No description available.

Transthyretin (TTR) amyloidosis is a disease that appears in three variants. One variant affects the elderly population with heart failure, the other two variants are hereditary and caused by an amino acid substitution in the gene, resulting in polyneuropathy and/or heart issues depending on the amino acid substitution. However, in all three variants, other organs may also be affected with amyloid deposition in the disease course. Amyloid fibrils of TTR (ATTR) contains a mixture of full-length protein and fragments (50-127). Luminescent conjugated oligothiophenes (LCO’s) are novel amyloid binding probes used to stain amyloid fibrils and these amyloid probes have the feature of characterizing the amyloid structure in terms of fluorescence spectra. Apart from LCO’s, a few other amyloid binding probes are used to stain recombinant amyloid transthyretin and native transthyretin for binding studies. The majority of generated TTR aggregates in vitro did not have the characteristic fluorescence spectra when bound to LCO’s and was observed as a clumped gel-like aggregate. The generation of recombinant TTR fibrils in vitro using the mutant TTR-T49M to obtain an aggregation prone fragment (50-127) after being treated with cyanogen bromide had a low yield of in vivo amyloid-like fibrils, but with characteristic LCO spectra. Carpal tunnel ATTR often precedes ATTR deposition in heart tissue. Amyloid transthyretin in carpal tunnel tissues was stained with LCO’s and used as a reference in the comparison against the in vitro generated recombinant amyloid transthyretin fibrils. This project also includes quantification of amyloid transthyretin in a few selected parts of the carpal tunnel tissue using ImageJ. In the long run this method could help in diagnosing TTR amyloidosis.

Advances in protein topology mapping methods are urgently needed to complement the wealth of interactome data that is presently being generated at a rapid pace. Chemical crosslinking followed by mass spectrometry (MS) has evolved over the last decade as an attractive method for protein topology and interface mapping, and holds great promise as a counterpart to modern interactome studies in the field of proteomics. Furthermore, stabilization of proteins and protein complexes with crosslinking offers many advantages over high-resolution structural mapping methods, including the ability to study protein topologies in vivo. The reliance on direct detection of crosslinked peptides, however, continues to pose challenges to protein topology and interface mapping with chemical crosslinking plus MS. The present body of work aimed to develop a novel generic methodology that utilizes chemical crosslinking, cyanogen bromide (CNBr) cleavage and MS for the low-resolution mapping of protein topologies and interfaces. Through such low-resolution mapping of crosslinked regions, this novel strategy overcomes limitations associated with the direct detection of crosslinked peptides. Following optimization of various steps, the present method was validated with the bacterial DNA-directed RNA polymerase core complex and was subsequently applied to probe the tetrameric assembly of yeast Skp1p-Cdc4p heterodimers. Further improvements were made through the enrichment of crosslinked CNBr-cleaved protein fragments prior to their identification via MS. Two enrichment strategies were developed which depended upon the conjugation of tags to CNBr-cleaved peptide C-termini followed by either tandem affinity purification or tandem reversed-phase HPLC purification. These strategies were successfully applied for the efficient purification of disulfide-linked peptides from peptide mixtures. It is expected that the potential to achieve sensitive mapping of topologies and interfaces of multi-subunit protein complexes in vivo, in combination with further enhancements to permit studies on complex protein samples, will extend the utility of this method to complement large-scale interactome studies.

Advances in protein topology mapping methods are urgently needed to complement the wealth of interactome data that is presently being generated at a rapid pace. Chemical crosslinking followed by mass spectrometry (MS) has evolved over the last decade as an attractive method for protein topology and interface mapping, and holds great promise as a counterpart to modern interactome studies in the field of proteomics. Furthermore, stabilization of proteins and protein complexes with crosslinking offers many advantages over high-resolution structural mapping methods, including the ability to study protein topologies in vivo. The reliance on direct detection of crosslinked peptides, however, continues to pose challenges to protein topology and interface mapping with chemical crosslinking plus MS. The present body of work aimed to develop a novel generic methodology that utilizes chemical crosslinking, cyanogen bromide (CNBr) cleavage and MS for the low-resolution mapping of protein topologies and interfaces. Through such low-resolution mapping of crosslinked regions, this novel strategy overcomes limitations associated with the direct detection of crosslinked peptides. Following optimization of various steps, the present method was validated with the bacterial DNA-directed RNA polymerase core complex and was subsequently applied to probe the tetrameric assembly of yeast Skp1p-Cdc4p heterodimers. Further improvements were made through the enrichment of crosslinked CNBr-cleaved protein fragments prior to their identification via MS. Two enrichment strategies were developed which depended upon the conjugation of tags to CNBr-cleaved peptide C-termini followed by either tandem affinity purification or tandem reversed-phase HPLC purification. These strategies were successfully applied for the efficient purification of disulfide-linked peptides from peptide mixtures. It is expected that the potential to achieve sensitive mapping of topologies and interfaces of multi-subunit protein complexes in vivo, in combination with further enhancements to permit studies on complex protein samples, will extend the utility of this method to complement large-scale interactome studies.

