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131.
Kai Budde Jacob Smith Pia Wilsdorf Fiete Haack Adelinde M. Uhrmacher 《PLoS computational biology》2021,17(8)
For many biological systems, a variety of simulation models exist. A new simulation model is rarely developed from scratch, but rather revises and extends an existing one. A key challenge, however, is to decide which model might be an appropriate starting point for a particular problem and why. To answer this question, we need to identify entities and activities that contributed to the development of a simulation model. Therefore, we exploit the provenance data model, PROV-DM, of the World Wide Web Consortium and, building on previous work, continue developing a PROV ontology for simulation studies. Based on a case study of 19 Wnt/β-catenin signaling models, we identify crucial entities and activities as well as useful metadata to both capture the provenance information from individual simulation studies and relate these forming a family of models. The approach is implemented in WebProv, a web application for inserting and querying provenance information. Our specialization of PROV-DM contains the entities Research Question, Assumption, Requirement, Qualitative Model, Simulation Model, Simulation Experiment, Simulation Data, and Wet-lab Data as well as activities referring to building, calibrating, validating, and analyzing a simulation model. We show that most Wnt simulation models are connected to other Wnt models by using (parts of) these models. However, the overlap, especially regarding the Wet-lab Data used for calibration or validation of the models is small. Making these aspects of developing a model explicit and queryable is an important step for assessing and reusing simulation models more effectively. Exposing this information helps to integrate a new simulation model within a family of existing ones and may lead to the development of more robust and valid simulation models. We hope that our approach becomes part of a standardization effort and that modelers adopt the benefits of provenance when considering or creating simulation models. 相似文献
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133.
Karl M Stuhlmeier Janet J Kao Pia Wallbrandt Maria Lindberg Barbro Hammarstr?m Hans Broell Beverly Paigen 《European journal of biochemistry》2003,270(2):334-341
Antioxidant protein 2 (AOP2) is a member of a family of thiol-specific antioxidants, recently renamed peroxiredoxins, that evolved as part of an elaborate system to counteract and control detrimental effects of oxygen radicals. AOP2 is found in endothelial cells, erythrocytes, monocytes, T and B cells, but not in granulocytes. AOP2 was found solely in the cytoplasm and was not associated with the nuclear or membrane fractions; neither was it detectable in plasma. Further experiments focused on the function of AOP2 in erythrocytes where it is closely associated with the hemoglobin complex, particularly with the heme. An investigation of the mechanism of this interaction demonstrated that the conserved cysteine-47 in AOP2 seems to play a role in AOP2-heme interactions. Recombinant AOP2 prevented induced as well as noninduced methemoglobin formation in erythrocyte hemolysates, indicating its antioxidant properties. We conclude that AOP2 is part of a sophisticated system developed to protect and support erythrocytes in their many physiological functions. 相似文献
134.
Virulence of parasites in hosts under environmental stress: experiments with anoxia and starvation 总被引:4,自引:0,他引:4
Most environments periodically impose severe stress that may cause high mortality and alter population structure, for example, by removing sick and old individuals. We examined how anoxic conditions and starvation of the host affect virulence of two closely related trematode parasites, Rhipidocotyle campanula and R. fennica . These parasites differ by prevalence of infection and by exploitation rate of individual hosts (freshwater clam, Anodonta piscinalis ). Infection by R. campanula is rare (<5% prevalence of infection) and destroys on average 90% of the gonad tissue of the individual host. Infection by R. fennica is more common (20–60% prevalence of infection) and leads to on average 30% gonad destruction. In the end, both infections lead to host infertility. We predicted that R. campanula induces higher host mortality than R. fennica under host stress. In two laboratory experiments, we exposed naturally-infected and uninfected clams to anoxia and to starvation. Anoxia occasionally takes place during winter in eutrophic lakes, while some degree of starvation should occur seasonally. We found that mortality rate of clams was much higher under anoxia than under starvation, and that infection increased mortality rate under both types of host stress. As predicted, R. campanula induced higher host mortality than R. fennica . Host survival was population-specific, suggesting that clams of different origins carried different amount of energy reserves. Severe environmental perturbation may remove R. campanula infected individuals from the host population, but recolonization from the fish host is likely to prevent extinction of the parasite suprapopulation. The observed high host mortality induced by R. campanula may be one ecological explanation for the consistently lower prevalence of infection of R. campanula when compared to R. fennica . 相似文献
135.
Azzurra Stefanucci Andrea Angeli Marilisa Pia Dimmito Grazia Luisi Sonia Del Prete Clemente Capasso 《Journal of enzyme inhibition and medicinal chemistry》2018,33(1):945-950
Six tripeptides incorporating acidic amino acid residues were prepared for investigation as activators of β- and γ-carbonic anhydrases (CAs, EC 4.2.1.1) from the pathogenic bacteria Vibrio cholerae, Mycobacterium tuberculosis, and Burkholderia pseudomallei. The primary amino acid residues that are involved in the catalytic mechanisms of these CA classes are poorly understood, although glutamic acid residues near the active site appear to be involved. The tripeptides that contain Glu or Asp residues can effectively activate VchCAβ and VchCAγ (enzymes from V. cholerae), Rv3273 CA (mtCA3, a β-CA from M. tuberculosis) and BpsCAγ (γ-CA from B. pseudomallei) at 0.21–18.1?µM levels. The position of the acidic residues in the peptide sequences can significantly affect bioactivity. For three of the enzymes, tripeptides were identified that are more effective activators than both l-Glu and l-Asp. The tripeptides are also relatively selective because they do not activate prototypical α-CAs (human carbonic anhydrases I and II). Because the role of CA activators in the pathogenicity and life cycles of these infectious bacteria are poorly understood, this study provides new molecular probes to explore such processes. 相似文献
136.
Tel1/ATM prevents degradation of replication forks that reverse after topoisomerase poisoning 下载免费PDF全文
Luca Menin Sebastian Ursich Camilla Trovesi Ralph Zellweger Massimo Lopes Maria Pia Longhese Michela Clerici 《EMBO reports》2018,19(7)
In both yeast and mammals, the topoisomerase poison camptothecin (CPT) induces fork reversal, which has been proposed to stabilize replication forks, thus providing time for the repair of CPT‐induced lesions and supporting replication restart. We show that Tel1, the Saccharomyces cerevisiae orthologue of human ATM kinase, stabilizes CPT‐induced reversed forks by counteracting their nucleolytic degradation by the MRX complex. Tel1‐lacking cells are hypersensitive to CPT specifically and show less reversed forks in the presence of CPT. The lack of Mre11 nuclease activity restores wild‐type levels of reversed forks in CPT‐treated tel1Δ cells without affecting fork reversal in wild‐type cells. Moreover, Mrc1 inactivation prevents fork reversal in wild‐type, tel1Δ, and mre11 nuclease‐deficient cells and relieves the hypersensitivity of tel1Δ cells to CPT. Altogether, our data indicate that Tel1 counteracts Mre11 nucleolytic activity at replication forks that undergo Mrc1‐mediated reversal in the presence of CPT. 相似文献
137.
Julius Pia 《Molecular & general genetics : MGG》1922,30(1):63-98
Ohne ZusammenfassungVergleiche: J. Pia: DieSiphoneae verticillatae vom Karbon bis zur Kreide. Abhandl. Zool.-bot. Ges. Wien. Bd. 11. Heft 2. 1920. Mit Literaturliste. Seit dem Erscheinen dieser Arbeit sind mir folgende wichtigere einschlägige Veröffentlichungen bekannt geworden:A. Andreae: Ein Beitrag zur Kenntnis des Elsässer Tertiärs. Abhandl. z. geol. Spezialk. v. Elsaß-Lotr. vol. 2. fasc. 3. Straßburg 1884.A. Baretti: Contributo allo studio delleSiphoneae Verticillatae del calcare di Villanova-Mondovi. Atti soc. Ital. sc. nat. vol. 58. Pavia 1919. p. 216.F. Börgesen: The Marine Algae of the Danish West Indies. Part. 1.Chlorophyceae. Dansk. Bot. Arkiv. vol. 1. No. 4. 1913.F. Börgesen: The Marine Algae of the Danish West Indies. III.Rhodophyceae with Addenda to theChlorophyceae, Phaeophyceae andRhodophyceae. Ebendort. vol. 3. No. 1a–f. 1917–20.S. v. Bubnoff: Die ladinische Fauna von Forno (Mezzovalle) bei Predazzo. Verhandl. Heidelb. Naturh.-mediz. Vereins 1920. N. F. Bd. 14. S. 257.E. Fossa-Mancini:Sifoneae verticillatae triasiche e liassiche dell' Appennino umbro-marchigiano. Pro. verb. soc. Tosc. sc. nat. vol. 30. 10. III. 1921.M. Gortani: La fauna permocarbonifera del Col Mezzodi presso Forni Avoltri. Pal. Ital. vol. 12. 1906. p. 1.J. Kiaer: Oversigt over Kalkalgefloraerna i Norges Ordovicium og Silur. Norsk Geol. Tidskr. vol. 6. 1921. p. 113.O. Lignier: Végétaux fossiles de Normandie. VI. — Flore jurassique de Mamers (Sarthe). Mém. soc. Linn. Normandie. vol. 24. 1911–13. fasc. 1. p. 1.O. Lignier: Végétaux fossiles de Normandie. VII. — Contribution à la flore jurassique. Ebendort fasc. 2. 1913. p. 67.L. Morellet: Deux Algues siphonées verticillées du Thanétien de Boncourt (Oise). Bull. soc. géol. France ser. 4. vol. 8. 1908. p. 96.L. Morellet et J. Morellet: Les Dasycladacées du Tertiaire Parisien. Mém. soc. géol. France, Paléontologie. vol. 21. fasc. 1. Mém. No. 47. 1913.L. Morellet: Note sur les algues siphonées. In H. Douvillé: Le crétacé et l'éocène du Tibet central. Pal. Indica, New Ser. vol. 5. Mém. No. 3. p. 47. 1916.Munier-Chalmas: Notes préliminaires pour servir à l'étude des terrains crétacées. Bull. soc. géol. France. ser. 3. vol. 25. 1897. p. 82.Ph. Négris: Roches cristallophylliennes et tectonique de la Grèce. 2e appendice. Athènes 1919.S. Squinabol: Di una specie fossile di Acetabularia. Atti e Mem. Acc. sc. Padova, n. s. vol. 18. 1902. p. 151.Mit Tafel 1. 相似文献
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