxide by forming inner-sphere complexes. Carboxylic groups governed the complexation of DHBAs with aluminum hydroxide at low pH or in cases when the two hydroxyl groups were not adjacent to each other and neither of them was ortho to the carboxylic group. The involvement of the phenolic groups, ortho to another phenolic group or ortho to the carboxylic groups, in the complexation increased with increasing pH as the deprotonation of phenolic groups was easier at higher pH. The presence of phenolic groups increased the electron density of the carboxylic groups and facilitated the inner-sphere complexation of the carboxylic groups with metal hydroxide. The correlation between the pK(a) values and the amount of organic acid adsorbed on the aluminum hydroxide revealed that the adsorption of DHBAs at acidic pH was largely dependent on the surface chelate formation rather than on the electronic effect.

Aluminum Hydroxide↗
PubMed2006

ATR homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.

DNA polymerase zeta (Polzeta) and Rev1 contribute to the bypassing of DNA lesions, termed translesion DNA synthesis (TLS). Polzeta consists of two subunits, one encoded by REV3 (the catalytic subunit) and the other encoded by REV7. Rev1 acts as a deoxycytidyl transferase, inserting dCMP opposite lesions. Polzeta and Rev1 have been shown to operate in the same TLS pathway in the budding yeast Saccharomyces cerevisiae. Here, we show that budding yeast Polzeta and Rev1 form a complex and associate together with double-strand breaks (DSBs). As a component of the Polzeta-Rev1 complex, Rev1 plays a noncatalytic role in the association with DSBs. In budding yeast, the ATR-homolog Mec1 plays a central role in the DNA-damage checkpoint response. We further show that Mec1-dependent phosphorylation promotes the Polzeta-Rev1 association with DSBs. Rev1 association with DSBs requires neither the function of the Rad24 checkpoint-clamp loader nor the Rad6-Rad18-mediated ubiquitination of PCNA. Our results reveal a novel role of Mec1 in the localization of the Polzeta-Rev1 complex to DNA lesions and highlight a linkage of TLS polymerases to the checkpoint response.

DNA Damage↗
PubMed2004

A conserved truncated isoform of the ATR-X syndrome protein lacking the SWI/SNF-homology domain.

Mutations in the ATRX gene cause a severe X-linked mental retardation syndrome that is frequently associated with alpha thalassemia (ATR-X syndrome). The previously characterized ATRX protein (approximately 280 kDa) contains both a Plant homeodomain (PHD)-like zinc finger motif as well as an ATPase domain of the SNF2 family. These motifs suggest that ATRX may function as a regulator of gene expression, probably by exerting an effect on chromatin structure, although the exact cellular role of ATRX has not yet been fully elucidated. Here we characterize a truncated (approximately 200 kDa) isoform of ATRX (called here ATRXt) that has been highly conserved between mouse and human. In both species, ATRXt arises due to the failure to splice intron 11 from the primary transcript, and the use of a proximal intronic poly(A) signal. We show that the relative expression of the full length and ATRXt isoforms is subject to tissue-specific regulation. The ATRXt isoform contains the PHD-like domain but not the SWI/SNF-like motifs and is therefore unlikely to be functionally equivalent to the full length protein. We used indirect immunofluorescence to demonstrate that the full length and ATRXt isoforms are colocalized at blocks of pericentromeric heterochromatin but unlike full length ATRX, the truncated isoform does not associate with promyelocytic leukemia (PML) nuclear bodies. The high degree of conservation of ATRXt and the tight regulation of its expression relative to the full length protein suggest that this truncated isoform fulfills an important biological function.

Amino Acid Sequence↗
PubMed2004

ATR-FTIR characterization of transport properties of benzoic acid ion-pairs in silicone membranes.

A novel technique based on Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy was used to study the transport of benzoic acid ion-pairs/salts in silicone membranes. The benzoic acid ion-pairs were prepared using various counter-ions with different degrees of lipophilicity, e.g. triethylamine (TA), diethylamine (DE), tert-butylamine (t-BA), 2-amino-2-methyl-propanol (AMP), and 2-amino-2-methyl-propanediol (AMPD). Silicone membrane, treated or untreated with propylene glycol (PG), was placed on the surface of a ZnSe crystal and the transport solution was applied to the upper surface of the membrane. A mathematical model, based on Fick's second law describing the build up of permeant concentration at the membrane/crystal interface with time was applied to determine diffusion coefficients. Absorption due to the acid (1700 cm(-1)) or benzoate anion (1555 cm(-1)) was observed at different regions without the interference from PG or silicone membrane. Benzoate anion, a charged species, was observed to permeate the membrane. The permeation of benzoate anion from sodium benzoate and polar ion-pairs of AMP and AMPD was very low in contrast to their high-saturated concentrations in PG as compared to the t-BA ion-pair. This indicated that benzoate anion preferentially permeates the membrane as an ion-pair rather than a single anion; otherwise its permeation should correspond to its concentration in PG instead of the lipophilicity of the ion-pairs. Additionally, the diffusion coefficient values of benzoic acid and benzoate anions through the treated and untreated membranes were not statistically different.

