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Stabilisation mechanism of the human transthyretin transporter protein by rosmarinic acid
Get PDFDedna transtiretinska amiloidoza je avtosomno dominantna bolezen. Nastane kot posledica mutacije v proteinu transtiretinu. Mutacije povzročajo strukturne spremembe proteina, ki jim sledi disociacija v monomere in kasneje agregacija monomerov ter tvorba amiloidnih vlakenc. Vlakenca se nalagajo v tkivih kot so živčevje, srce in ledvice. Nestabilno strukturo proteina, ki jo povzročajo mutacije, je možno stabilizirati z vezavo majhnih molekul na protein. Ena izmed takšnih molekul je rožmarinska kislina.
V magistrskem delu smo z uporabo računalniških simulacij molekulske dinamike ugotavljali, kako mutacija V30M vpliva na stabilnost strukture proteina transtiretina. Na protein smo vezali tudi rožmarinsko kislino in opazovali, ali se z vezavo stabilnost proteina spremeni. Pri tem smo uporabili dva različna načina parametrizacije polja sil za rožmarinsko kislino.
Za pripravo 6 simulacij molekulske dinamike smo uporabili program CHARMM-GUI, za samo izvedbo simulacij pa program NAMD. Rezultate smo vizualno pregledali in analizirali s programoma Chimera in Cytoscape. Analiza trajektorij molekulskih dinamik je obsegala izračun srednjega kvadrata odstopanja, analizo vodikovih vezi in analizo vseh nekovalentnih kontaktov.
Rezultati, ki smo jih pri tem dobili, kažejo, da mutacija V30M povzroči manj stabilno strukturo transtiretina. Avtomatsko parametrizirana rožmarinska kislina na stabilnost kompleksa protein-ligand za nemutirani protein ni imela velikega vpliva, medtem ko je ročno parametrizirana rožmarinska kislina zmanjšala število kontaktov med nemutiranim proteinom in ligandom. V primeru vezave ročno parametrizirane rožmarinske kisline pa smo zaznali veliko število kontaktov med proteinom in ligandom. Ob vezavi rožmarinske kisline na nemutirani protein smo zaznali manjšo stabilnost proteina. Vezava rožmarinske kisline na mutirani protein pa izboljša stabilnost proteina.Hereditary transthyretin amyloidosis is an autosomal dominant disease. The disease is caused by a mutation in the transthyretin protein. Mutations cause structural changes in the protein, followed by dissociation into monomers and subsequent aggregation of the monomers to form amyloid fibrils. Fibrils are deposited in organs such as the nervous system, heart and kidneys. The unstable protein structure caused by mutations can be stabilised by binding small molecules to the protein. One such molecule is rosmarinic acid.
In this thesis, we used computational molecular dynamics simulations to determine how the V30M mutation affects the stability of the structure of the transthyretin protein. We also bound rosmarinic acid to the protein and observed whether the binding changes the stability of the protein. Two different ways of the force field parameterisation for rosmarinic acid were used.
We applied CHARMM-GUI to prepare the 6 molecular dynamics simulations and NAMD to run them. The results were visually examined and analysed using Chimera and Cytoscape. The analysis of the molecular dynamics trajectories included the calculation of the Root Mean Square Deviation, the analysis of hydrogen bonds and the analysis of all non-covalent contacts.
The results obtained show that the V30M mutation results in a less stable transthyretin structure. The stability of the protein-ligand complex for the non-mutated protein was not significantly affected by the automatically parameterised rosmarinic acid, whereas the manually parameterised rosmarinic acid reduced the number of contacts between the non-mutated protein and the ligand. However, in the case of binding manually parameterised rosmarinic acid, a high number of contacts between the protein and the ligand was detected. Binding of rosmarinic acid to the mutated protein improves the stability of the protein. However, when rosmarinic acid was bound to the non-mutated protein, we detected lack of stability of the protein itself
Synthesis of functionalized magnetic nanoparticles with microwave oven for application in forward osmosis
Get PDFKonvencionalne tehnologije čiščenja vode so v preteklih letih zelo pripomogle k čiščenju odpadnih voda, vendar so vedno večje potrebe po čisti pitni vodi te tehnologije potisnile do njihovih skrajnih meja. Ena izmed rešitev problema čiščenja vode je proces napredne osmoze, ki za svoje delovanje potrebuje gonilno raztopino, ki ustvarja ustrezen osmotski tlak. V sklopu diplomske naloge smo sintetizirali magnetne nanodelce (MND) v mikrovalovni pečici in jih uspešno funkcionalizirali s (poli)akrilno kislino. Preučevali smo, kako vplivata čas in temperatura sinteze na končni osmotski tlak pripravljenih raztopin. Potrdili smo, da tako daljši čas kot tudi višja temperatura pri sintezi pripomoreta k višjemu osmotskemu tlaku raztopine MND. Visoki osmotski tlaki sintetiziranih magentnih nanodelcev nakazujejo, da bi takšne raztopine lahko uporabili kot gonilne raztopine v procesu napredne osmoze. MND smo karakterizirali s Fourierovo transformacijsko infrardečo spektroskopijo (FTIR), termogravimetrično analizo (TGA), dinamičnim sipanjem svetlobe (DLS), rentgensko praškovno difrakcijo (RTG) ter z merjenjem osmotskega tlaka. S pomočjo karakterizacije smo ugotovili, da so sintetizirani nanodelci mešanica goetita in maghemita. V diplomski nalogi so predstavljeni rezultati in meritve vseh opravljenih sintez, kot tudi diskusija rezultatov.Conventional water treatment technologies have made a significant contribution to wastewater treatment over the pase years, but the increasing demand for clean drinking water has pushed these technologies to their limits. One solution to the water treatment problem is the forward osmosis process, which requieres drive solutions to generate the sufficient osmotic pressure. In this work, magnetic nanoparticles were synthesised in a microwave oven and successfully functionalized with poly(acrylic acid). We investigated how the time and temperature of synthesis affect the final osmotic pressure of the synthesised solutions. We confirmed that longer synthesis time and higher synthesis temperature lead to higher osmotic pressure of the magnetic nanoparticle solution. The high osmotic pressures of the synthesised solutions indicate that these solutions could be used as driving solutions in the forward osmosis process. The magnetic nanoparticles were characterised by Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), dynamic light scattering (DLS), X – ray diffraction (RTG) and osmotic pressure measurements. The characterization revealed that the synthesised nanoparticles are a mixture of goethite and maghemite. The results and measurements of all the syntheses we performed, as well as a discussion of the results, are presented in the thesis. Graphs and figures are shown to illustrate the work that has been carried out
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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