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101.
María Isabel Ponferrada-Marín María Isabel Martínez-Macías Teresa Morales-Ruiz Teresa Roldán-Arjona Rafael R. Ariza 《The Journal of biological chemistry》2010,285(30):23032-23039
DNA cytosine methylation is an epigenetic mark that promotes gene silencing and performs critical roles during reproduction and development in both plants and animals. The genomic distribution of DNA methylation is the dynamic outcome of opposing methylation and demethylation processes. In plants, active demethylation occurs through a base excision repair pathway initiated by 5-methycytosine (5-meC) DNA glycosylases of the REPRESSOR OF SILENCING 1 (ROS1)/DEMETER (DME) family. To gain insight into the mechanism by which Arabidopsis ROS1 recognizes and excises 5-meC, we have identified those protein regions that are required for efficient DNA binding and catalysis. We have found that a short N-terminal lysine-rich domain conserved in members of the ROS1/DME family mediates strong methylation-independent binding of ROS1 to DNA and is required for efficient activity on 5-meC·G, but not for T·G processing. Removal of this domain does not significantly affect 5-meC excision from short molecules, but strongly decreases ROS1 activity on long DNA substrates. This region is not required for product binding and is not involved in the distributive behavior of the enzyme on substrates containing multiple 5-meC residues. Altogether, our results suggest that methylation-independent DNA binding allows ROS1 to perform a highly redundant search for efficient excision of a nondamaged, correctly paired base such as 5-meC in long stretches of DNA. These findings may have implications for understanding the evolution of structure and target specificity in DNA glycosylases. 相似文献
102.
Carles Pons Marco D’Abramo Dmitri I. Svergun Pau Bernadó Juan Fernández-Recio 《Journal of molecular biology》2010,403(2):217-230
X-ray crystallography and NMR can provide detailed structural information of protein-protein complexes, but technical problems make their application challenging in the high-throughput regime. Other methods such as small-angle X-ray scattering (SAXS) are more promising for large-scale application, but at the cost of lower resolution, which is a problem that can be solved by complementing SAXS data with theoretical simulations. Here, we propose a novel strategy that combines SAXS data and accurate protein-protein docking simulations. The approach has been benchmarked on a large pool of known structures with synthetic SAXS data, and on three experimental examples. The combined approach (pyDockSAXS) provided a significantly better success rate (43% for the top 10 predictions) than either of the two methods alone. Further analysis of the influence of different docking parameters made it possible to increase the success rates for specific cases, and to define guidelines for improving the data-driven protein-protein docking protocols. 相似文献
103.
Tracking down human contamination in ancient human teeth 总被引:1,自引:0,他引:1
Sampietro ML Gilbert MT Lao O Caramelli D Lari M Bertranpetit J Lalueza-Fox C 《Molecular biology and evolution》2006,23(9):1801-1807
DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental, problem that affects the reliability of ancient DNA (aDNA) studies. We have typed the mitochondrial DNA hypervariable region I of the only 6 people involved in the excavation, washing, and subsequent anthropological and genetic study of 23 Neolithic remains excavated from Granollers (Barcelona, Spain) and searched for their presence among the 572 clones generated during the aDNA analyses of teeth from these samples. Of the cloned sequences, 17.13% could be unambiguously identified as contaminants, with those derived from the people involved in the retrieval and washing of the remains present in higher frequencies than those of the anthropologist and genetic researchers. This finding confirms, for the first time, previous hypotheses that teeth samples are most susceptible to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time: contaminants that are >10 years old have approximately 5 times more damage than those that are recent. Furthermore, we demonstrate that in this data set, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA sequences can be used to support data authenticity is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results are accurate. 相似文献
104.
Noy A Meyer T Rueda M Ferrer C Valencia A Pérez A de la Cruz X López-Bes JM Pouplana R Fernandez-Recio J Luque FJ Orozco M 《Journal of biomolecular structure & dynamics》2006,23(4):447-456
Analysis, storage, and transfer of molecular dynamic trajectories are becoming the bottleneck of computer simulations. In this paper we discuss different approaches for data mining and data processing of huge trajectory files generated from molecular dynamic simulations of nucleic acids. 相似文献
105.
106.
beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus 下载免费PDF全文
Maiques E Ubeda C Campoy S Salvador N Lasa I Novick RP Barbé J Penadés JR 《Journal of bacteriology》2006,188(7):2726-2729
Antibiotics that interfere with DNA replication and cell viability activate the SOS response. In Staphylococcus aureus, the antibiotic-induced SOS response promotes replication and high-frequency horizontal transfer of pathogenicity island-encoded virulence factors. Here we report that β-lactams induce a bona fide SOS response in S. aureus, characterized by the activation of the RecA and LexA proteins, the two master regulators of the SOS response. Moreover, we show that β-lactams are capable of triggering staphylococcal prophage induction in S. aureus lysogens. Consequently, and as previously described for SOS induction by commonly used fluoroquinolone antibiotics, β-lactam-mediated phage induction also resulted in replication and high-frequency transfer of the staphylococcal pathogenicity islands, showing that such antibiotics may have the unintended consequence of promoting the spread of bacterial virulence factors. 相似文献
107.
