Detecting similarities among distant homologous proteins by comparison of domain flexibilities

Aim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons of protein domain flexibilities is proposed. CONCOORD is confirmed as a reliable method for fast conformational sampling. The root mean square fluctuation of alpha carbon positions in the essential dynamics subspace is employed as a measure of local flexibility and a synthetic index of similarity is presented. The dynamics of a large collection of protein domains from ASTRAL/SCOP40 is analyzed and the possibility to identify relationships, at both the family and the superfamily levels, on the basis of the dynamical features is discussed. The obtained picture is in agreement with the SCOP classification, and furthermore suggests the presence of a distinguishable familiar trend in the flexibility profiles. The results support the complementarity of the dynamical and the structural information, suggesting that information from dynamics analysis can arise from functional similarities, often partially hidden by a static comparison. On the basis of this first test, flexibility annotation can be expected to help in automatically detecting functional similarities otherwise unrecoverable. © 2007 The Author(s)

A Holistic Approach to Functional Safety for Networked Cyber-Physical Systems

Functional safety is a significant concern in today's networked cyber-physical systems such as connected machines, autonomous vehicles, and intelligent environments. Simulation is a well-known methodology for the assessment of functional safety. Simulation models of networked cyber-physical systems are very heterogeneous relying on digital hardware, analog hardware, and network domains. Current functional safety assessment is mainly focused on digital hardware failures while minor attention is devoted to analog hardware and not at all to the interconnecting network. In this work we believe that in networked cyber-physical systems, the dependability must be verified not only for the nodes in isolation but also by taking into account their interaction through the communication channel. For this reason, this work proposes a holistic methodology for simulation-based safety assessment in which safety mechanisms are tested in a simulation environment reproducing the high-level behavior of digital hardware, analog hardware, and network communication. The methodology relies on three main automatic processes: 1) abstraction of analog models to transform them into system-level descriptions, 2) synthesis of network infrastructures to combine multiple cyber-physical systems, and 3) multi-domain fault injection in digital, analog, and network. Ultimately, the flow produces a homogeneous optimized description written in C++ for fast and reliable simulation which can have many applications. The focus of this thesis is performing extensive fault simulation and evaluating different functional safety metrics, \eg, fault and diagnostic coverage of all the safety mechanisms

Electron tomography of meiotic spindles in males of the trioecious nematode Auanema rhodensis

