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Dissertation
Identificatie van nonfermenters en mycobacteria Sequencing en MALDI-TOF MS
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Year: 2013 Publisher: Gent : s.n.,

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Bij de moeilijk te identificeren bacteriën, zoals nonfermenters en mycobacteria, dienden alternatieve targetgenen gesequeneerd te worden om meer informatie te verschaffen betreffende de species status van de onbekende isolaat. Het recA gen en gyrB gen werden om deze reden onderzocht voor identificatie van het Burkholderia cepacia complex, Acinetobacter spp. en mycobacteria. Na analyse blijkt het recA gen in staat te zijn om een verbeterde identificatie tot op species niveau te geven bij leden van het Burkholderia cepacia complex. Een ultieme identi ficatieprocedure tot op species niveau voor alle kiemen, enkel en alleen op basis van sequencing van één of meerdere targetgenen, is nog niet mogelijk. Bijkomende alternatieve methodes zijn hierbij noodzakelijk.Als geen identificatie kan worden verkregen d.m.v. MALDI-TOF MS kan sequencing van het 16S rRNA worden aanzien als de eerste stap waarbij in de meeste gevallen een identificatie tot op species niveau kan worden verkregen. Als dit echter niet het geval is, kan sequencing van alternatieve targetgenen worden uitgevoerd om een verbeterde identificatie te verkrijgen tot op species niveau. Correcte identificatie van klinische bacteriële isolaten is belangrijk voor het opstarten van de geschikte behandeling en eventuele controlemaatregelen. Vooral bij immuunverzwakte patiënten, waaronder mucoviscidose patiënten, is een snelle en accurate identificatie van hun koloniserende pathogenen cruciaal, maar echter veelal problematisch gezien hun specifieke klinische context.Matrix asissted laser desorption/ionization time-of-flight massaspectrometrie (MALDI-TOF MS) is een moleculaire identificatiemethode die recent zijn opmars heeft gemaakt in de klinische laboratoria. Deze techniek is snel en eenvoudig in gebruik, maar bevat nog een aantal tekortkomingen vooral bij de moeilijk te identificeren bacteriën, zoals nonfermenters en mycobacteria. Ter validatie van de MALDI-TOF MS identificatie van nonfermenters en mycobacteria kan identificatie door middel van sequencing dienst doen als alternatieve identificatiemethode.Sequencing van het 16S rRNA wordt in de literatuur beschreven als een goede identificatiemethode voor de meeste bacteriën, echter identificatie tot op species niveau bij nauw verwante bacteriën, waarbij onderling het 16S rRNA sterk gelijkend is, zorgt soms voor problemen. Dit blijkt na toepassing van de volledige sequencing procedure op een set van eenvoudig te identificeren Grampositieve en Gramnegatieve bacteriën, die via sequentie van het 16S rRNA gen aanleiding gaf tot een eenduidige identificatie.


Digital
How Free Cationic Polymer Chains Promote Gene Transfection
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ISBN: 9783319003368 Year: 2013 Publisher: Heidelberg Springer International Publishing

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In this PhD thesis, Yue Yanan addresses a long-overlooked and critical question in the development of non-viral vectors for gene delivery. The author determines that those uncomplexed and cationic polymer chains free in the solution mixture of polymer and DNA facilitate and promote gene transfection. Furthermore, by using a combination of synthetic chemistry, polymer physics and molecular biology, Yue confirms that it is those cationic polymer chains free in the solution mixture, rather than those bound to DNA chains, that play a decisive role in intracellular trafficking. Instead of the previously proposed and widely accepted “proton sponge” model, the author's group propose a new hypothesis based on the results of several well-designed and decisive experiments. These results show that free polycationic chains with a length of more than ~10 nm are able to partially block the fusion between different endocytic vesicles, including the endocytic-vesicle-to-endolysosome pathway. This thesis is highly original and its results greatly deepen our understanding of polymer-mediated gene transfection. More importantly, it provides new insights into the rational design of next-generation superior polymeric gene-delivery vectors.


