1,720,957 research outputs found
The bottleneck for maternal transmission of mtDNA is linked to purifying selection by autophagy
No full textMammalian mitochondrial DNA (mtDNA) inheritance differs fundamentally from nuclear inheritance owing to exclusive maternal transmission, high mutation rate, and lack of recombination. Two key mechanisms shape this inheritance: the bottleneck, which drives stochastic transmission of maternal mtDNA variants, and purifying selection, which actively removes mutant mtDNA. Whether these mechanisms interact has been unresolved. To address this question, we generated a series of mouse models with random mtDNA mutations alongside alleles altering mtDNA copy number or decreasing autophagy. We demonstrate that tightening the mtDNA bottleneck increases heteroplasmic variance between individuals, causing lower mutational burden and nonsynonymous-to-synonymous ratios. In contrast, reduced autophagy weakens purifying selection, leading to decreased interoffspring heteroplasmic variance and increased mutational burden with higher nonsynonymous-to-synonymous ratios. These findings provide experimental evidence that the mtDNA bottleneck size modulates the efficacy of purifying selection. Our findings yield fundamental insights into the processes governing mammalian mtDNA transmission with direct implications for the origin and propagation of mtDNA mutations causing human disease.Revealing mechanisms of mtDNA transmission is critical for combating human disease.Mammalian mitochondrial DNA (mtDNA) inheritance differs fundamentally from nuclear inheritance owing to exclusive maternal transmission, high mutation rate, and lack of recombination. Two key mechanisms shape this inheritance: the bottleneck, which drives stochastic transmission of maternal mtDNA variants, and purifying selection, which actively removes mutant mtDNA. Whether these mechanisms interact has been unresolved. To address this question, we generated a series of mouse models with random mtDNA mutations alongside alleles altering mtDNA copy number or decreasing autophagy. We demonstrate that tightening the mtDNA bottleneck increases heteroplasmic variance between individuals, causing lower mutational burden and nonsynonymous-to-synonymous ratios. In contrast, reduced autophagy weakens purifying selection, leading to decreased interoffspring heteroplasmic variance and increased mutational burden with higher nonsynonymous-to-synonymous ratios. These findings provide experimental evidence that the mtDNA bottleneck size modulates the efficacy of purifying selection. Our findings yield fundamental insights into the processes governing mammalian mtDNA transmission with direct implications for the origin and propagation of mtDNA mutations causing human disease.Revealing mechanisms of mtDNA transmission is critical for combating human disease.LifeArc http://dx.doi.org/10.13039/100012357LifeArc http://dx.doi.org/10.13039/100012357Swedish Cancer Foundation http://dx.doi.org/10.13039/100012538Rosetrees Trust http://dx.doi.org/10.13039/501100000833Knut och Alice Wallenbergs Stiftelse http://dx.doi.org/10.13039/501100004063Knut och Alice Wallenbergs Stiftelse http://dx.doi.org/10.13039/501100004063EMBO long-term fellowshipWenner-Gren foundation postdoctoral fellowshipVetenskapsrådet http://dx.doi.org/10.13039/501100004359Wellcome Discovery AwardWellcome Collaborative AwardMedical Research Council Mitochondrial Biology UnitBiological and Biotechnology Research CouncilLifeArc Centre to Treat Mitochondrial DiseasesNIHR Cambridge Biomedical Research CentreEuropean Research Council Advanced GrantSwedish Brain Foundation 501100003792Novo Nordisk Fonden http://dx.doi.org/10.13039/501100009708Region of Stockhol
Development of novel clinical markers for the assessment of atherosclerotic diseases development in humans