The nematode Auanema rhodensis has recently been established as a new model organism. A. rhodensis is characterized by the simultaneous existence of three phenotypical sexes (males, females and hermaphrodites; called trioecy), skewed sex ratios which do not follow Mendel's laws, and variant segregation patterns according to sex and type of gametogenesis. Recently, A. rhodensis has been used to study the possible mechanisms for sex determination in three-sexed species and the variability of basic processes during sexual reproduction including meiotic divisions. During male meiosis, a diploid primary spermatocyte undergoes two consecutive divisions to form four haploid spermatids. Surprisingly, male meiosis in A. rhodensis results in two functional and two nonfunctional spermatids depending on the presence of an X-chromatid. A. rhodensis males exhibit a set of paired autosomes and one single X-chromosome, like males of the wellestablished nematode model organism Caenorhabditis elegans. In contrast to C. elegans, however, the X-chromosome in A. rhodensis divides precociously into its sister chromatids during the first meiotic division followed by a lagging X-chromatid and its uneven distribution during meiosis II. Additionally, the second meiotic divi-sion within this species is characterized by an asymmetric organelle distribution and a spindle structure reminiscent of a monopolar spindle. In this study, serial section electron tomography was used to analyse the ultrastructure of the microtubule skeleton in spermatocytes of A. rhodensis. The analysis of spermiogenesis using electron tomography posed some key advantages compared to standard transmission electron microscopy. First, the microtubule (MT) network could be studied in detail including spindle formation, organization of spindle poles, rearrangement of MTs, and inter-action between MTs and chromosomes. Second, the number and shape of chromosomes could be visualized. And third, the morphology of organelles could be observed at high resolution, and different organelles as well as their distribution pattern could be distinguished and quantified. This study provides highresolution 3D information about male meiosis in A. rhodensis. The results of this thesis confirm the complexity of the male meiotic program and the promi-nent position of the X-chromatid in meiosis II in this organism. Like previous light microscopic studies, electron tomography supports the hypothesis of an X-chromatid-dependent distribution of cellular organelles such as fibrousbody membranousorganelles (FB-MOs) and mitochondria. Furthermore, the formation of an asymmetric spindle could be observed with progressing anaphase II and might be associated with the X-chromatid distribution. Additionally, the analysis of the number of chromosome-associating MTs and their association character gives new insights into possible chromosome segregation mechanisms. Finally, significant differences to the male meiotic program in C. elegans have been identified. For the first time, the MT network in A rhodensis spermatocytes of different division stages has been observed in detail, and several different analyses could be done, including an analysis of the length distribution of MTs in the spindles. Because this ultrastructural analysis is based on fixed samples, live-cell imaging should be performed in the future to gain further information on the chromosome dynamics in this species.Der Fadenwurm Auanema rhodensis hat sich in den letzten Jahren mehr und mehr zu einem neuen Modellorganismus entwickelt. Typisch für A. rhodensis ist das zeitgleiche Vor-kommen dreier phänotypischer Geschlechter (Männchen, Weibchen und Hermaphroditen; die sogenannte Triözie) und deren zahlenmäßig ungleiches Verhältnis zueinander, welches sich nicht durch Mendelsche Regeln erklären lässt. Ebenfalls auffällig sind nach Geschlecht und Gametogenese (Oogenese oder Spermatogenese) abweichende chromosomale Segregationsmuster. Unlängst hat A. rhodensis zu Erkenntnissen über die Geschlechtsdeterminierung in dreigeschlechtlichen Arten und die Varianz grundlegender Prozesse in der Meiose beigetragen. Während der männlichen Meiose (Spermatogenese) teilt sich eine diploide primäre Vorläuferzelle (primäre Spermatozyte) in zwei aufeinanderfolgenden Teilungen in insgesamt vier haploide Spermatiden. Bei A. rhodensis führt die Spermatogenese ungewöhnlicher-weise zu zwei funktionalen und zwei nicht-funktionalen Spermatiden, wobei die Funktionsfähigkeit vom Auftreten eines X-Chromatids abhängt. Männchen von A. rhodensis besitzen, ähnlich wie im Modellorganismus Caenorhabditis elegans, eine Reihe gepaarter Autosomen sowie ein einzelnes X-Chromosom. Im Gegensatz zu C. elegans teilt sich das ungepaarte X-Chromosom in A. rhodensis vorzeitig schon während der ersten meiotischen Teilung in seine Chromatiden, wodurch es zu einer verzögerten und ungleichen Verteilung des X-Chromatids während der zweiten meiotischen Teilung kommt. Diese zweite meiotische Teilung bei A. rhodensis ist außerdem durch eine asymmetrische Verteilung der Organellen und Mikrotubuli gekennzeichnet, letztere ähneln einer monopolaren Spindel. In dieser Arbeit wurde die Methode der seriellen Elektronentomographie genutzt, um die Ultrastruktur der Mikrotubuli in meiotischen Spindeln in Spermatozyten von A. rhodensis zu untersuchen. Zum einen wurden mittels Elektronentomographie das Netzwerk der Mikrotubuli und die Spindelorganisation, die Struktur der Spindelpole sowie die Interaktion zwischen Mikrotubli und Chromosomen drei-dimensional (3D) analysiert. Zum anderen wurde die Form der Chromosomen und die Morphologie und Verteilung der verschiedenen Organellen quantitativ erfasst. Somit stellt diese Studie hochauflösende 3D-Information über den Ablauf der männlichen Meiose in A. rhodensis zur Verfügung und bestätigt damit die Komplexität der männlichen Meiose und die zentrale Rolle des X-Chromatids während der zweiten meiotischen Teilung in diesem Organismus. Basierend auf vorangegangenen lichtmikroskopischen Experimenten an fixierten Proben unterstützt die Elektronentomographie die Hypothese einer vom X-Chromatid abhängigen Verteilung zellulärer Organellen wie spermienspezifischer FB-MOs oder Mitochondrien während der zweiten meiotischen Teilung. Außerdem konnte die Ausbildung einer asymmetrischen Spindel beobachtet werden, welche ebenfalls mit der ungleichen Verteilung des X-Chromatids in Zusammenhang stehen könnte. Eine zusätzliche Analyse chromosomenassoziierter Mikrotubuli brachte erste Erkenntnisse über mögliche zugrundeliegende Mechanismen der Chromosomensegregation. Die Ergebnisse dieser Arbeit konnten mit ähnlichen Untersuchungen in C. elegans verglichen und Unterschiede herausgearbeitet werden. Zum ersten Mal wurden hier meiotische Spindeln unterschiedlicher Teilungsstadien in 3D untersucht und unterschiedliche quantitative Analysen zur Längenverteilung der Mikrotubuli durchgeführt. Da alle hier gewonnenen Ultrastrukturdaten auf fixierten Proben basieren, sollte eine Betrachtung einer transgenen Wurmlinie mit Fluoreszenzmarkern mittels live-cell imaging auf diese Ultrastrukturanalyse folgen

