TreeViewJ: An Application for Viewing and Analyzing Phylogenetic Trees

BACKGROUND. Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization software available, but limitations in these programs often require researchers to use multiple programs for analysis, annotation, and the production of publication-ready images. RESULTS. We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches that they wish to highlight, and add names to nodes. If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order. CONCLUSION. TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at http://treeviewj.sourceforge.net

Automated methods in aircraft ground analyses: modelling process improvements by automated simulations

The purpose of this work is to investigate about the processes adopted to perform some Aircraft Level analyses and to create new methods and approaches in order to automate them, to speed them up, and to re-use the model created for all the aircraft. This approach is in compliance with the principles of the Lean Philosophy developed by Toyota (based on mapping the processes, finding what is value adding, non value adding and what the sources of waste are, and trying to continuously improve the process). The analyses taken into account for this work are Groundlines, Jacking Groundlines and Ground Manoeuvrability. The programmes the work refers to are A350XWB, A380 and the A320 family, but the methods will be applied for the same analyses on all the other aircraft

Design of general-purpose sampling strategies for geometric shape measurement

Quality inspection is a preliminary step for different further analyses (process monitoring, control and optimisation) and requires one to select a measuring strategy, i.e., number and location of measurement points. This phase of data gathering usually impacts on inspection times and costs (via sample size) but it also affects the performance of the following tasks (process monitoring, control and optimisation). While most of the approaches for sampling design are specifically presented with reference to a target application (namely, monitoring, control or optimisation), this paper presents a general-purpose procedure, where the number and location of measurement points are selected in order to retain most of the information related to the feature under study. The procedure is based on principal component analysis and its application is shown with reference to a real case study concerning the left front window of a car. A different approach based on multidimensional scaling is further applied as validation tool, in order to show the effectiveness of the PCA solution

Biogeochemical characterisation of extreme environments

There is currently a considerable interest in characterising extreme environments, since they offer the opportunity to envision practical applications and to understand microbial diversity as an adaptive response that reflects environmental diversity. It is now well recognized that microorganisms thrive in extreme conditions such as contaminated soils/sediments and the pressurised depth of the Earth. Morphological, physiological, biochemical and genetic adaptations to extreme environments by these microorganisms have generated immense interest amongst scientists who continuously discover new occurrences and modes of microbial life on Earth. In this thesis, biogeochemical processes are investigated in two different extreme environments. (i) The deep biosphere, with a focus on shale gas basin and coal-bed methane (CBM). These environments are currently gaining momentum across the scientific community for the production of gaseous fuel. (i) [sic] Coal tar-contaminated soil and concentrated organic-phase coal tar, which was studied for bioremediation purposes. The core of this thesis consists of three articles dedicated to combination of different molecular and chromatographic methods of experimentation, analysis and interpretation. These include molecular tools such as DNA extraction techniques, PCR, 454-pyrosequencing and culturing-based approaches. The chemical experiments were metabolomic and isotopic chromatographic analyses. This study presented an extensive review of the biogeochemistry of unconventional gas systems, which provide an improved level of information of such environments. A robust culture-independent methodology was developed for the characterisation of microbial life in extreme environments, which was applied to describe, for the first time, the presence of bacteria in concentrated organic-phase coal tar. The deep sequencing methods were then used in combination with multidimensional compound specific isotope analysis (CSIA) to investigate community structure. The combined approach of deep sequencing methods with multidimensional CSIA was confirmed by statistics. Thus, high-throughput 16S rRNA gene sequencing and multidimentional CSIA, can be applied to investigate microbial community structure in extreme environments.There is currently a considerable interest in characterising extreme environments, since they offer the opportunity to envision practical applications and to understand microbial diversity as an adaptive response that reflects environmental diversity. It is now well recognized that microorganisms thrive in extreme conditions such as contaminated soils/sediments and the pressurised depth of the Earth. Morphological, physiological, biochemical and genetic adaptations to extreme environments by these microorganisms have generated immense interest amongst scientists who continuously discover new occurrences and modes of microbial life on Earth. In this thesis, biogeochemical processes are investigated in two different extreme environments. (i) The deep biosphere, with a focus on shale gas basin and coal-bed methane (CBM). These environments are currently gaining momentum across the scientific community for the production of gaseous fuel. (i) [sic] Coal tar-contaminated soil and concentrated organic-phase coal tar, which was studied for bioremediation purposes. The core of this thesis consists of three articles dedicated to combination of different molecular and chromatographic methods of experimentation, analysis and interpretation. These include molecular tools such as DNA extraction techniques, PCR, 454-pyrosequencing and culturing-based approaches. The chemical experiments were metabolomic and isotopic chromatographic analyses. This study presented an extensive review of the biogeochemistry of unconventional gas systems, which provide an improved level of information of such environments. A robust culture-independent methodology was developed for the characterisation of microbial life in extreme environments, which was applied to describe, for the first time, the presence of bacteria in concentrated organic-phase coal tar. The deep sequencing methods were then used in combination with multidimensional compound specific isotope analysis (CSIA) to investigate community structure. The combined approach of deep sequencing methods with multidimensional CSIA was confirmed by statistics. Thus, high-throughput 16S rRNA gene sequencing and multidimentional CSIA, can be applied to investigate microbial community structure in extreme environments