Sandrine Vuillaumier-Barrot Céline Bouchet-Séraphin Malika Chelbi Louise Devisme Samuel Quentin Steven Gazal Annie Laquerrière Catherine Fallet-Bianco Philippe Loget Sylvie Odent Dominique Carles Anne Bazin Jacqueline Aziza Alix Clemenson Fabien Guimiot Maryse Bonnière Sophie Monnot Christine Bole-Feysot Jean-Pierre Bernard Laurence Loeuillet Marie Gonzales Koryna Socha Bernard Grandchamp Tania Attié-Bitach Férechté Encha-Razavi Nathalie Seta 《American journal of human genetics》2012,91(6):1135-1143
Cobblestone lissencephaly is a peculiar brain malformation with characteristic radiological anomalies. It is defined as cortical dysplasia that results when neuroglial overmigration into the arachnoid space forms an extracortical layer that produces agyria and/or a “cobblestone” brain surface and ventricular enlargement. Cobblestone lissencephaly is pathognomonic of a continuum of autosomal-recessive diseases characterized by cerebral, ocular, and muscular deficits. These include Walker-Warburg syndrome, muscle-eye-brain disease, and Fukuyama muscular dystrophy. Mutations in POMT1, POMT2, POMGNT1, LARGE, FKTN, and FKRP identified these diseases as alpha-dystroglycanopathies. Our exhaustive screening of these six genes, in a cohort of 90 fetal cases, led to the identification of a mutation in only 53% of the families, suggesting that other genes might also be involved. We therefore decided to perform a genome-wide study in two multiplex families. This allowed us to identify two additional genes: TMEM5 and ISPD. Because TMEM has a glycosyltransferase domain and ISPD has an isoprenoid synthase domain characteristic of nucleotide diP-sugar transferases, these two proteins are thought to be involved in the glycosylation of dystroglycan. Further screening of 40 families with cobblestone lissencephaly identified nonsense and frameshift mutations in another four unrelated cases for each gene, increasing the mutational rate to 64% in our cohort. All these cases displayed a severe phenotype of cobblestone lissencephaly A. TMEM5 mutations were frequently associated with gonadal dysgenesis and neural tube defects, and ISPD mutations were frequently associated with brain vascular anomalies. 相似文献
108.
Sandrine Vuillaumier-Barrot Céline Bouchet-Séraphin Malika Chelbi Louise Devisme Samuel Quentin Steven Gazal Annie Laquerrière Catherine Fallet-Bianco Philippe Loget Sylvie Odent Dominique Carles Anne Bazin Jacqueline Aziza Alix Clemenson Fabien Guimiot Maryse Bonnière Sophie Monnot Christine Bole-Feysot Jean-Pierre Bernard Laurence Loeuillet Marie Gonzales Koryna Socha Bernard Grandchamp Tania Attié-Bitach Férechté Encha-Razavi Nathalie Seta 《American journal of human genetics》2012
109.
Harvesting the microalgae Phaeodactylum tricornutum with polyaluminum chloride, aluminium sulphate, chitosan and alkalinity-induced flocculation 总被引:1,自引:0,他引:1
Sema ?irin Rosa Trobajo Carles Ibanez Joan Salvadó 《Journal of applied phycology》2012,24(5):1067-1080
The purpose of this study was to explore efficient methods of harvesting the microalga Phaeodactylum tricornutum. Natural sedimentation experiments, performed at different light and temperature conditions, did not yield significant improvements in efficiency even after 1?week. When alkalinity-induced flocculation was performed, both the flocculation efficiency and the concentration factor dramatically improved at pH?=?9.75 (0.5–0.7 units over the original pH of the culture) after 10?min settling time. Sedimentation rates are documented at pH ranging between pH?9.75 and 11.0. The results of the application of two conventional flocculants used in wastewater treatment, polyaluminium chloride and aluminium sulphate, are also presented. Chitosan was also used as a natural flocculating agent to improve possible contamination problems in the downstream process. pH was adjusted in order to determine optimum flocculation efficiency of chitosan in combination with a high concentration factor. Satisfactory results were found with chitosan at an adjusted pH of 9.9 using concentrations as low as 20?mg?L?1, after testing a flocculant range of 5–200?mg?L?1. 相似文献