Principles and Applications of Deoxyribonucleic Acid Microarray: a Review
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Detection of Dna Hybridization on a Configurable Digital Microfluidic
DETECTION OF DNA HYBRIDIZATION ON A CONFIGURABLE DIGITAL MICROFLUIDIC BIO- CHIP USING SPR IMAGING Lidija Malic1, Teodor Veres2 and Maryam Tabrizian1 1Biomedical Engineering Department, McGill University, CANADA and 2Industrial Materials Institute, National Research Council, CANADA ABSTRACT This paper presents a configurable digital microfluidic-based surface plasmon resonance (SPR) biochip platform comprising an electrowetting-on-dielectric (EWOD) microfluidic device coupled to SPR imaging (SPRi). We demonstrate its application for dynamic on-chip simultaneous immobilization of different DNA probes in combination with multichannel label-free real-time detection of subse- quent hybridization reactions. The integrated EWOD-SPRi system would enable the development of high-throughput, rapid and ultrasensitive biomolecular detection strategies beyond DNA microarray applications. KEYWORDS: Digital microfluidics, EWOD, SPR imaging, DNA hybridization INTRODUCTION EWOD microfluidics has attracted considerable attention in the past decade and the most recent efforts are directed towards its application in biomedical research [1- 3]. While these studies demonstrate the versatility of EWOD devices, the reported applications involve homogeneous phase reactions [4] and detection methods that require labeled biomolecules [2] or sample extraction from the chip [1]. This in- creases both the time and complexity of the assay. To introduce new applications relying on label-free, real-time surface sensitive detection techniques such as SPRi, it would be advantageous to use droplet-based EWOD actuation for surface specific biomolecule immobilization. However, the need of hydrophobic properties for EWOD actuation renders immobilization of biomolecules such as DNA on the sur- face of the chip impossible [3, 4]. In this paper, we demonstrate for the first time the use of an EWOD microfluidic chip to dynamically immobilize DNA probes in a two-dimensional array, followed by SPRi detection of bioaffinity interactions. -
To DNA Microarrays
Glass slides to DNA microarrays by Samuel D. Conzone* and Carlo G. Pantano† A tremendous interest in deoxyribonucleic acid Most individuals, outside of academic circles focused (DNA) characterization tools was spurred by the on genomics, became aware of the potential mapping and sequencing of the human genome. commercial, technical, and social importance of the New tools were needed, beginning in the early 1990s, human genome project during the late 1990s. The human genome project was formally initiated in to cope with the unprecedented amount of genomic 19901 and was expected to last 15 years. It had the information that was being discovered. Such needs major goals of identifying all the genes in human led to the development of DNA microarrays; tiny DNA, determining the sequences of those genes, and gene-based sensors traditionally prepared on coated storing the information in public databases. glass microscope slides. The following review is However, the project moved quickly from the onset intended to provide historical insight into the advent and, by 1998, the Department of Energy (DOE) and of the DNA microarray, followed by a description of the National Institutes of Health (NIH) predicted the technology from both the application and that the human genome project would be completed by 2003. fabrication points of view. Finally, the unmet challenges and needs associated with DNA The big buzz about biotech microarrays will be described to define areas of The tremendous success in rapidly mapping and sequencing potential future developments for the materials the human genome (a working draft sequence of the human researcher. genome was completed in 2000), has led many commentators to predict that similar achievements would follow on the applications side, giving rise to unprecedented discoveries related to human health2,3. -
Architecture of Thermal Adaptation in an Exiguobacterium Sibiricum Strain
BMC Genomics BioMed Central Research article Open Access Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach Debora F Rodrigues*1, Natalia Ivanova2, Zhili He3, Marianne Huebner4, Jizhong Zhou3 and James M Tiedje1 Address: 1Michigan State University, NASA Astrobiology Institute and Center for Microbial Ecology, East Lansing, MI 48824, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598-1604, USA, 3Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA and 4Michigan State University, Department of Statistics and Probability, East Lansing, MI, USA Email: Debora F Rodrigues* - [email protected]; Natalia Ivanova - [email protected]; Zhili He - [email protected]; Marianne Huebner - [email protected]; Jizhong Zhou - [email protected]; James M Tiedje - [email protected] * Corresponding author Published: 18 November 2008 Received: 23 May 2008 Accepted: 18 November 2008 BMC Genomics 2008, 9:547 doi:10.1186/1471-2164-9-547 This article is available from: http://www.biomedcentral.com/1471-2164/9/547 © 2008 Rodrigues et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Many microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth temperature range through a holistic view of its physiology, genome, and transcriptome. -
Introducing the IMED Biotech Unit What Science Can Do Introduction What Science Can Do
Introducing the IMED Biotech Unit What science can do Introduction What science can do At AstraZeneca, our purpose is to push the Our IMED Biotech Unit applies its research and Our approach to R&D development capabilities and technologies to The IMED Biotech Unit plays a critical boundaries of science to deliver life-changing accelerate the progress of our pipeline. Through role in driving AstraZeneca’s success. Working together with MedImmune, medicines. We achieve this by placing science great collaboration across our three science units, our global biologics arm and Global we are confident that we can deliver the next wave Medicines Development (GMD), our at the centre of everything we do. late-stage development organisation, of innovative medicines to transform the lives of we are ensuring we deliver an innovative patients around the world. and sustainable pipeline. Pancreatic beta cells at different Eosinophil prior to Minute pieces of circulating tumour DNA stages of regeneration apoptosis (ctDNA) in the bloodstream IMED Biotech Unit MedImmune Global Medicines Development Focuses on driving scientific advances Focuses on biologics research and Focuses on late-stage development in small molecules, oligonucleotides and development in therapeutic proteins, of our innovative pipeline, transforming other emerging platforms to push the monoclonal antibodies and other next- exciting science into valued new boundaries of medical science. generation molecules to attack a range medicines and ensuring patients of diseases. around the world can access them. It’s science that compels us to push the boundaries of what is possible. We trust in the potential of ideas and pursue them, alone and with others, until we have transformed the treatment of disease. -
Opto-Fluidic Manipulation of Microparticles and Related Applications
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 11-10-2020 Opto-Fluidic Manipulation of Microparticles and Related Applications Hao Wang University of South Florida Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Biomedical Engineering and Bioengineering Commons Scholar Commons Citation Wang, Hao, "Opto-Fluidic Manipulation of Microparticles and Related Applications" (2020). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/8601 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Opto-Fluidic Manipulation of Microparticles and Related Applications by Hao Wang A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Engineering Department of Medical Engineering College of Engineering University of South Florida Major Professor: Anna Pyayt, Ph.D. Robert Frisina, Ph.D. Steven Saddow, Ph.D. Sandy Westerheide, Ph.D. Piyush Koria, Ph.D. Date of Approval: October 30, 2020 Key words: Thermal-plasmonic, Convection, Microfluid, Aggregation, Isolation Copyright © 2020, Hao Wang Dedication This dissertation is dedicated to the people who have supported me throughout my education. Great appreciation to my academic adviser Dr. Anna Pyayt who kept me on track. Special thanks to my wife Qun, who supports me for years since the beginning of our marriage. Thanks for making me see this adventure though to the end. Acknowledgments On the very outset of this dissertation, I would like to express my deepest appreciation towards all the people who have helped me in this endeavor. -
Structure and Function Of
8/5/2019 Micro Array /DNA chip` It is collection of microscopic DNA spots attached to a solid surface usually glass, plastic or silicon biochip Each DNA spot contains • picomoles (10−12 moles) of a specific DNA sequence • known as probes or reporters . • These can be a short section of a gene • Other DNA element that are used to hybridize a cDNA The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm Micro Array /DNA chip` Micro Array /DNA chip` cRNA sample (called target) • Probe-target hybridization • Detected • Quantified • detection of fluorophore- silver-, or chemiluminescence-labeled targets Example of an approximately 40,000 probe spotted 1 8/5/2019 Micro Array /DNA chip` Micro Array/ DNA chip` Use • To determine relative abundance of nucleic acid sequences in the target. • To measure the expression levels of large numbers of genes simultaneously • detect RNA (most commonly as cDNA after reverse transcription) • To genotype multiple regions of a genome. Microarray Analysis Techniques Microarray Analysis Techniques Microarray manufacturers LIMMA • Affymetrix • A set of tools for background correction • Agilent MA plots Comparing two different arrays • To plot the data. • Two different samples • R, MATLAB, and Excel • Hybridized to the same array • For adjustments for systematic errors introduced • Differences in procedures • Dye intensity effects. 2 8/5/2019 Protein synthesis • Messenger RNA (mRNA) molecules direct Median polish Algorithm the assembly of proteins on ribosomes. The median polish is an exploratory data analy sis procedure proposed by the statistician John Tukey. • Transfer RNA (tRNA) molecules are used Data Normalization to to deliver amino acids to the ribosome • Ribosomal RNA (rRNA) then links amino acids together to form proteins. -
Lab-On-Chip Microdevices for Capturing, Imaging and Counting White Blood Cells
LAB-ON-CHIP MICRODEVICES FOR CAPTURING, IMAGING AND COUNTING WHITE BLOOD CELLS by Anurag Tripathi A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Mechanical Engineering) in The University of Michigan 2012 Doctoral Committee: Associate Professor Nikolaos Chronis, Chair Associate Professor Katsuo Kurabayashi Assistant Professor Jianping Fu Assistant Professor Sunitha Nagrath To The Almighty And To My Family & Friends ii ACKNOWLEDGEMENTS It is my honor and absolute pleasure to acknowledge people who made this thesis possible. First and foremost, I would like to thank my advisor Dr. Nikos Chronis whose guidance and training enabled me to develop skills in microfabrication and microfluidics technology. More than the technical knowledge I gained from Dr. Chronis in the past five years, he taught me the virtues of hard work, sincerity and integrity. In the toughest of situations, his patience and understanding provided me with courage and confidence and enabled me to see through those hard times. He inculcated a strong aptitude for research in me and his ‘never give up’ principle left an indelible impression on my problem solving approach. I would be eternally grateful to Dr. Chronis for mentoring me and transforming me into a better researcher and a better human being. A big gratitude is in order for the other three members of my thesis dissertation committee, Dr. Katsuo Kurabayashi, Dr. Jianping Fu and Dr. Sunitha Nagrath. It was a privilege to have them on my committee. I thank them wholeheartedly for their valuable inputs during the Ph.D. preliminary examinations. I acknowledge the encouragement they provided to my research and would like to thank them for their support and motivation all this while. -
The Bio Revolution: Innovations Transforming and Our Societies, Economies, Lives
The Bio Revolution: Innovations transforming economies, societies, and our lives economies, societies, our and transforming Innovations Revolution: Bio The The Bio Revolution Innovations transforming economies, societies, and our lives May 2020 McKinsey Global Institute Since its founding in 1990, the McKinsey Global Institute (MGI) has sought to develop a deeper understanding of the evolving global economy. As the business and economics research arm of McKinsey & Company, MGI aims to help leaders in the commercial, public, and social sectors understand trends and forces shaping the global economy. MGI research combines the disciplines of economics and management, employing the analytical tools of economics with the insights of business leaders. Our “micro-to-macro” methodology examines microeconomic industry trends to better understand the broad macroeconomic forces affecting business strategy and public policy. MGI’s in-depth reports have covered more than 20 countries and 30 industries. Current research focuses on six themes: productivity and growth, natural resources, labor markets, the evolution of global financial markets, the economic impact of technology and innovation, and urbanization. Recent reports have assessed the digital economy, the impact of AI and automation on employment, physical climate risk, income inequal ity, the productivity puzzle, the economic benefits of tackling gender inequality, a new era of global competition, Chinese innovation, and digital and financial globalization. MGI is led by three McKinsey & Company senior partners: co-chairs James Manyika and Sven Smit, and director Jonathan Woetzel. Michael Chui, Susan Lund, Anu Madgavkar, Jan Mischke, Sree Ramaswamy, Jaana Remes, Jeongmin Seong, and Tilman Tacke are MGI partners, and Mekala Krishnan is an MGI senior fellow. -
WHOI-R-06-006 Ahn, S. Fiber-Optic Microarra
..... APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2006, p. 5742-5749 Vol. 72, No.9 0099-2240/06/$08.00+0 doi:10.1128/AEM.00332-06 Copyright © 2006, American Society for Microbiology. All Rights ReseiVed. ' Fiber-Optic Microarray for Simultaneous Detection of Multiple Harmful Algal Bloom Species Soohyoun Ahn,lt David M. Kulis,2 Deana L. Erdner,2 Donald M. Anderson,2 and David R. Wale* Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, Massachusetts 02155, 1 and Biology Department, WoodY Hole Oceanographic Institution, Woods Hole, Massachusetts 025432 Received 9 February 2006/Accepted 12 June 2006 Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alex/lndrium fundyense, AleXIlndrium ostenfeldii, and Pseudo-nitzschia australis. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 J.tm) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration ofHAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. -
Guide to Biotechnology 2008
guide to biotechnology 2008 research & development health bioethics innovate industrial & environmental food & agriculture biodefense Biotechnology Industry Organization 1201 Maryland Avenue, SW imagine Suite 900 Washington, DC 20024 intellectual property 202.962.9200 (phone) 202.488.6301 (fax) bio.org inform bio.org The Guide to Biotechnology is compiled by the Biotechnology Industry Organization (BIO) Editors Roxanna Guilford-Blake Debbie Strickland Contributors BIO Staff table of Contents Biotechnology: A Collection of Technologies 1 Regenerative Medicine ................................................. 36 What Is Biotechnology? .................................................. 1 Vaccines ....................................................................... 37 Cells and Biological Molecules ........................................ 1 Plant-Made Pharmaceuticals ........................................ 37 Therapeutic Development Overview .............................. 38 Biotechnology Industry Facts 2 Market Capitalization, 1994–2006 .................................. 3 Agricultural Production Applications 41 U.S. Biotech Industry Statistics: 1995–2006 ................... 3 Crop Biotechnology ...................................................... 41 U.S. Public Companies by Region, 2006 ........................ 4 Forest Biotechnology .................................................... 44 Total Financing, 1998–2007 (in billions of U.S. dollars) .... 4 Animal Biotechnology ................................................... 45 Biotech -
Beating the Reaction Limits of Biosensor Sensitivity with Dynamic Tracking of Single Binding Events
Beating the reaction limits of biosensor sensitivity with dynamic tracking of single binding events Derin Sevenlera,b,1, Jacob Truebc, and M. Selim Ünlüa,1 aDepartment of Electrical and Computer Engineering, Boston University, Boston, MA 02215; bCenter for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129; and cDepartment of Mechanical Engineering, Boston University, Boston, MA 02215 Edited by David R. Walt, Brigham and Women’s Hospital–Harvard Medical School, Boston, MA, and accepted by Editorial Board Member John A. Rogers January 19, 2019 (received for review September 13, 2018) The clinical need for ultrasensitive molecular analysis has moti- species (e.g., genomic DNA) with single-copy sensitivity and vated the development of several endpoint-assay technologies precision (10), while the detection limits of other analytes (e.g., capable of single-molecule readout. These endpoint assays are microRNA) are many orders of magnitude worse (11–13). Probe now primarily limited by the affinity and specificity of the affinity can also vary between samples. Variations in extensive molecular-recognition agents for the analyte of interest. In properties of the sample such as pH and ion content change the contrast, a kinetic assay with single-molecule readout could free energy of binding, and variable amounts of nonspecific distinguish between low-abundance, high-affinity (specific ana- background binding further complicates quantitation. lyte) and high-abundance, low-affinity (nonspecific background) Current leading single-molecule detection technologies rely on binding by measuring the duration of individual binding events at signal-amplification reactions. These are endpoint assays: the equilibrium. Here, we describe such a kinetic assay, in which probe molecules are incubated with the sample for a set amount individual binding events are detected and monitored during of time, after which the reaction is halted so that amplification sample incubation. -
Lab on a Chip Systems for Biochemical Analysis, Biology and Synthesis
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Lab on a Chip Systems for Biochemical Analysis, Biology and Synthesis Towards Simple, Scalable Microfabrication Technologies Based on COC and LTCC Miguel Berenguel Alonso Tesi Doctoral Programa de Doctorat en Qu´ımica Directors: Mar Puyol and Juli´anAlonso Chamarro Departament de Qu´ımica Facultat de Ci`encies 2017 Mem`oriapresentada per aspirar al Grau de Doctor per Miguel Berenguel Alonso Vist i plau Mar Puyol Juli´anAlonso Chamarro Professora Agregada Catedr`atic Departament de Qu´ımica Departament de Qu´ımica Bellaterra, 6 de Juny de 2017 iii The present dissertation was carried out with the following financial support: CTQ2009-12128 Nuevas plataformas microflu´ıdicaspara la miniaturizaci´on de sistemas (bio)anal´ıticos integrados e intensificaci´onde procesos de producci´onde nanomateriales. Ministerio de Ciencia e Innovaci´on,co- funded by FEDER. 2009SGR0323 Convocat`oriade suport als Grups de Recerca de Catalunya. Departament d'Universitats, Recerca i Societat de la Informaci´o,Gen- eralitat de Catalunya. FI-DGR 2012 Pre-doctoral scholarship FI-DGR granted by the Ag`enciade Gesti´od'Ajuts Universitaris i de Recerca, Generalitat de Catalunya, and co-funded by the ESF.