Antifungal Agents↗
PubMed2005

A new method for gaining insight into the chemistry of drying mineral surfaces using ATR-FTIR.

Although it is understood that the chemical environment at a drying surface is likely to be quite different from that at a fully hydrated surface, the difficulty of quantitative measurement has meant that this potentially crucial aspect of surface chemistry has gone largely overlooked. As a result, most of our understanding comes from measurement before and after drying, with a gray region of speculation in between. An interesting natural example is the paradoxical reduction of Mn oxides in moist soils as they dry, because drying is usually considered an oxidative process. This phenomenon indicates that important chemical changes are occurring during drying and an approach is needed to probe the chemistry of drying surfaces. Here we show the suitability of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy for real-time, in situ investigation of the drying solid-water interface, using the change in surface pH as an example. This was achieved by adsorbing thymol blue pH indicator (pK(a)=1.65) onto a natural Mn-rich clay and observing the real-time pH change, which dropped from pH 5 to below pH 1.65 with the removal of free water from the surface.

Journal Article↗
PubMed2005

An in situ ATR-FTIR study of polyacrylamide adsorption at the talc surface.

The adsorption of a low molecular weight unmodified polyacrylamide (Polymer-N) and a hydroxyl-substituted polyacrylamide (Polymer-H) onto talc was studied using in situ particle film ATR-FTIR spectroscopy in the multiple internal reflection mode. Spectra of the adsorbed polymer were collected as a function of increasing concentration and as a function of time. Measurement of the peak intensities of the adsorbed polymer allowed adsorption isotherms and adsorption kinetics to be determined for both polymers. Langmuir adsorption isotherm analysis of in situ data yielded Gibbs free energies of adsorption (deltaG0(ads)) for Polymer-N and Polymer-H of -44.5 and -45.7 kJ/mol, respectively, which correlate well with similar values determined from ex situ adsorption isotherms. Kinetic analysis indicated that the adsorption of both polymers was a pseudo-first-order process. The apparent rate constants for Polymer-N and Polymer-H were 0.10 and 0.15 min(-1), respectively. Absence of spectral shifts in the spectra of adsorbed polymer is indicative of a hydrophobic interaction between the polyacrylamides and the talc surface.

Journal Article↗
PubMed2005

Drawing out the structural information of the first layer of hydrated ions: ATR-FTIR spectroscopic studies on aqueous NH4NO3, NaNO3, and Mg(NO3)2 solutions.

ATR-FTIR technique was used to obtain the difference spectra of aqueous NH4NO3 NaNO3, and Mg(NO3)2 solutions, with NO3- concentrations ranging from 0 to 4.00 mol dm(-3). The water monomers weakly hydrogen bonded with NO3- ions showed a positive peak near at 3565 cm(-1) for both Mg(NO3)2 and NH4NO3 solutions. The positive peak was shift to approximately 3543 cm(-1) for NaNO3 solutions due to the total contributions of the hydrated NO3- (approximately 3565 cm(-1)) and the hydrated Na+ (approximately 3440 cm(-1)). Compared with perchlorate solutions, the positive peak of nitrate solutions has a red shift of about 20 cm(-1) and the peak area is about half of that of perchlorate solutions with the same concentrations, indicating that the hydrogen bonding between NO3- and water monomers is relative stronger than that between ClO4- and water monomers, and NO3- has a strict requirement on the orientation of water molecules when hydrogen bonded with water monomers due to its planar structure. The ab initio calculations were used to understand the splitting of the nu3 band and hydration effect on the infrared activation of the nu1. The absorbance of nu3b, nu1 and nu2 bands, dependent on the type of cations, was observed to departed from Beer low with increasing concentrations, which is considered as the results of the interactions between cations and nitrate ions.

Magnesium Compounds↗
PubMed2005

ATR-FTIR spectroscopy as a way to identify natural protein-based materials, tortoiseshell and horn, from their protein-based imitation, galalith.