Spindle organization in three dimensions

During cell division, chromosome segregation takes place on bipolar, microtubulebased spindles. Here, C. elegans is used to analyze spindle organization under both mitotic and meiotic conditions. First, the role of SAS-4 in organizing centrosome structure was analyzed. Partial depletion of SAS-4 in early embryos results in structurally defective centrioles. The study of this protein sheds light on the poorly understood role of the centrioles in dictating centrosome size. Second, the ultrastructure of wild-type mitotic spindle components was analyzed by electron tomography. This 3-D analysis reveals morphologically distinct microtubule end morphologies in the mitotic spindle pole. These results have structural implications for models of microtubule interactions with centrosomes Third, spindle assembly was studied in female meiosis. Specifically, the role of the microtubule severing complex katanin in spindle organization was analyzed. Electron tomography reveals fragmentation of spindle microtubules and suggests a novel katanin-dependent mechanism of meiotic spindle assembly. In this model, relatively long microtubules seen near the meiotic chromatin are converted into numerous short fragments, thus increasing the total number of polymers in an acentrosomal environment. Taken together, these results provide novel insights into the three-dimensional organization of microtubules during spindle assembly.Die Segregation der Chromosomen während der Zellteilung wird duch bipolare, von Microtubuli-aufgebauten Spindlen gewährleistet. In der vorliegenden Arbeit wird C. elegans zur Analyse der Spindelorganisation unter mitotischen und meiotischen Bedingungen herangezogen. Erstens wird die Rolle von SAS-4 in der Organisation von Zentrosomen untersucht. Die partielle Depletierung von SAS-4 in frühen Embryonen führt zu strukturell defekten Zentriolen und wirft somit Licht auf die wenig verstandene Rolle der Zentriolen in der Bestimmung der Zentrosomengröße. Zweitens wird die Ultrastruktur der mitotischen Spindelkomponenten im Wildtyp durch Elektronentomographie untersucht. Diese 3-D-Analyse zeigt, dass im mitotischen Spindlepol unterschiedliche Morphologien der Mikrotubulienden zu finden sind. Diese Ergebnisse haben strukturelle Implikationen für Modelle der Mikrotubuli-Zentrosomen-Interaktionen. Drittens wird der Aufbau der Spindel in der weiblichen Meiose, speziell die Rolle des Mikrotubuli-schneidenden Kataninkomplexes in der Spindelorganisation, untersucht. Die Elektronentomographie zeigt hier eine Fragmentierung der Spindelmikrotubuli. Basierend auf diesem Ergebnis wird ein neues Katanin-abhängiges Modell der Formierung der Meiosespindel entwickelt, in dem relativ lange Microtubuli in Nähe des meiotischen Chromatins in zahlreiche kurze Mikrotubuli “zerschnitten” werden. Dies erhöht die Anzahl der verfügbaren Polymere in dieser azentrosomalen Situation. Zusammenfassend bringen diese Ergebnisse neue Einsichten in die räumliche Organisation der Mikrotubuli während des Spindelaufbaus

Integrated mining of feature spaces for bioinformatics domain discovery

One of the major challenges in the field of bioinformatics is the elucidation of protein folding for the functional annotation of proteins. The factors that govern protein folding include the chemical, physical, and environmental conditions of the protein\u27s surroundings, which can be measured and exploited for computational discovery purposes. These conditions enable the protein to transform from a sequence of amino acids to a globular three-dimensional structure. Information concerning the folded state of a protein has significant potential to explain biochemical pathways and their involvement in disorders and diseases. This information impacts the ways in which genetic diseases are characterized and cured and in which designer drugs are created. With the exponential growth of protein databases and the limitations of experimental protein structure determination, sophisticated computational methods have been developed and applied to search for, detect, and compare protein homology. Most computational tools developed for protein structure prediction are primarily based on sequence similarity searches. These approaches have improved the prediction accuracy of high sequence similarity proteins but have failed to perform well with proteins of low sequence similarity. Data mining offers unique algorithmic computational approaches that have been used widely in the development of automatic protein structure classification and prediction. In this dissertation, we present a novel approach for the integration of physico-chemical properties and effective feature extraction techniques for the classification of proteins. Our approaches overcome one of the major obstacles of data mining in protein databases, the encapsulation of different hydrophobicity residue properties into a much reduced feature space that possess high degrees of specificity and sensitivity in protein structure classification. We have developed three unique computational algorithms for coherent feature extraction on selected scale properties of the protein sequence. When plagued by the problem of the unequal cardinality of proteins, our proposed integration scheme effectively handles the varied sizes of proteins and scales well with increasing dimensionality of these sequences. We also detail a two-fold methodology for protein functional annotation. First, we exhibit our success in creating an algorithm that provides a means to integrate multiple physico-chemical properties in the form of a multi-layered abstract feature space, with each layer corresponding to a physico-chemical property. Second, we discuss a wavelet-based segmentation approach that efficiently detects regions of property conservation across all layers of the created feature space. Finally, we present a unique graph-theory based algorithmic framework for the identification of conserved hydrophobic residue interaction patterns using identified scales of hydrophobicity. We report that these discriminatory features are specific to a family of proteins, which consist of conserved hydrophobic residues that are then used for structural classification. We also present our rigorously tested validation schemes, which report significant degrees of accuracy to show that homologous proteins exhibit the conservation of physico-chemical properties along the protein backbone. We conclude our discussion by summarizing our results and contributions and by listing our goals for future research

