Approaches towards the automated interpretation and prediction of ES-MS/MS spectra of non-peptidic, pharmaceutical, combinatorial compounds

Electrospray tandem mass spectrometry is currently widely used in protein sequencing. The knowledge of the dissociation trends of peptides molecules allows detailed identification of the amino acid residues and to a certain extent successful characterisation of unknown peptidic compounds. The process of protein identification is frequently aided by interpretive A1 software packages that offer fast and simple ways for manipulating the ES-MS/MS data. Identification of non-peptide molecules using a similar automated approach is, at the moment, a challenge. The dissociation pathways of non-peptidic compounds vary for each class of molecules and general rules have not been established. The isonisation and fragmentation mechanisms taking place under ES-MS/MS conditions have also not been identified and therefore electron ionisation rules are often employed by the A1 packages in order to overcome this problem. This approach leads to a very low success rate when it comes to identifying an unknown non-peptide molecule from its ES-MS/MS spectrum. The aim of this investigation was to develop existing interpretive software packages such that they take account of the specific fragmentation pathways and mechanisms involved in ES-MS/MS. Sub-libraries of non-peptidic, combinatorial molecules were studied and specific rules for their dissociation were established. This allowed pattern recognition methods to be used.  Throughout this work, detailed mechanisms and fragmentation pathways together with the sites of ionisation have been investigated. Incorporation of the findings into an A1 software package should enable the rapid characterisation of the components of combinatorial libraries using ES-MS/MS only.</p

Η Παιδαγωγική και διδακτική διάσταση στα προοίμια των έργων του Αγίου Νικοδήμου του Αγιορείτου:περιεχόμενο, ορολογία, πηγές.

ΠΕΡΙΛΗΨΗ Ο Άγιος Νικόδημος αποτέλεσε ένα σημαντικό πρόσωπο της Αθωνικής ζωής που έδρασε σε μία κρίσιμη για τους Έλληνες περίοδο: την περίοδο της κυριαρχίας της Οθωμανικής Αυτοκρατορίας και της διάδοσης των ιδεών του Διαφωτισμού. Τα γραπτά του κείμενα είναι επηρεασμένα από το κίνημα των Κολλυβάδων, ενώ η σημαντική του συνεισφορά βρίσκεται στην προώθηση του πνεύματος της Φιλοκαλίας, της ησυχαστικής ασκητικής παράδοσης, της νοερής προσευχής. Ωστόσο, η μεγάλη συνεισφορά του δεν αφορά μόνο στα δόγματα της Εκκλησίας και των Ιερών Κανόνων, τα οποία κωδικοποίησε, απλοποίησε και ερμήνευσε, αλλά και στον ορισμό των σχέσεων μεταξύ τους, καθώς και στην πνευματικότητα της Ορθοδοξίας. Τα Προοίμια των γραπτών του κειμένων, δώδεκα από τα οποία αποτελούν το αντικείμενο ανάλυσης αυτής της εργασίας, διακρίνονται για την παιδαγωγική και τη διδακτική τους διάσταση. Μέσα από τα προοίμια των έργων του, ο άγιος Νικόδημος, στόχευε στη μετάδοση των αξιών ενός Χριστιανού, στις αρχές που θα πρέπει να διέπουν το έργο των κληρικών, στην εδραίωση της άρρηκτης σχέσης μεταξύ Ελληνισμού και Ορθοδοξίας, στον γλωσσικό εμπλουτισμό των Ελλήνων και στην προετοιμασία τους για την πνευματική αναγέννηση, στη βάση της