This paper presents a new totally non-destructive methodology, for the identification of protein-based materials, tortoiseshell, horn and galalith, on heritage objects. Attenuated total reflexion (ATR) infrared spectroscopy combined to a deconvolution procedure of amide I band was performed to characterize the secondary structure of these materials and allows us to identify each material. The component at 1639 cm(-1), attributed to the amide group involved in hydrated random-coil domains, allows us to distinguish horn from galalith and tortoiseshell. A second component, at 1614 cm(-1), assigned to amide group involved in protein self-association, allows us to differentiate galalith and tortoiseshell. This differentiation is applicable to both raw and manufactured materials. Then, we applied our models to identify what unknown object was made of.

Animal Structures↗
PubMed2006

Applications of diamond crystal ATR FTIR spectroscopy to the characterization of ambers.

Diamond crystal ATR FTIR spectroscopy is a rapid technique with virtually no sample preparation which requires small sample amounts and showed potential in the study of ambers. FTIR spectra of ambers present discriminating patterns and can be used to distinguish amber from immature resins as copal, to determine local or Baltic origin of archaeological ambers and to detect most of the falsifications encountered in the amber commercialisation.

Amber↗
PubMed2006

Radiation and new molecular agents part I: targeting ATM-ATR checkpoints, DNA repair, and the proteasome.

In response to DNA breaks, human cells delay their progression through the G1, S, and G2 phases of the cell cycle. This response requires the coordinated effort of the ATM-CHK2-p53 and ATR-CHK1 DNA damage-sensing pathways and DNA repair (eg, DNA-PK and RAD51 complexes). The turnover of many of these DNA damage-associated proteins is controlled by the 26S proteasome. In this article, we review molecular strategies that target each of these pathways using silencing RNA (siRNA), antisense, or small-molecule inhibition. Although these agents can radiosensitize tumor cells, little data are available regarding potential effects on normal tissues to determine the potential therapeutic ratio of these strategies after fractionated radiotherapy. Clinical trials using such agents will require novel correlative science endpoints to track DNA repair and cell-cycle arrest and will need careful assessment of normal tissue toxicity and stability.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2002

ATR-FTIR difference spectroscopy of the P(M) intermediate of bovine cytochrome c oxidase.

Perfusion-induced attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was used to investigate changes induced in protein and cofactors of bovine cytochrome c oxidase when it was converted from the oxidised state to the catalytic P(M) intermediate. The transition was induced in a film of detergent-depleted 'fast' oxidase with a buffer containing CO and O(2). The extent of formation of the P(M) state was quantitated simultaneously by monitoring formation of its characteristic 607-nm band with a scanned visible beam reflected off the top surface of the prism. The P(M) minus O FTIR difference spectrum is distinctly different from the redox spectra reported to date and includes features that can be assigned to changes of haem a(3) and surrounding protein. Tentative assignments are made based on vibrational data of related proteins and model compounds.

Animals↗
PubMed2001

Attenuated total reflection (ATR) Fourier transform infrared spectroscopy of dimyristoyl phosphatidylserine-cholesterol mixtures.

Mixtures of cholesterol with dimyristoyl phosphatidylserine or deuterated dimyristoyl phosphatidylserine were investigated by polarized and non polarized attenuated total reflection (ATR) Fourier transform infrared (FTIR) Spectroscopy. From polarized spectra the dichroic ratios of various vibrations as a function of cholesterol were calculated. Dichroic ratios of methylene vibration (CH(2)) 2934 cm(-1) of cholesterol decreases with increase of cholesterol concentration leveling off in the region where cholesterol phase separation takes place. The orientation of deuterated methylene (CD(2)) symmetric and asymmetric bands of the deuterated dimyristoyl phosphatidylserine is influenced little by cholesterol. In the polar region of dimyristoyl phosphatidylserine no effect of cholesterol on the dichroic ratios of carbonyl (C==O) and asymmetric phosphate (PO(2)(-)) vibrations were detected. For nonpolarized spectra the broad bands in the polar region of the phospholipid were deconvoluted. The carbonyl band (C==O) in pure dimyristoyl phosphatidylserine is composed of five bands; in the presence of increasing concentrations of cholesterol conformational change of these vibrations takes place evolving into one predominant band. Similar conformational change takes place in the presence of 75 molecules water/molecule DMPS. For the asymmetric phosphate band very small shifts due to interaction with cholesterol were detected.