Projections for fast protein structure retrieval

BACKGROUND: In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniques, for retrieving protein structures similar to a query structure from a large protein structure database. Each protein structure is specified by the 3D coordinates of residues of the protein. The algorithm is based on a novel characterization of the residues, called projections, leading to a similarity measure between the residues of the two proteins. This measure is exploited to efficiently compute the optimal equivalences. RESULTS: Experimental results show that, the current algorithm outperforms the state of the art on benchmark datasets in terms of speed without losing accuracy. Search results on SCOP 95% nonredundant database, for fold similarity with 5 proteins from different SCOP classes show that the current method performs competitively with the standard algorithm CE. The algorithm is also capable of detecting non-topological similarities between two proteins which is not possible with most of the state of the art tools like Dali

Investigating the structure and binding mechanism of QseM, a novel dual-target protein-inhibitor

This thesis details the structural characterisation of a novel protein, QseM, through the use of X-ray crystallography and nuclear magnetic resonance. QseM contains the uncharacterised DUF2285 domain, which, through this work, has been revealed to be a novel helix-turn-helix motif

Using Formal Methods for Building more Reliable and Secure e-voting Systems

Deploying a system in a safe and secure manner requires ensuring the tech- nical and procedural levels of assurance also with respect to social and regu- latory frameworks. This is because threats and attacks may not only derive from pitfalls in complex security critical system, but also from ill-designed procedures. However, existing methodologies are not mature enough to em- brace procedural implications and the need for multidisciplinary approach on the safe and secure operation of system. This is particularly common in electronic voting (e-voting) systems. This dissertation focuses along two lines. First, we propose an approach to guarantee a reasonable security to the overall systems by performing for- mal procedural security analysis. We apply existing techniques and define novel methodologies and approaches for the analysis and verification of procedural rich systems. This includes not only the definition of adequate modeling convention, but also the definition of general techniques for the injection of attacks, and for the transformation of process models into rep- resentations that can be given as input to model checkers. With this it is possible to understand and highlight how the switch to the new tech- nological solution changes security, with the ultimate goal of defining the procedures regulating system and system processes that ensure a sufficient level of security for the system as well as for its procedures. We then investigate the usage of formal methods to study and analyze the strength and weaknesses of currently deployed (e-voting) system in order to build the next generation (e-voting) systems. More specifically, we show how formal verification techniques can be used to model and reason about the security of an existing e-voting system. To do that, we reuse the methodology propose for procedural security analysis. The practical applicability of the approaches is demonstrated in several case studies from the domain of public administrations in general and in e-voting system in particular. With this it can be possible to build more secure, reliable, and trustworthy e-voting system

Evolutionary diversification and historical biogeography of orchidaceae in Central America with emphasis on Costa Rica and Panama

In this thesis, I targeted the orchid genus Lepanthes, one of the six genera of angiosperms that surpasses 1,000 species in the Neotropics, as a study model to investigate the evolutionary processes that promoted species diversifications. To investigate this, we improved the taxonomy of the group integrating a solid phylogenetic framework with morphological evolution, assessing inter-specific relationships in species complexes with hundreds of DNA markers using anchored hybrid enrichment approach, and describing new species. In addition, we addressed the pollination of Trichosalpinx through the study of floral anatomy, pollinator behavior, and floral traits. Trichosalpinx flowers are pollinated exclusively by female biting midges that are attracted by the small quantities of proteins secreted on the flowers. Finally, we inferred the biogeographical history and diversification dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using densely sampled phylogenies coupled with geological datasets and discussed the impact of biogeographical events and orogeny on the species richness of Lepanthes. Species diversification is correlated with Andean orogeny, and multiple migrations and recolonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales. This thesis provides new insights into the complex evolution of one of the most species-rich angiosperm.Leiden University/[]//Países BajosCentro de Biodiversidad Naturalis/[]//Países BajosUniversidad de Costa Rica/[]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL