排序方式: 共有315条查询结果,搜索用时 46 毫秒
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Mateusz Chwastyk Albert Galera–Prat Mateusz Sikora Àngel Gómez‐Sicilia Mariano Carrión‐Vázquez Marek Cieplak 《Proteins》2014,82(5):717-726
We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single‐molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single‐molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force‐extension patterns of the guest protein. We study examples of such systems within a coarse‐grained structure‐based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force‐displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single‐molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure. Proteins 2014; 82:717–726. © 2014 Wiley Periodicals, Inc. 相似文献
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Katarzyna Pogoda Mateusz Cieluk Piotr Deptua Grayna Tokajuk Ewelina Piktel Grzegorz Krl Joanna Resze Robert Bucki 《Translational oncology》2021,14(7)
Oral leukoplakia is a clinical term relating to various morphological lesions, including squamous cell hyperplasia, dysplasia and carcinoma. Leukoplakia morphologically manifested as hyperplasia with epithelial dysplasia is clinically treated as precancerous condition. Nevertheless, there is a lack of good markers indicating the transformation of premalignancies towards cancer. A better understanding of the mechanical environment within the tissues where tumors grow might be beneficial for the development of prevention, diagnostic, and treatment methods in cancer management. Atomic force microscopy (AFM) and immunohistology techniques were used to assess changes in the stiffness and morphology of oral mucosa and leukoplakia samples at different stages of their progression towards cancer. The Young''s moduli of the tested leukoplakia samples were significantly higher than those of the surrounding mucus. Robust inhomogeneity of stiffness within leukoplakia samples, reflecting an increase in regeneration and collagen accumulation (increasing density) in the extracellular matrix (ECM), was observed. Within the histologically confirmed cancer samples, Young''s moduli were significantly lower than those within the precancerous ones. Inhomogeneous stiffness within leukoplakia might act as “a mechanoagonist” that promotes oncogenesis. In contrast, cancer growth might require the reorganization of tissue structure to create a microenvironment with lower and homogenous stiffness. The immunohistology data collected here indicates that changes in tissue stiffness are achieved by increasing cell/ECM density. The recognition of new markers of premalignancy will aid in the development of new therapies and will expand the diagnostic methods. 相似文献
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G-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully understood at the molecular level. Here, we used all-atom molecular dynamics to probe the microscopic origin of the G4 motif stability. By computing the free energy profiles governing the dissociation of the 3′-terminal G-tetrad in the telomeric parallel-stranded G4, we examined the thermodynamic and kinetic stability of a single G-tetrad, as a common structural unit of G4 DNA. Our results indicate that the energetics of guanine association alone does not explain the overall stability of the G-tetrad and that interactions involving sugar–phosphate backbone, in particular, the constrained minimization of the phosphate–phosphate repulsion energy, are crucial in providing the observed enthalpic stabilization. This enthalpic gain is largely compensated by the unfavorable entropy change due to guanine association and optimization of the backbone topology. 相似文献
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Mateusz Baca Danijela Popović Anna Lemanik Sandra Bañuls-Cardona Nicholas J. Conard Gloria Cuenca-Bescós Emmanuel Desclaux Helen Fewlass Jesus T. Garcia Tereza Hadravova Gerald Heckel Ivan Horáček Monika Vlasta Knul Loïc Lebreton Juan Manuel López-García Elisa Luzi Zoran Marković Jadranka Mauch Lenardić Xabier Murelaga Pierre Noiret Alexandru Petculescu Vasil Popov Sara E. Rhodes Bogdan Ridush Aurélien Royer John R. Stewart Joanna Stojak Sahra Talamo Xuejing Wang Jan M. Wójcik Adam Nadachowski 《Journal of Biogeography》2023,50(1):183-196
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Katarzyna Zmudczyńska-Skarbek Mateusz Barcikowski Adrian Zwolicki Lech Iliszko Lech Stempniewicz 《Polar Biology》2013,36(11):1659-1669