No full textThe present doctorate thesis has led to the development of simple and innovative methodologies for the isolation, characterization and fractionation of low density lipoproteins (LDLs) into their main molecular components. The ultimate aim of this thesis is to study/measure the specific oxidative modifications present on LDL components, that characterize the oxidized LDL (oxLDL) particles, which in turn are causally related to the development of atheromatous plaques and therefore to the risk of subsequent cardiovascular diseases (CVDs). The methods developed in the present thesis include: (a) A simple, relatively fast and low-cost method for the isolation of LDL particles (LDLP)from human blood serum, in order to avoid the disadvantages of the currently used ultracentrifugation and affinity chromatography methods. (b) Confirmation of the purity of the, isolated with the proposed methodology, LDL-P through SDS-PAGE electrophoresis of their protein component (apolipoprotein B100, apoB100), and determination of the size of LDL-P. The latter as well as the concentration of LDL-P in serum are estimated by means of a developed simple, clinically applicable - in comparison with existing nuclear magnetic resonance (NMR)methodologies - method while their value as risk indicators for the development of CVDs is also evaluated. (c) A method for the fractionation of LDL, for the first time, into its individual protein/lipid (apoB100, cholesterol esters, triglycerides, free cholesterol, phospholipids) and antioxidant (carotenoids, tocopherols) components. (d) Methods for the quantification, for the first time, of certain specific - representative of the initial effects of oxidative stress - oxidative modifications/markers in the molecular components of LDL (cholesteryl ester-OOH, triglyceride-OOH, free cholesterol-OOH, phospholipid-OOH, apoB100- MDA, apoB100-DiTyr), out of the many (known/unknown/under development) oxidative modifications that collectively characterize the oxidative state of oxLDL. These methods for oxLDL state evaluation differ significantly when compared to the existing non-specific and unreliable methods for assessing the oxidative status ofoxLDL. The aforementioned oxLDL markers are being studied for the first time in patients prone to atherosclerosis development as well as in patients with established atherosclerotic lesions and CVDs. Specifically, the selected patient groups include: patients with chronic kidney disease(CKD) on hemodialysis, patients with CKD on peritoneal dialysis, patients with abdominal aortic aneurysm patients and patients with carotid artery disease. Additionally, within the framework of the present thesis, a structural study of the apoB100 protein of LDL particles was carried out, as this remains a poorly studied protein with an unknown structure. Initially, a biophysical characterization of the solubilized apoB100 was performed by studying its secondary structure (by circular dichroism analysis, CD analysis), its thermal stability (by differential scanning fluorescence, nanoDSF) and the existence of aggregates in its solution (by dynamic scattering light, DLS). The biophysical characterization of apoB100 was followed by LCP (Liquid Cubic Phase) crystallization screens of the protein and measurement of the resulting crystals by X-ray diffraction. In summary, the isolation of LDL particles and their fractionation into their individual protein, lipid and antioxidant components paves the way for future studies regarding the investigation and quantification of all possible LDL oxidative modifications and thus paves the way for the full characterization of the so far unknown oxidative status of oxLDL particles. This may also lead to further studies for the identification of the oxLDL modifications that are responsible for their recognition by the macrophages and the impending transformation of the latter into foam cells, which are responsible for the formation of atherosclerotic lesions that in turn lead to the development of CVDs. Lastly, the biophysical characterization experiments and the LCP crystallization screens of apoB100, performed for the first time in the framework of this thesis, are the trigger for further apoB100 crystallization studies that will lead to the solving the so far unknown structure of apoB100 and to the elucidation its function and role in the development of atherosclerotic lesions.Η παρούσα διδακτορική διατριβή οδήγησε στην ανάπτυξη απλών και καινοτόμων μεθοδολογιών για την απομόνωση, το χαρακτηρισμό και την κλασμάτωση των λιποπρωτεϊνών χαμηλής πυκνότητας (LDL) στα κύρια μοριακά τους συστατικά. Απώτερος σκοπός της παρούσας διατριβής είναι η μελέτη σε αυτά συγκεκριμένων οξειδωτικών τροποποιήσεων οι οποίες χαρακτηρίζουν τα αιτιακώς σχετιζόμενα με την ανάπτυξη αθηρωματικών πλακών και άρα και με τον κίνδυνο εμφάνισης των επακόλουθων καρδιαγγειακών παθήσεων, οξειδωμένα LDL (oxLDL) σωματίδια. Οι αναπτυχθείσες στην παρούσα διατριβή μέθοδοι περιλαμβάνουν: (α) Μία απλή, σχετικά γρήγορη και χαμηλού κόστους μέθοδο για την απομόνωση των LDL σωματιδίων (LDL-P) από τον ορό του αίματος, προς αποφυγή των μειονεκτημάτων των έως τώρα εφαρμοζόμενων υπερφυγοκεντρικών μεθόδων και μεθόδων χρωματογραφίας συγγένειας. (β) Επιβεβαίωση της καθαρότητας των απομονωμένων με την προτεινόμενη μεθοδολογία LDL, μέσω SDS-PAGE ηλεκτροφόρησης της πρωτεΐνης αυτών (απολιποπρωτεΐνη Β100, apoB100), και προσδιορισμός του μεγέθους των LDL-P. Το τελευταίο καθώς και η συγκέντρωση των LDL-P στον ορό υπολογίζονται στην παρούσα διατριβή μέσω μίας αναπτυχθείσας απλής, κλινικά εφαρμόσιμης μεθόδου - σε σύγκριση με τις υπάρχουσες μεθοδολογίες μαγνητικού πυρηνικού συντονισμού (NMR) – ενώ αξιολογείται και η αξία τους ως δείκτες εκτίμησης του κινδύνου εμφάνισης καρδιαγγειακών παθήσεων. (γ) Μία μέθοδος για την κλασμάτωση των LDL, για πρώτη φορά, στα επιμέρους πρωτεϊνικά/λιπιδικά (apoB100, εστέρες χοληστερίνης, τριγλυκερίδια, ελεύθερη χοληστερίνη, φωσφολιπίδια) και αντιοξειδωτικά (καροτενοειδή, τοκοφερόλες) συστατικά τους. (δ) Μέθοδοι για την ποσοτικοποίηση, για πρώτη φορά, ορισμένων συγκεκριμένων - αντιπροσωπευτικών των αρχικών επιδράσεων του οξειδωτικούς στρες - οξειδωτικών τροποποιήσεων/δεικτών στα μοριακά συστατικάτων LDL (cholesteryl ester-OOH, triglyceride-OOH, free cholesterol-OOH, phospholipid-OOH,apoB100-MDA, apoB100-DiTyr) εκ των πολλών (γνωστών/άγνωστων/υπό ανάπτυξη) οξειδωτικών τροποποιήσεων που συλλογικά χαρακτηρίζουν την οξειδωτική κατάσταση των oxLDL. Οι μέθοδοι αυτοί έρχονται σε αντίθεση με τις υπάρχουσες μη-εξειδικευμένες και αναξιόπιστες μεθόδους γιατην αξιολόγηση της οξειδωτικής κατάστασης των oxLDL. Οι προαναφερθέντες oxLDL δείκτες μελετώνται για πρώτη φορά σε ασθενείς επιρρεπείς στην εμφάνιση και σε ασθενείς με εγκατεστημένες αθηρωματικές πλάκες και καρδιαγγειακές νόσους. Συγκεκριμένα, οι ομάδες ασθενών που επιλέχθηκαν είναι: ασθενείς με χρόνια νεφρική νόσο υπό αιμοκάθαρση, ασθενείς με χρόνια νεφρική νόσο υπό περιτοναϊκή κάθαρση, ασθενείς με ανεύρυσμα κοιλιακής αορτής και ασθενείς με στένωση καρωτίδων. Επιπροσθέτως, στα πλαίσια της παρούσας διατριβής πραγματοποιήθηκε δομική μελέτη της apoB100 των LDL σωματιδίων, καθώς αυτή αποτελεί μέχρι και σήμερα μία πρωτεΐνη ελάχιστα μελετημένη και με άγνωστη δομή. Αρχικά, πραγματοποιήθηκε χαρακτηρισμός των βιοφυσικών ιδιοτήτων του διαλύματος της apoB100 μέσω μελέτης της δευτεροταγούς της δομής (με ανάλυση κυκλικού διχρωισμού, CD analysis), της θερμικής της σταθερότητας (με διαφορική φθορισμομετρία σάρωσης, nanoDSF) και της ύπαρξης συσσωματωμάτων στο διάλυμα αυτής (μέσω δυναμικής σκέδασης φωτός, DLS). Έπειτα, ακολούθησαν δοκιμές LCP (Liquid Cubic Phase) κρυστάλλωσης της πρωτεΐνης και μέτρηση των προκύψαντων κρυστάλλων με περίθλαση ακτίνων Χ. Συνοψίζοντας, η απομόνωση των LDL σωματιδίων και η κλασμάτωσή τους στα επιμέρους πρωτεϊνικά, λιπιδικά και αντιοξειδωτικά συστατικά τους ανοίγει το δρόμο για μελλοντικές μελέτες διερεύνησης και ποσοτικοποίησης όλων των πιθανών οξειδωτικών τροποποιήσεων των LDL και συνεπώς του πλήρους χαρακτηρισμού της, άγνωστης μέχρι σήμερα, οξειδωτικής κατάστασης των oxLDL σωματιδίων. Το γεγονός αυτό μπορεί να οδηγήσει σε περαιτέρω μελέτες ταυτοποίησης των οξειδωτικών τροποποιήσεων των oxLDL οιοποίες αναγνωρίζονται από τα μακροφάγα και είναι υπεύθυνες για τη μετατροπή των τελευταίωνσε αφρώδη κύτταρα, τα οποία ευθύνονται για το σχηματισμό των αθηρωματικών πλακών που με τη σειρά τους οδηγούν στην εμφάνιση των καρδιαγγειακών παθήσεων. Τέλος, ο βιοφυσικός χαρακτηρισμός και οι δοκιμές LCP κρυστάλλωσης της apoB100, που πραγματοποιήθηκαν για πρώτη φορά στην υπάρχουσα βιβλιογραφία στην παρούσα διατριβή, αποτελούν το έναυσμα για την πραγματοποίηση περαιτέρω μελετών κρυστάλλωσης της apoB100 με στόχο την επίλυση της, άγνωστης μέχρι σήμερα, δομής αυτής και της διαλεύκανσης της λειτουργίας και του ρόλου της στην ανάπτυξη αθηρωματικών πλακών
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Full text linkWe 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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