Ορθοδοξίας και όχι των ιδεών του δυτικοευρωπαϊκού φαινομένου του Διαφωτισμού. Ο Άγιος Νικόδημος δεν έγραψε ποτέ με αποκλειστικά ακαδημαϊκό τόνο, αλλά πάντα με πρακτική και ποιμαντική πρόθεση. Σχεδόν όλα τα έργα του απευθύνονταν στους λαϊκούς, καθώς και στους κληρικούς και μοναχούς. Μέσα από την ανάλυση των προοιμίων των έργων του, καταδεικνύεται ότι η παιδαγωγική και διδακτική τους διάσταση έγκειται στην κοινή ωφέλεια όλων των Ορθοδόξων Χριστιανών, κυρίως των απλών και αγράμματων ανθρώπων, ώστε να γίνεται κατανοητός ο λόγος του Θεού και τα διδάγματα των εκκλησιαστικών κειμένων για τη σωτηρία της ψυχής των πιστών, για την αποτελεσματική εφαρμογή των Ιερών Μυστηρίων και κατ’ επέκταση για τη διαμόρφωση χριστιανικών και πνευματικών προσωπικοτήτων. Όλη αυτή η προσπάθεια επιχειρείται σε συνδυασμό και με την επιθυμία και την ανάγκη της εποχής για πνευματική αφύπνιση, υπό το πρίσμα της Οθωμανικής κυριαρχίας και της επιρροής του ορθού λόγου του Διαφωτισμού. Λέξεις-κλειδιά: Άγιος Νικόδημος, Άθως, ησυχαστική παράδοση, παιδαγωγική, διδασκαλία, πνευματική αναγέννηση, Διαφωτισμός.ABSTRACT Saint Nicodemus was an important person of the Athonian life who acted during a critical period for the Greeks: the domination of the Ottoman Empire and the dissemination of the ideas of Enlightenment. His writings are influenced by the Kollyvad movement, and his important contribution was the promotion of the spirit of Philokalia, the hesychastic ascetic tradition, and prayer. However, his great contribution was not only related to the doctrines of the Church and the Sacred Canons, which he codified, simplified and interpreted, but also the definition of the relations between them, as well as the spirituality of Orthodoxy. The preambles of his writings, some of which are the subject of analysis of this thesis, are distinguished for their pedagogical dimension. Through his writings he aimed at the transmission of the Christian values, the principles that should govern the work of the clergy, the consolidation of the inextricable relationship between Hellenism and Orthodoxy, the linguistic enrichment of the Greeks and their preparation for spiritual regeneration, on the basis of Orthodoxy and not on the ideas of the Western European phenomenon of Enlightenment. Saint Nicodemus never wrote based on an exclusively academic tone, but he had always a practical and pastoral intention. Almost all his works were addressed to the people, as well as to the monks and clergymen. Through the analysis of the preambles of his works, it is indicated that their pedagogical dimension lies in the common benefit of all Orthodox Christians, especially the simple and non-literary people, in order to understand the word of God and the teachings of ecclesiastical texts for the salvation of the believers, the effective application of the Sacred Sacraments, and ultimately the formation of Christian, spiritual personalities, in the midst of the effort of spiritual awakening seen from the point of view of Ottoman domination and the influence of the reasonable word of Enlightenment. Keywords: Saint Nicodemus, Athos, hesychastic tradition, pedagogy, teaching, spiritual regeneration, Enlightenment