In the resource-limited Arctic environment, vegetation developing near seabird colonies is exceptionally luxuriant. Nevertheless, there are very few detailed quantitative studies of any specific plant species responses to ornithogenic manuring. Therefore, we studied variability of polar scurvygrass Cochlearia groe nlandica individual biomass and leaf width along a seabird influenced gradient determining environmental conditions for vegetation in south-west Spitsbergen. We found seabird colony effect being a paramount factor responsible for augmented growth of C. groenlandica. The species predominated close to the colony and reached the highest mean values of individual biomass (1.4 g) and leaf width (26.6 mm) 10 m below the colony. Its abundance and size declined towards the coast. Both C. groenlandica individual traits significantly decreased with distance from the colony, soil water and organic matter content and increased with guano deposition, soil δ 15N, conductivity, acidity and nitrate, phosphate and potassium ion content. Our study supports the hypothesis that seabirds have fundamental importance for vegetation growth in poor Arctic environment. Highly plastic species such as C. groenlandica may be a useful instrument in detecting habitat condition changes, for instance resulting from climate change. 相似文献
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Mateusz Tałanda 《Zoologica scripta》2016,45(1):1-8
Amphisbaenians are highly specialized limbless burrowing lizards of controversial relationships. Among fossil lizards, the Eocene (47 Ma) Cryptolacerta is allegedly closest to the amphisbaenian ancestor, but this is put in doubt in this study. Similarities between Cryptolacerta and amphisbaenians, such as limb reduction and expansion of the skull roof, may be a result of parallel evolution. Instead, the Late Cretaceous lizard Slavoia with well‐developed limbs and several plesiomorphic skull characters is proposed to be the oldest known stem amphisbaenian. This is supported by two different phylogenetic analyses and observations on numerous specimens together representing almost the whole skeleton. Among the unique features, that Slavoia shares with amphisbaenians, the most significant are vomers strongly underlapping palatines and pterygoid quadrate ramus tightly wrapping around posteromedial surface of quadrate. The anatomy of Slavoia suggests that the reinforcement of the snout in amphisbaenian evolution preceded the elongation of the postorbital part of the skull, and that of the body, as well as modification of the limbs. Reduction of its hindlimbs was more advanced than that of the forelimbs. The ancient geological age of the central Asiatic Slavoia suggests that diversification of the main North American amphisbaenian groups may have resulted from a faunal dispersals from Asia after the Late Cretaceous. 相似文献
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Mateusz Konczal Karolina J. Przesmycka Ryan S. Mohammed Karl P. Phillips Francisco Camara Sebastian Chmielewski Christoph Hahn Roderic Guigo Jo Cable Jacek Radwan 《Molecular ecology》2020,29(8):1494-1507
Determining the molecular basis of parasite adaptation to its host is an important component in understanding host–parasite coevolution and the epidemiology of parasitic infections. Here, we investigate short‐ and long‐term adaptive evolution in the eukaryotic parasite Gyrodactylus bullatarudis infecting Caribbean guppies (Poecilia reticulata), by comparing the reference genome of Tobagonian G. bullatarudis with other Platyhelminthes, and by analysing resequenced samples from local Trinidadian populations. At the macroevolutionary timescale, we observed duplication of G‐protein and serine proteases genes, which are probably important in host–parasite arms races. Serine protease also showed strong evidence of ongoing, diversifying selection at the microevolutionary timescale. Furthermore, our analyses revealed that a hybridization event, involving two divergent genomes, followed by recombination has dramatically affected the genetic composition of Trinidadian populations. The recombinant genotypes invaded Trinidad and replaced local parasites in all populations. We localized more than 300 genes in regions fixed in local populations for variants of different origin, possibly due to diversifying selection pressure from local host populations. In addition, around 70 genes were localized in regions identified as heterozygous in some, but not all, individuals. This pattern is consistent with a very recent spread of recombinant parasites. Overall, our results are consistent with the idea that recombination between divergent genomes can result in particularly successful parasites. 相似文献
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ABSTRACT Capsule: The Crested Lark Galerida cristata as an example of a species which selects habitats which have undergone agricultural intensification. Aims: To describe habitat preferences of the Crested Lark in western Poland. Methods: We surveyed 30 randomly chosen study plots (1?km2) in western Poland to detect breeding pairs of Crested Larks. Sentinel and direct observations in the field were used to provide habitat data. Generalized linear mixed models were used to determine what type of environments habitats were selected by the Crested Larks. Results: We recorded a total of 106 pairs of Crested Larks in 30 study plots. Birds inhabited farmland environments, where their preferred habitats included buildings, silage, and arable land with cereals. Conclusion: Silage, which is associated with agricultural intensification within agricultural landscapes, increased the chances of the occurrence of Crested Larks. 相似文献