Digital
Biophysical approaches to translational control of gene expression
Author:
ISBN: 9781461439912 Year: 2013 Publisher: New York, NY Springer

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When quantum mechanics was first proposed a century ago, nobody could have anticipated how deeply it would affect our lives.  Today, we are connected and powered through devices whose existence is predicated on the basic principles of this strange physics.  Not even the biological sciences have escaped its reach.  As scientists query the deepest mysteries of the living world, the physical scales probed and the types of questions asked are increasingly blurring the lines between biology and physics.  The hybrid field of biophysics represents the new frontier of the 21st century. The ribosome has been at the heart of three Nobel Prizes.  Understanding its essential nature and how it interacts with other proteins and nucleic acids to control protein synthesis has been one of the central foundations in our understanding of the biology at the molecular level.  With the advent of atomic scale structures, methods to visualize and separate individual molecules, and the computational power to model the complex interactions of over a million atoms at once, our understanding of how gene expression is controlled at the level of protein translation is now deeply ensconced in the biophysical realm. This book provides a premier resource to a wide audience, whether it be the general reader seeking a broad view of the field, a clinician interested in the role of protein translation in human disease, the bench researcher looking for state-of-the-art technologies, or computational scientists involved in cutting edge molecular modeling.


Digital
Biophysics of RNA Folding
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ISBN: 9781461449546 Year: 2013 Publisher: New York, NY Springer

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Structured RNAs are everywhere, functioning throughout gene expression with key roles ranging from catalysis to regulation. New functional RNAs are being discovered all the time; in fact, it is now clear that a much greater fraction of eukaryotic genomes is devoted to coding for RNA than protein. Many of these RNAs must traverse complex energy landscapes to find their functional three-dimensional structures. Along the way, they may encounter native and non-native folding intermediates, chaperone proteins, and assemble with partner proteins. This volume, written by experts in the field, discusses the current understanding of the biophysical principles that govern RNA folding, with featured RNAs including the ribosomal RNAs, viral RNAs, and self-splicing introns. In addition to the fundamental features of RNA folding, the central experimental and computational approaches in the field are presented with an emphasis on their individual strengths and limitations, and how they can be combined to be more powerful than any method alone; these approaches include NMR, single molecule fluorescence, site-directed spin labeling, structure mapping, comparative sequence analysis, graph theory, course-grained 3D modeling, and more. This volume will be of interest to professional researchers and advanced students entering the field of RNA folding.


Digital
Bio-synthetic Polymer Conjugates
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ISBN: 9783642343506 Year: 2013 Publisher: Berlin, Heidelberg Springer

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H. Menzel Polypeptide-Polymer Conjugates   B. Jung P. Theato Chemical Strategies for the Synthesis of Protein-Polymer Conjugates A. M. Eissa N. R. Cameron Glycopolymer Conjugates D. Kedracki I. Safir N. Gour K. Ngo C. Vebert-Nardin DNA-Polymer Conjugates: From Synthesis, Through Complex Formation and Self-assembly to Applications J. Zhao H. Schlaad Synthesis of Terpene-Based Polymers.


Digital
Quadruplex Nucleic Acids
Authors: ---
ISBN: 9783642347436 Year: 2013 Publisher: Berlin, Heidelberg Springer

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Gaining Insights into the Small Molecule Targeting of the G-Quadruplex in the c-MYC Promoter Using NMR and an Allele-Specific Transcriptional Assay, by Christine E. Kaiser, Vijay Gokhale, Danzhou Yang and Laurence H. Hurley.- Higher-Order Quadruplex Structures, by Luigi Petraccone.- Investigation of Quadruplex Structure Under Physiological Conditions Using In-Cell NMR, by Robert Hänsel, Silvie Foldynová-Trantírková, Volker Dötsch and Lukás Trantírek.- Circular Dichroism of Quadruplex Structures, by Antonio Randazzo, Gian Piero Spada and Mateus Webba da Silva.- Molecular Crowding and Hydration Regulating of G-Quadruplex Formation, by Daisuke Miyoshi, Takeshi Fujimoto and Naoki Sugimoto.- Visualizing the Quadruplex: From Fluorescent Ligands to Light-Up Probes, by Eric Largy, Anton Granzhan, Florian Hamon, Daniela Verga and Marie-Paule Teulade-Fichou.- Calculation of Hydrodynamic Properties for G-Quadruplex Nucleic Acid Structures from in silico Bead Models, by Huy T. Le, Robert Buscaglia, William L. Dean, Jonathan B. Chaires and John O. Trent.- Energetics of Ligand Binding to G-Quadruplexes, Concetta Giancola and Bruno Pagano.- Tetramolecular Quadruplex Stability and Assembly, by Phong Lan Thao Tran, Anne De Cian, Julien Gros, Rui Moriyama and Jean-Louis Mergny.


Digital
DNA Nanotechnology : From Structure to Function
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ISBN: 9783642360770 Year: 2013 Publisher: Berlin, Heidelberg Springer

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DNA nanotechnology: From structure to function presents an overview of various facets of DNA nanotechnology, with a particular focus on their promising applications. This book is composed of three parts. Part I, Elements of DNA Nanotechnology, provides extensive basic information on DNA nanotechnology. Part II, Static and Dynamic DNA Nanotechnology, describes the design and fabrication of static and dynamic DNA nanostructures. Recent advances in DNA origami, DNA walkers and DNA nanodevices are all covered in this part. Part III, Applications of DNA Nanotechnology, introduces a variety of applications of DNA nanotechnology, including biosensing, computation, drug delivery, etc. Together these provide a comprehensive overview of this emerging area and its broad impact on biological and medical sciences. This book is intended for post-graduates, post-doctoral researchers and research scientists who are interested in expanding their knowledge of DNA nanotechnology. It provides readers an impression of the latest developments in this exciting filed.


Digital
DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases
Authors: ---
ISBN: 9783642368530 Year: 2013 Publisher: Berlin, Heidelberg Springer

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DNA and RNA nanobiotechnologies have currently reached the status of one of the most dynamic research areas in the field of drug delivery in molecular medicine. Scientists and bio-engineers are creating totally new nanometer-scale structures with unique biological properties for a wide range of medical applications. The book, written by world-leading scientists in this new field, gives an overview of various aspects and applications of DNA and RNA nanotechnologies. These include the design and synthesis of DNA and RNA nanostructures with the aim of using them for different kinds of drug deliveries, for genetic immunization, for metabolite and nucleic acid detection, gene regulation, siRNA delivery for cancer treatment, and even analytical and therapeutic applications of aptamer-based nanoparticles. This volume will be of interest not only to graduate students and researchers in the field of molecular medicine and molecular biology, but also to chemists interested in the biological fields. As a matter of fact, the book contains so many new and unique approaches to this area of molecular medicine that it may inspire the interested reader to undertake research into nucleic acid nanotechnologies.


Digital
Molecular Beacons
Authors: ---
ISBN: 9783642391095 Year: 2013 Publisher: Berlin, Heidelberg Springer

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Molecular Beacons explains working principle of molecular beacons, discusses their design, synthesis, purification and characterization, explores their thermodynamic and kinetic properties, and more importantly, reviews their in vivo and in vitro applications with the emphasis on the design and modification of molecular beacons for in vivo mRNA imaging applications. This book is designed to bring together in a single resource an organized and comprehensive view of molecular beacons and will be a valuable resource for academic, clinical and industrial scientists and graduate students who may consider exploring molecular beacons in their research or practice. Chaoyong James Yang is the Lu Jiaxi Professor of Chemistry at Xiamen University, China. Weihong Tan is a Distinguished Professor of Chemistry and Biomedical Engineering at Hunan University, China and also a University of Florida Distinguished Professor and V. T. and Louis Jackson Professor of Chemistry at the University of Florida, USA.


Book
Moleculaire diagnostiek
Authors: ---
ISBN: 9789077423950 Year: 2013 Publisher: Utrecht Syntax Media

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Met moleculaire diagnostiek worden laboratoriumtechnieken aangeduid waarmee op het niveau van DNA of RNA ziekten bij mens, plant en dier worden gekarakteriseerd. Pathogenen en afwijkingen in het erfelijk materiaal zijn onderwerp van de moleculaire analyses. Sinds de 1e druk van dit boek in 2001 zijn de beschikbare technieken sterk toegenomen en op veel terreinen sneller, goedkoper, gevoeliger en grootschaliger geworden. Deze geheel vernieuwde 2e druk behandelt nu ook real-time PCR, sequensen, microarrays, DNA-chips en enkele fysische technieken. De ongeveer twintig auteurs zijn allen gezaghebbend op hun terrein.

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