Identification of cellular targets of the adenovirus E1B 55-kDa protein

La protéine d'adénovirus (Ad) ElB 55-kDa est essentielle à la croissance virale et à la transformation complète des cellules infectées par adénovirus. Les mécanismes détaillés de l'action d'ElB ne sont pas encore bien connus. Afin déterminer les fonctions de cette oncoprotéine virale, il est essentiel de déterminer ses cibles cellulaires. La méthode de deux-hybride de levure a été utilisée pour cribler la bibliothèque genomique de Saccharomyces cerevisiae et la bibliothèque d' ADNc Hela humaine avec la protéine d'Ad2 ElB 55-kDa. Le criblage partiel de la bibliothèque genomique de S. cerevisiae (106 transformants) a indiqué plusieurs protéines de levure qui se lient à ElB. Parmi elles: UFD l, impliqué dans la voie de dégradation de fusion par ubiquitination, une voie importante pour la dégradation sélective des protéines dans les eukaryotes, RIS 1, une membre de la famille SWI/SNF2 d' ADN-dépendente ATPases, et Bdf2 qui contient deux copies du bromodomaine, domaine hautement conservé durant l'évolution et qui est homologue à la moitié C-terminale de TAFII250 de mammifères. Un criblage partiel de la bibliothèque d' ADNc de Hela humaine (7 x 105 transformants) a permis d'identifier des protéines humaines positives pour l'association avec Ad2 El B 55-kDa. UbcH7 est l'une d'entre elles. UbcH7 est une enzyme d'ubiquitination-conjugaison, impliquée dans la dégradation du suppresseur de tumeur p53, celui-ci reconnu pour être stabilisé et inactivé par Ad ElB 55-k.Da. Il y a aussi ubiquitine elle-même, SUM0-1, une protéine semblable aux protéines d'ubiquitination, qui modifie d'un nombre limité de protéines par un procédé similaire à l'ubiquitination, et DAXX, impliquée dans l'apoptose induite par Fas. L'identification d'une interaction entre DAXX et Ad E 1 B 55-kDa propose des implications intéressantes pour le rôle d'E l B dans la transformation de cellules. Les capacités pro-apoptotiques de DAXX semblent dépendre de l'interaction physique de DAXX avec une suppresseur de tumeur, PML. La liaison de DAXX par PML provoque la localisation de DAXX dans des corps nucléaires, connus sous le nom de domaines oncogènes de PML (PODs). La liaison d'Ad ElB 55-kDa à la portion C-terminale de DAXX est requise pour la liaison a PML et la localisation dans les PODs. Les expériences de co-localisation par immunofluorescence ont démontré que dans des lignées de cellulaires exprimant les protéines Ad ElB 55-k.Da il y a dissociation du complexe PML-DAXX. La formation des PODs dans ces cellules est aussi perturbée. Ces observations suggèrent un autre mécanisme par lequel la protéine d'Ad E 18 55-kDa contribuerait à la transformation cellulaire: celles-ci pour interférer avec un processus apoptotique qui agit par l'intermédiaire de DAXX.Abstract: The adenovirus (Ad) ElB 55-k.Da protein is vital to viral growth and complete transformation of adenovirus-infected cells. The detailed mechanisms of E 1 B action are not yet clear. ln order to shed light on the functions of this viral oncoprotein it is essential to determine its cellular targets. The yeast two-hybrid method was utilized to screen the Saccharomyces cerevisiae genomic library and the human Hela cONA library with the Ad2 ElB 55-kDa protein as hait. Partial screening of the S. erevisiae genomic library (106 transformants) has revealed several yeast proteins that bind to El B. Among these are: UFOl, involved in the ubiquitin fusion degradation pathway, a major pathway for selective protein degradation in eukaryotes, RIS 1, a member of the S Wl/SNF2 family of DNA-dependent ATPases, and Bdt2 which contains two copies of the evolutionarily conserved bromodomain, homologous to the C-terminal half of mammalian T Af 11250. Human proteins positive for Ad2 ElB 55-k.Da binding were identified through partial screening of the Hela cONA library (7 x 105 transformants). Among them are: UbcH7, a ubiquitin-conjugating enzyme involved in the ubiquitin-mediated degradation of the tumor suppressor protein p53, known to be stabilized and inactivated by Ad ElB 55-kDa. SUM0-1, a ubiquitin-like protein which covalently modifies a limited number of proteins in a manner similar to ubiquitination, ubiquitin itself, and DAXX, implicated in Fasinduced apoptosis

Multiple aspects of natural killer cell expansion in relevance to immunotherapy for hematologic malignancies

Natural Killer (NK) cells are a subset of lymphocytes that regulate adaptive immune responses and utilize missing self recognition to activate anti-tumor and anti-viral cytotoxicity. Clinical research, as well as murine and ex vivo models, have shown that a variety of NK cell applications have proven useful as immunotherapeutic treatments for patients with hematologic malignancies. However, the selective expansion of NK cells to yield relevant amounts of these lymphocytes has been a major hurdle in the development of methods for clinical therapeutic use. Here, we demonstrate a novel ex vivo expansion method utilizing k562 leukemic cell lines and soluble cytokines as well as a novel method utilizing isolated plasma membranes of genetically engineered tumor cell lines that could be of relevance to in vivo NK cell expansion. Also, the ligand expression by canonical feeder cell lines used for NK cell expansion and our isolated plasma membranes were compared via ligand quantification by western blot quantification of 4-1BB ligand. In an adjunct study, we sought to better characterize these expansion environments by investigating the glucose metabolism of NK cells using fluorescent glucose analog 2-(N-(7-Nitrobenz-2-oxa-1, 3-diazol-4-yl)Amino)-2-Deoxyglucose (2-NBDG) and the glycolysis inhibitor 2-Deoxy-D-Glucose (2-DG)