Δυναμική πρόσδεσης μεταγραφικών παραγόντων κυτταρικού επαναπρογραμματισμού στο γονιδίωμα

Ο κυτταρικός επαναπρογραμματισμός σωματικών κυττάρων προς πολυδύναμα βλαστικά μέσω της συνέκφρασης των μεταγραφικών παραγόντων Oct4, Sox2, Klf4 και c-Myc (παράγοντες OSKM) είναι μια στοχαστική διαδικασία που παράγει ένα μικρό υποπληθυσμό επαγώμενων πολυδύναμων βλαστικών κυττάρων (iPSCs). Την τελευταία δεκαετία, τεχνολογίες υψηλής ανάλυσης έχουν προσφέρει μια ατελείωτη λίστα πιθανών ρυθμιστικών περιοχών που σχετίζονται με τον κυτταρικό επαναπρογραμματισμό αλλά παρ’ όλ’ αυτά, δεν μπορούν να εξακριβώσουν τον ακριβή ρόλο τους. Εδώ κάναμε μια μετα-ανάλυση προηγούμενων ChIP-seq πειραμάτων του εργαστηρίου κατά τα οποία μετρήθηκε η πρόσδεση των OSKM στο DNA κατά τον κυτταρικό επαναπρογραμματισμό. Αναγνωρίσαμε μια περιοχή κοντά στο γονίδιο του Oct4 πάνω στην οποία οι OSKM προσδένονται με δυναμικό τρόπο σε αλληλοεπικαλυπτόμενα DNA μοτίβα. Η επαγωγή του ενδογενούς γονιδίου Oct4 είναι ένα όψιμο, αλλά σπουδαίο γεγονός κατά τον επαναπρογραμματισμό, καθώς το Oct4 είναι μέλος του βασικού δικτύου πολυδυναμίας που σταθεροποιεί και προστατεύει την επίκτητη πολυδυναμία στα iPSCs. Οπότε, κάναμε επιπλέον πειράματα ChIP-PCR έναντι των OSKM σ’ αυτή την περιοχή ώστε να παρακολουθήσουμε την ακριβή διαδοχή των γεγονότων όσον αφορά τη δυναμική πρόσδεσή τους κατά τον επαναπρογραμματισμό. In vitro πειράματα πρόσδεσης στο DNA αποκάλυψαν ότι οι OSKM προσδένονται σ’ αυτό το στοιχείο DNA συνεργατικά, επιβεβαιώνοντας τα in vivo δεδομένα του ChIP. Υποθέσαμε λοιπόν ότι αυτό το στοιχείο δρα ως ενισχυτής που ελέγχει τη στοχαστική έκφραση του γονιδίου Oct4 και άρα έμμεσα εγκαθιδρύει την πολυδυναμία. Για να ελέγξουμε αυτή την ιδέα, δημιουργήσαμε ένα λεντιϊκό σύστημα όπου χρησιμοποιήθηκε το GFP ως γονίδιο αναφοράς κάτω από τον έλεγχο αυτού του πιθανού ενισχυτή και το εισαγάγαμε σε εμβρυϊκούς ινοβλάστες ποντικού που επαναπρογραμματίστηκαν. Ανακαλύψαμε ότι αυτή η περιοχή λειτουργεί ως πραγματικός ενισχυτής που ρυθμίζει τη στοχαστική έκφραση του γονιδίου αναφοράς, με τρόπο παρόμοιο με την έκφραση του ενδογενούς Oct4 γονιδίου. Συμπερασματικά, τα δεδομένα μας υποδεικνύουν έναν επαγόμενο-κατά-τον-επαναπρογραμματισμό ενισχυτή που μπορεί να λειτουργήσει ως ένα πολύτιμο εργαλείο απομόνωσης επαναπρογραμματιζόμενων κυττάρων για τον καθορισμό των βιοχημικών υπογραφών τους και να προσφέρει νέα δεδομένα για την κατανόηση ουσιωδών βιολογικών μηχανισμών.Cellular reprogramming of somatic cells to ground state pluripotency by the co-expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM factors) is a stochastic process generating a small subpopulation of induced Pluripotent Stem Cells (iPSCs). During the last decade, high-throughput technologies have produced an enormous list of putative regulatory regions associated with cellular reprogramming but, however, provide no evidence concerning their particular role in the process. Here, we carried out a meta-analysis of our previous ChIP-seq experiments measuring OSKM DNA binding during the entire process of cellular reprogramming. We identified a genomic region located near Oct4 gene on which the OSKM factors bind in a dynamic fashion to highly overlapping DNA motifs. Induction of the endogenous Oct4 gene is a late plus significant event during cellular reprogramming as Oct4 is a member of the core pluripotency network that stabilizes and safeguards the acquired pluripotency in iPSCs. So, we performed further ChIP-PCR experiments against OSKM on this region to follow in detail the exact sequence of events regarding the dynamic binding during the course of reprogramming. In vitro DNA binding assays revealed that OSKM bind cooperatively to this DNA element, thus confirming the in vivo ChIP experiments. We hypothesized that this element functions as enhancer controlling the stochastic expression of the Oct4 gene, thus establishing the stemness phenotype. To test this idea, we generated lentiviral reporter bearing GFP under the control of this putative enhancer and transduced mouse embryonic fibroblasts undergoing cellular reprogramming. Remarkably, we discovered that this region functions as true enhancer element driving the stochastic expression of the GFP reporter in a manner similar to the endogenous Oct4 gene. Taken together, our data identified a reprogramming inducible enhancer which can serve as an invaluable tool to isolate cells during the dynamic process of reprogramming in order to determine their biochemical signatures and provide novel insights to understand essential biological mechanisms

Approaches towards the automated interpretation and prediction of electrospray tandem mass spectra of non-peptidic combinatorial compounds

Combinatorial chemistry is widely used within the pharmaceutical industry as a means of rapid identification of potential drugs. With the growth of combinatorial libraries, mass spectrometry (MS) became the key analytical technique because of its speed of analysis, sensitivity, accuracy and ability to be coupled with other analytical techniques. In the majority of cases, electrospray mass spectrometry (ES-MS) has become the default ionisation technique. However, due to the absence of fragment ions in the resulting spectra, tandem mass spectrometry (MS/MS) is required to provide structural information for the identification of an unknown analyte. This work discusses the first steps of an investigation into the fragmentation pathways taking place in electrospray tandem mass spectrometry. The ultimate goal for this project is to set general fragmentation rules for non-peptidic, pharmaceutical, combinatorial compounds. As an aid, an artificial intelligence (AI) software package is used to facilitate interpretation of the spectra. This initial study has focused on determining the fragmentation rules for some classes of compound types that fit the remit as outlined above. Based on studies carried out on several combinatorial libraries of these compounds, it was established that different classes of drug molecules follow unique fragmentation pathways. In addition to these general observations, the specific ionisation processes and the fragmentation pathways involved in the electrospray mass spectra of these systems were explored. The ultimate goal will be to incorporate our findings into the computer program and allow identification of an unknown, non-peptidic compound following insertion of its ES-MS/MS spectrum into the AI package. The work herein demonstrates the potential benefit of such an approach in addressing the issue of high-throughput, automated MS/MS data interpretation

High-throughput approaches towards the definitive identification of pharmaceutical drug metabolites. 1. Evidence for an ortho effect on the fragmentation of 4-benzenesulfinyl-3-methylphenylamine using electrospray ionisation mass spectrometry

A 50 m/z unit loss from protonated 4-benzenesulfinyl-3-methylphenylamine has been observed and investigated using electrospray ionisation quadrupole ion trap mass spectrometry (ESI-QIT-MS). It was hypothesised that the specific fragmentation was affected by the presence of an ortho methyl group in relation to the sulfoxide functionality, i.e. an ortho effect influences the preferred dissociation pathway. This was because the des-methyl homologue did not display a 50 m/z unit loss. This fragmentation was shown to be a two-step process with sequential losses of a hydroxyl radical and a thiol radical. Molecular modelling calculations showed that the most favourable site of protonation for 4-benzenesulfinyl-3-methylphenylamine was the sulfoxide oxygen, which would facilitate the loss of a hydroxyl radical. Subsequent deuterium-exchange experiments confirmed that the loss was a hydroxyl radical and afforded definitive assignment of the site of protonation. Furthermore, the involvement of a single exchangeable hydrogen atom in the overall 50 m/z unit loss was demonstrated. Thus, supportive evidence was provided for the involvement of the ortho methyl group in the second stage of the fragmentation, leading to the loss of the thiol radical. Accurate mass measurements, performed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS), verified the elemental formulae of the individual losses. The ion structure following the 50 m/z unit loss was proposed to be a protonated aminofluorene and was supported by comparing the product ion spectrum of commercially available protonated 2-aminofluorene with the MS4 data of protonated 4-benzenesulfinyl-3-methylphenylamine. Fragmentation mechanisms are proposed. The relevance of the loss with regards to pharmaceutical drug metabolite identification is discussed

Towards a universal product ion mass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers

Product ion spectra produced by collision-induced dissociation (CID) in tandem mass spectrometry experiments can differ markedly between instruments. There have been a number of attempts to standardise the production of product ion spectra; however, a consensus on the most appropriate approach to the reproducible production of spectra has yet to be reached. We have previously reported the comparison of product ion spectra on a number of different types of instruments - a triple quadrupole, two ion traps and a Fourier transform ion cyclotron resonance mass spectrometer (Bristow AWT, Webb KS, Lubben AT, Halket JM. Rapid Commun. Mass Spectrom. 2004; 18: 1). The study showed that a high degree of reproducibility was achievable. The goal of this study was to improve the comparability and reproducibility of CID product ion mass spectra produced in different laboratories and using different instruments. This was carried out experimentally by defining a spectral calibration point on each mass spectrometer for product ion formation. The long-term goal is the development of a universal (instrument independent) product ion mass spectral library for the identification of unknowns. The spectra of 48 compounds have been recorded on eleven mass spectrometers: six ion traps, two triple quadrupoles, a hybrid triple quadrupole, and two quadrupole time-of-flight instruments. Initially, 4371 spectral comparisons were carried out using the data from eleven instruments and the degree of reproducibility was evaluated. A blind trial has also been carried out to assess the reproducibility of spectra obtained during LC/MS/MS. The results suggest a degree of reproducibility across all instrument types using the tuning point technique. The reproducibility of the product ion spectra is increased when comparing the tandem in time type instruments and the tandem in space instruments as two separate groups. This may allow the production of a more limited, yet useful, screening library for LC/MS/MS identification using instruments of the same type from different manufacturers