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PubMed2004

Chromosomal instability and ATR amplification gene in patients with persistent and polyclonal B-cell lymphocytosis (PPBL).

Forty-three patients with persistent and polyclonal B-cell lymphocytosis (PPBL) were studied. The PPBL diagnosis was based on the presence of a polyclonal lymphocytosis and the detection of binucleated lymphoid cells on peripheral blood examination. In order to define the cytogenetic profile in these patients, conventional cytogenetic analysis and fluorescence in situ hybridization were performed at diagnosis in all patients and also at follow-up in 10 patients. When excluding + i(3q) and PCC, chromosomal instability is a common occurrence in PPBL and is characterized by other independent clonal abnormalities, del(6q), + der(8) or + 8, polyploid karyotype, structural changes, aneuploidy and/or non clonal chromosomal aberrations with either loss or more frequently gain of chromosomes. These data show the presence of a chromosomal instability in 67.5% of PPBL patients. Finally, ATR amplification was detected by hybridization with BAC probe 26217 in + i(3q) positive metaphase cells. No ATR deletion was observed in the + i(3q) negative B-cells. As the natural history of PPBL remains unclear, it is necessary to diagnose PPBL patients and useful to recommend a careful and continued long follow-up in all PPBL patients.

Adult↗
PubMed2006

Direct requirement for Xmus101 in ATR-mediated phosphorylation of Claspin bound Chk1 during checkpoint signaling.

TopBP1-like proteins, which include Xenopus laevis Xmus101, are required for DNA replication and have been linked to replication checkpoint control. A direct role for TopBP1/Mus101 in checkpoint control has been difficult to prove, however, because of the requirement for replication in generating the DNA structures that activate the checkpoint. Checkpoint activation occurs in X. laevis egg extracts upon addition of an oligonucleotide duplex (AT70). We show that AT70 bypasses the requirement for replication in checkpoint activation. We take advantage of this replication-independent checkpoint system to determine the role of Xmus101 in the checkpoint. We find that Xmus101 is essential for AT70-mediated checkpoint signaling and that it functions to promote phosphorylation of Claspin bound Chk1 by the ataxia-telangiectasia and Rad-3-related (ATR) protein kinase. We also identify a separation-of-function mutant of Xmus101. In extracts expressing this mutant, replication of sperm chromatin occurs normally; however, the checkpoint response to stalled replication forks fails. These data demonstrate that Xmus101 functions directly during signal relay from ATR to Chk1.

Adaptor Proteins, Signal Transducing↗
PubMed1996

ATRX encodes a novel member of the SNF2 family of proteins: mutations point to a common mechanism underlying the ATR-X syndrome.

It was shown recently that mutations of the ATRX gene give rise to a severe, X-linked form of syndromal mental retardation associated with alpha thalassaemia (ATR-X syndrome). In this study, we have characterised the full-length cDNA and predicted structure of the ATRX protein. Comparative analysis shows that it is an entirely new member of the SNF2 subgroup of a superfamily of proteins with similar ATPase and helicase domains. ATRX probably acts as a regulator of gene expression. Definition of its genomic structure enabled us to identify four novel splicing defects by screening 52 affected individuals. Correlation between these and previously identified mutations with variations in the ATR-X phenotype provides insights into the pathophysiology of this disease and the normal role of the ATRX protein in vivo.

Amino Acid Sequence↗
PubMed1994

Adaptive acid tolerance response (ATR) in Aeromonas hydrophila.

Aeromonas hydrophila, a gastrointestinal pathogen of humans, was shown to exhibit a significant adaptive acid tolerance response (ATR) capable of protecting cells from severe acid at a pH of 3.5. The ATR was induced by exposure to a relatively mild pH level of 5.0 for 20 min. Adaptation required protein synthesis since treatment with chloramphenicol during adaptation to pH 5.0 prevented the development of acid tolerance. The adaptation to acid environment was found to be a non-transient phenomenon. Also, iron was not required for acid adaptation in A. hydrophila. Two-dimensional protein analyses revealed an increased production of 28 proteins and decreased synthesis of 10 following pH shifts from 7.2 to 5.0. The mild pH treatment must act as a signal to A. hydrophila to adapt and survive in acid environments by producing 'protective' proteins. The adaptation and survival of this pathogen in low pH may provide valuable information about its ability to withstand acid environments in nature and in the human gastrointestinal tract.

Acids↗
PubMed2002

A requirement for replication in activation of the ATR-dependent DNA damage checkpoint.

Using the Xenopus egg extract system, we investigated the involvement of DNA replication in activation of the DNA damage checkpoint. We show here that DNA damage slows replication in a checkpoint-independent manner and is accompanied by replication-dependent recruitment of ATR and Rad1 to chromatin. We also find that the replication proteins RPA and Polalpha accumulate on chromatin following DNA damage. Finally, damage-induced Chk1 phosphorylation and checkpoint arrest are abrogated when replication is inhibited. These data indicate that replication is required for activation of the DNA damage checkpoint and suggest a unifying model for ATR activation by diverse lesions during S phase.

Animals↗
PubMed2004

ATR couples FANCD2 monoubiquitination to the DNA-damage response.

Fanconi anemia (FA) is a multigenic autosomal recessive cancer susceptibility syndrome. The FA pathway regulates the monoubiquitination of FANCD2 and the assembly of damage-associated FANCD2 nuclear foci. How FANCD2 monoubiquitination is coupled to the DNA-damage response has remained undetermined. Here, we demonstrate that the ATR checkpoint kinase and RPA1 are required for efficient FANCD2 monoubiquitination. Deficiency of ATR function, either in Seckel syndrome, which clinically resembles Fanconi anemia, or by siRNA silencing, results in the formation of radial chromosomes in response to the DNA cross-linker, mitomycin C (MMC), thus mimicking the chromosome instability of FA cells.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2000

Requirement for Atr in phosphorylation of Chk1 and cell cycle regulation in response to DNA replication blocks and UV-damaged DNA in Xenopus egg extracts.

The checkpoint kinase Xchk1 becomes phosphorylated in Xenopus egg extracts in response to DNA replication blocks or UV-damaged DNA. Xchk1 is also required for the cell cycle delay that is induced by unreplicated or UV-damaged DNA. In this report, we have removed the Xenopus homolog of ATR (Xatr) from egg extracts by immunodepletion. In Xatr-depleted extracts, the checkpoint-associated phosphorylation of Xchk1 is abolished, and the cell cycle delay induced by replication blocks is strongly compromised. Xatr from egg extracts phosphorylated recombinant Xchk1 in vitro, but not a mutant form of Xchk1 (Xchk1-4AQ) containing nonphosphorylatable residues in its four conserved SQ/TQ motifs. Recombinant human ATR, but not a kinase-inactive mutant, phosphorylated the same sites in Xchk1. Furthermore, the Xchk1-4AQ mutant was found to be defective in mediating a checkpoint response in egg extracts. These findings suggest that Xchk1 is a functionally important target of Xatr during a checkpoint response to unreplicated or UV-damaged DNA.

Amino Acid Motifs↗
PubMed2002

ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones.

Budding yeast Mec1, homolog of mammalian ATR, is an essential protein that mediates S-phase checkpoint responses and meiotic recombination. Elimination of Mec1 function leads to genomewide fork stalling followed by chromosome breakage. Breaks do not result from stochastic collapse of stalled forks or other incidental lesions; instead, they occur in specific regions of the genome during a G2 chromosomal transition. Break regions are found to be genetically encoded replication slow zones (RSZs), a newly discovered yeast chromosomal determinant. Thus, Mec1 has important functions in normal S phase and the genome instability of mec1 (and, analogously, ATR-/-) mutants stems from defects in these basic roles.

Chromosome Breakage↗
PubMed2002

Quantitative analysis of the relative transcript levels of ABC transporter Atr genes in Aspergillus nidulans by real-time reverse transcription-PCR assay.

The development of assays for quantitative analysis of the relative transcript levels of ABC transporter genes by real-time reverse transcription-PCR (RT-PCR) might provide important information about multidrug resistance in filamentous fungi. Here, we evaluate the potential of real-time RT-PCR to quantify the relative transcript levels of ABC transporter Atr genes from Aspergillus nidulans. The AtrA to AtrD genes showed different and higher levels in the presence of structurally unrelated drugs, such as camptothecin, imazalil, itraconazole, hygromycin, and 4-nitroquinoline oxide. We also verified the relative transcript levels of the Atr genes in the A. nidulans imazalil-resistant mutants. These genes displayed a very complex pattern in different ima genetic backgrounds. The imaB mutant has higher basal transcript levels of AtrB and -D than those of the wild-type strain. The levels of these two genes are comparable when the imaB mutant is grown in the presence and absence of imazalil. The imaC, -D, and -H mutants have higher basal levels of AtrA than that of the wild type. The same behavior is observed for the relative transcript levels of AtrB in the imaG mutant background.

ATP-Binding Cassette Transporters↗
PubMed2005

Inhibition of human Chk1 causes increased initiation of DNA replication, phosphorylation of ATR targets, and DNA breakage.

Human checkpoint kinase 1 (Chk1) is an essential kinase required to preserve genome stability. Here, we show that Chk1 inhibition by two distinct drugs, UCN-01 and CEP-3891, or by Chk1 small interfering RNA (siRNA) leads to phosphorylation of ATR targets. Chk1-inhibition triggered rapid, pan-nuclear phosphorylation of histone H2AX, p53, Smc1, replication protein A, and Chk1 itself in human S-phase cells. These phosphorylations were inhibited by ATR siRNA and caffeine, but they occurred independently of ATM. Chk1 inhibition also caused an increased initiation of DNA replication, which was accompanied by increased amounts of nonextractable RPA protein, formation of single-stranded DNA, and induction of DNA strand breaks. Moreover, these responses were prevented by siRNA-mediated downregulation of Cdk2 or the replication initiation protein Cdc45, or by addition of the CDK inhibitor roscovitine. We propose that Chk1 is required during normal S phase to avoid aberrantly increased initiation of DNA replication, thereby protecting against DNA breakage. These results may help explain why Chk1 is an essential kinase and should be taken into account when drugs to inhibit this kinase are considered for use in cancer treatment.

Ataxia Telangiectasia Mutated Proteins↗
PubMed1994

X linked mental retardation with non-deletional alpha thalassaemia (ATR-X): further delineation of the phenotype.

Two sibs with non-deletional alpha thalassaemia and mental retardation (ATR-X) have been ascertained showing variable neurological features. The proband had a complex neurological picture with recurrent apnoea, complex partial seizures, and prolonged periods of semiconsciousness between 12 and 17 months of age. Episodes of spontaneous laughter were also a feature. An EEG was initially normal. Hb H inclusions were present but rare in this family. The sole genital anomaly was deficiency of the foreskin, a feature not previously described in ATR-X.

Abnormalities, Multiple↗
PubMed2000

ATR-X mutations cause impaired nuclear location and altered DNA binding properties of the XNP/ATR-X protein.

Mutations in the XNP/ATR-X gene, located in Xq13.3, are associated with several X linked mental retardation syndromes, the best known being alpha thalassaemia with mental retardation (ATR-X). The XNP/ATR-X protein belongs to the family of SWI/SNF DNA helicases and contains three C2-C2 type zinc fingers of unknown function. Previous studies have shown that 65% of mutations of XNP have been found within the zinc finger domain (encoded by exons 7, 8, and the beginning of exon 9) while 35% of the mutations have been found in the helicase domain extending over 3 kb at the C-terminus of the protein. Although different types of mutations have been identified, no specific genotype-phenotype correlation has been found, suggesting that gene alteration leads to a loss of function irrespective of mutation type. Our aims were to understand the function of the XNP/ATR-X protein better, with specific attention to the functional consequences of mutations to the zinc finger domain. We used monoclonal antibodies directed against the XNP/ATR-X protein and performed immunocytochemical and western blot analyses, which showed altered or absent XNP/ATR-X expression in cells of affected patients. In addition, we used in vitro experiments to show that the zinc finger domain can mediate double stranded DNA binding and found that the DNA binding capacity of mutant forms in ATR-X patients is severely reduced. These data provide insights into the understanding of the functional significance of XNP/ATR-X mutations.

Active Transport, Cell Nucleus↗
PubMed2006

Drosophila ATR in double-strand break repair.

The ability of a cell to sense and respond to DNA damage is essential for genome stability. An important aspect of the response is arrest of the cell cycle, presumably to allow time for repair. Ataxia telangiectasia mutated (ATM) and ATR are essential for such cell-cycle control, but some observations suggest that they also play a direct role in DNA repair. The Drosophila ortholog of ATR, MEI-41, mediates the DNA damage-dependent G2-M checkpoint. We examined the role of MEI-41 in repair of double-strand breaks (DSBs) induced by P-element excision. We found that mei-41 mutants are defective in completing the later steps of homologous recombination repair, but have no defects in end-joining repair. We hypothesized that these repair defects are the result of loss of checkpoint control. To test this, we genetically reduced mitotic cyclin levels and also examined repair in grp (DmChk1) and lok (DmChk2) mutants. Our results suggest that a significant component of the repair defects is due to loss of MEI-41-dependent cell cycle regulation. However, this does not account for all of the defects we observed. We propose a novel role for MEI-41 in DSB repair, independent of the Chk1/Chk2-mediated checkpoint response.

Animals↗
PubMed2003

FTIR-ATR evaluation of organic contaminant cleaning methods for SiO2 surfaces.

The effectiveness of cleaning organic contaminants from silicon dioxide (SiO2) surfaces was studied by conducting highly sensitive measurements using Fourier Transform Infrared Attenuated Total reflectance (FTIR-ATR) with a Si prism as the waveguide. To serve as an example, the surface of the prism was oxidized to an order of a few nanometers. The oxidized Si surface film was allowed to stand in the atmosphere and then wet-cleaned in a repeated manner; subsequently its thickness was measured by ellipsometry. Although, various wet-cleaning methods were tested, they only showed values of 0.1-0.2 nm larger than, but not equal to, the original thickness immediately after oxidation. FTIR-ATR measurements of the spectral change after exposure to air revealed that organic species, such as C-CH3 and -(CH2)n-, increased with time. Wet-cleaning the sample failed to remove the C-CH3 species, which indicates that they corresponded to the film thickness increment from the original.

Journal Article↗
PubMed2006

Evaluation of fine structure of tubular zeolite NaA membrane by FTIR-ATR and FIB-TEM.

A zeolite NaA (LTA) membrane supported by an alumina porous support tube for pervaporation (PV) dehydration of ethanol was characterized by transmission electron microscopy (TEM) using a focused ion beam (FIB) thin-layer specimen preparation technique and by Fourier transform infrared attenuated total reflectance method (FTIR-ATR) using a diamond prism as the waveguide. FIB-TEM clearly presented cross-section images up to about 15 microm depth from the membrane surface. FTIR-ATR monitored the Si-O asymmetric stretching vibration spectrum. The Si-O spectrum was compared with the TEM image and their relationships were discussed. By combining the two methods, we could study the thickness of surface LTA crystals, the grain boundary, the LTA/alumina interface structure and the crystallinity and density of materials inside of the alumina porous support. Consequently, fine structure changes of the LTA membrane corresponding to the hydrothermal synthesis condition could be sensitively detected.

Aluminum↗
PubMed2006

FTIR-ATR study of the surface of a tubular zeolite NaA membrane ultrasonically reacted with water and acetic acid.

For the dehydration process of biomass alcohol using a zeolite NaA (LTA) membrane supported by an alumina porous support tube, it is very important to understand damage of the surface crystal, which may be caused by acetic acid. Therefore, the surface structure and the chemical composition of the LTA membrane that reacted with water or acetic acid (pH 3-4) were investigated by the Fourier Transform Infrared Attenuated Total Reflectance method (FTIR-ATR), with a diamond prism as the waveguide, scanning electron microscope and an energy-dispersive X-ray analysis. For leaching experiments using water and acetic acid, ultrasonication was applied to promote the leaching rate and to surely prepare damaged membranes as a model experiment. The Si-O asymmetric stretching vibration spectra of the original LTA membranes showed a bimodal peak. LTA membranes after water leaching also showed the same peak. However, for the LTA membrane reacted with acetic acid of pH 3, damage of the surface LTA crystal and the loss of sodium by dissolution were clearly observed. Also, its Si-O spectral shape was broad, which suggests amorphous-like substances secondarily formed on the membrane surface. Sodium acetate was not detected for all LTA membranes reacted with acetic acid. To evaluate surface-damaged and sodium-loss membranes, FTIR-ATR can sensitively detect a Si-O spectral change corresponding to the surface structure and the chemical composition of the LTA membrane.

Journal Article↗
PubMed2004

ATR and ATM-dependent movement of BLM helicase during replication stress ensures optimal ATM activation and 53BP1 focus formation.

The BLM helicase, a deficiency that markedly increases cancer incidence in humans, is required for optimal repair during DNA replication. We show that BLM rapidly moves from PML nuclear bodies to damaged replication forks, returning to PML bodies several hours later, owing to activities of the DNA damage response kinases ATR and ATM, respectively. Immunofluorescence and cellular fractionation demonstrate that BLM partitions to different sub-cellular compartments after replication stress. Unexpectedly, fibroblasts lacking BLM were deficient in phospho-ATM (S-1981) and 53-binding protein-1 (53BP1), and these proteins failed to form foci following replication stress. Expression of a dominant p53 mutant or helicase-deficient BLM restored replication stress-induced 53BP1 foci, but only mutant p53 restored optimal ATM activation. Thus, optimal repair of damaged replication fork lesions likely requires both ATR and ATM. BLM recruits 53BP1 to these lesions independent of its helicase activity, and optimal activation of ATM requires both p53 and BLM helicase activities.

Adenosine Triphosphatases↗
PubMed2000

Investigation of drug release from suspension using FTIR-ATR technique: part II. Determination of dissolution coefficient of drugs.

Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy was applied to a release experiment in order to determine the dissolution coefficient of drug particles in heterogeneous semisolid formulations. The drug release experiment was carried out using ketoconazole suspended in Vaseline with various amounts of paraffinum liquidum as donor and an artificial dodecanol-collodion (DDC) membrane as acceptor compartment. Monitoring changes in IR bands due to ketoconazole the decrease of the drug content near the ATR crystal ointment was followed as a function of time. A mathematical model based on Fick's second law with a source term was used to derive the apparent dissolution coefficient Kdis by numerical fitting the experimental data. It was found that Kdis is dependent on the fraction of paraffinum liquidum in the suspension. Taking into account all experimental parameters required, the transport process was simulated and discussed in terms of drug concentration- time and drug concentration- distance profiles. Calculating the area under the mass-time curve it was tried to predict the 'dermal bioavailability' in the acceptor (AUCa).

Antifungal Agents↗