Τα τελευταία χρόνια, υπάρχει έντονο ερευνητικό ενδιαφέρον για την φασματοσκοπία πλάσματος, η οποία βασίζεται στην μελέτη της ηλεκτρομαγνητικής ακτινοβολίας που εκπέμπεται όταν η ύλη βρίσκεται σε κατάσταση ολικού ή μερικού ιονισμού. Έτσι προκειμένου να δημιουργηθεί πλάσμα, απαιτείται να προσφερθεί στο ουδέτερο αρχικά δείγμα, ενέργεια σημαντικής ποσότητας. Κατά τη διεξαγωγή των πειραμάτων, την απαιτούμενη ενέργεια την παρείχαν δύο διαφορετικές πηγές: ένα laser Nd-YAG και ένας ηλεκτρικός σπινθηριστής. Οι φασματοσκοπικές αυτές μέθοδοι ονομάζονται Libs (Laser Induced Breakdown Spectroscopy) και Sibs (Spark Induced Breakdown Spectroscopy) αντίστοιχα. Στην παρούσα ειδική ερευνητική εργασία, οι τεχνικές αυτές εφαρμόζονται για την επαγωγή πλάσματος σε δύο διαφορετικά δείγματα: σε ατμοσφαιρικό αέρα και σε προ-αναμεμειγμένα μίγματα υδρογονάνθρακα-αέρα. Αρχικά λοιπόν, μελετήθηκαν ποιοτικά τα φάσματα εκπομπής πλάσματος επαγόμενου από τους δύο σπινθήρες για να συλλεχθούν πληροφορίες για το οξειδωτικό μέσο, εν προκειμένω του αέρα και στη συνέχεια, συγκρίθηκαν με τα φάσματα εκπομπής πλάσματος σε φλόγες. Επιπλέον, η φασματοσκοπία πλάσματος χρησιμοποιήθηκε για την μελέτη μιγμάτων με διαφορετική αναλογία καυσίμου προς οξειδωτικό μέσο το κάθενα, μέγεθος που εκφράζεται μέσω του λόγου ισοδυναμίας,φ. Τέλος, συσχετίστηκε η ολική ένταση της μοριακής ταινίας του ελεύθερου ριζικού κυανίου (CN), ενδιάμεσο προϊόν της καύσης, με το φ όπου και διαπιστώθηκε η γραμμική σχέση που συνδέει τις παραπάνω ποσότητες. Αποτέλεσμα αυτής της εργασίας αποτελεί το γεγονός ότι οι τεχνικές αυτές θα μπορούσαν να χρησιμοποιηθούν σαν διαγνωστικά εργαλεία για τη μελέτη φλογών άγνωστης περιεκτικότητας σε καύσιμο όχι μόνο στους εργαστηριακούς χώρους αλλά και σε in-situ περιβάλλοντα. / Over the past few years, there has been an intense research interest over the plasma spectroscopy, which is based on the study of the electromagnetic radiation propagated by matter in total or partial ionized state. Hence, in order to create plasma, it is necessary to provide the neutral sample with a significant amount of energy. During the experimental procedures, the required energy was provided by two different energy sources, a laser Nd-YAG and an electrical scintillator. The afore-mentioned spectroscopic methods are called Libs (Laser Induced Breakdown Spectroscopy) and Sibs (Spark Induced Breakdown Spectroscopy), respectively. In the present study, these techniques are applied to induce plasma in atmospheric air and in premixed flammable hydrocarbon-air mixtures. At first, the emission spectra of plasma induced by the two sparks were qualitatively analyzed in order to capture data concerning the oxidizing agent, namely the air. Then the spectra were compared to the spectra of the plasma in flame. Moreover, plasma spectroscopy was used to study combustible mixtures of different fuel concentrations, which are characterized by the equivalence ratio, φ. Finally, the total intensity of the molecular band of the free radical cyanogens (CN), known meta-stable product of the combustion was correlated to φ. This correlation demonstrates that the growth of the CN band with the amount of fuel in the mixture is evident and simple linear correlation exists between them. The major result of this study is the fact that these techniques could possibly be used as diagnostic and analytical tools for the study of flames of unknown fuel concentration, not only in the laboratory but also in field conditions.