Cholesterol↗
PubMed2003

The effect of isoflurane on erythrocyte membranes studied by ATR-FTIR.

The effect of isoflurane on erythrocyte membranes has been investigated by means of attenuated total reflection infrared spectroscopy. Infrared spectra were measured on sonicated erythrocyte ghosts layered upon a ZnSe crystal covered with D(2)O saline solutions containing increasing amounts of isoflurane. At clinically relevant anesthetic concentrations and 37 degrees C, significant changes in the structural and dynamic properties of the membrane phospholipid bilayers are observed. Both the acyl chain methylene symmetric and asymmetric stretching modes and the carbonyl ester stretching band displayed frequency shifts interpreted as transitions toward disordered liquid-like structure accompanied by dehydration of the phospholipid polar heads. In turn, no secondary structure-linked changes are observed in the amide I region of membrane proteins. Higher anesthetic concentrations (500-900 microM), resulted in progressive detachment of the multilayers from the ATR crystal and irreversible formation of denatured protein. Polarization studies in correspondence of the acyl lipid methylene stretching bands indicated that isoflurane decreases the dichroic ratio thus inducing disorder in the orientation of the lipid acyl chains.

Deuterium Oxide↗
PubMed2001

Highly concentrated phenolic wastewater treatment by the photo-Fenton reaction, mechanism study by FTIR-ATR.

Phenol degradation by Photo-Fenton reaction has been studied in highly concentrated wastewaters and most intermediate species have been identified by Fourier Transform IR-Spectroscopy with ATR device. During the photodegradation of highly concentrated phenol solutions, the formation of dissolved and precipitate tannin has been observed. The possibility of a Fe3+-Pyrogallol complex formation, previous to the tannin formation, has been proposed too. The complex formation involving Fe3+ ions could be related to the observed Photo-Fenton activity decrease. Tannin formation inhibits the complete mineralization of phenol because *OH radicals attack will produce further condensation steps and the polymer size increase. This fact limits the applicability of the process for highly concentrated phenolic wastes mineralization. However, the tannin precipitation allows its separation from the solution by conventional filtration, and reduction of the corresponding dissolved organic carbon. These observations have been proved from the identification of primary degradation products, catechol and hydroquinone. Catechol is considered to be the first step for the formation of tannins. Degradation process for phenol, catechol and hydroquinone have been monitored by total organic carbon (TOC) measurements along the reaction time span. From these results, a global mechanism for the Photo-Fenton degradation of phenol is proposed.

Environmental Monitoring↗
PubMed2000

FTIR-ATR spectroscopy for monitoring polyanhydride/anhydride-amine reactions.

The reactivity of 1,3-bis(p-carboxyphenoxy) propane:sebacic acid anhydride copolymer (CPPSA1:6), myristic and benzoic anhydrides with amine nucleophiles were investigated in non-polar solvents. FTIR-ATR (attenuated total reflectance) spectroscopy was used to monitor the polyanhydride/anhydride reaction rates in dichloromethane, dichloroethane, chloroform, and 1,4-dioxane solutions at room temperature. The reaction kinetics was determined by measuring the anhydride peak loss with time. Aminolysis resulted from nucleophilic attack of the added amine on the carbonyl group of the anhydride moiety. Primary and secondary amines reacted to form amides and the reaction followed second-order kinetics. Second-order rate constants and reaction half-life (t(1/2)) were calculated from the semilog plots of [anhydride]/[amine] in 1,4-dioxane at room temperature. The aminolysis rate decreased with pK(a) of the amine reactant, and half-life (t(1/2)) decreased with increasing amine concentration, as expected. With trifluoroethylamine (pK(a) 5.8), myristic anhydride reacted about 6-fold faster than benzoic anhydride. The lower reaction rate of benzoic anhydride was due to the higher stability of the aromatic anhydride compared to aliphatic. The overall CPPSA1:6 copolymer reactivity was the sum of aliphatic-aliphatic (SA-SA), aliphatic-aromatic (SA-CPP), and aromatic-aromatic (CPP-CPP) anhydride linkage reactivities. Based on the monomer ratio, the probability of SA-SA, SA-CPP, and CPP-CPP dyads were calculated to be 0.74, 0.24, and 0.02, respectively. This indicated that CPPSA1:6 reactivity will mainly result from SA-SA and SA-CPP linkages. The second-order rate constants and t(1/2) obtained for CPPSA1:6 with TFEA were closer to those for myristic anhydride than benzoic anhydride with TFEA.

Algorithms↗