DR. LEROY E. HOOD Curriculum Vitae
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Comparison of ABI 3730XL Capillary Sequencer And
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Lehigh University: Lehigh Preserve Lehigh University Lehigh Preserve Theses and Dissertations 2008 Comparison of ABI 3730XL capillary sequencer and Megabace4500 capillary sequencer : the two machines are evaluated for their complexity, accuracy, reproducibility, productivity and cost effectiveness Jacques P. Thimote Lehigh University Follow this and additional works at: http://preserve.lehigh.edu/etd Recommended Citation Thimote, Jacques P., "Comparison of ABI 3730XL capillary sequencer and Megabace4500 capillary sequencer : the two machines are evaluated for their complexity, accuracy, reproducibility, productivity and cost effectiveness" (2008). Theses and Dissertations. Paper 1021. This Thesis is brought to you for free and open access by Lehigh Preserve. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Lehigh Preserve. For more information, please contact [email protected]. Thimote, Jacques P. t Comparison of ABI 3730XL Capillary Sequencer and Megabace 4500 .. Capillary Sequencer... September 2008 . COMPARISON OF ABI 3730XL CAPILLARY SEQUENCER AND MEGABACE4500 CAPILLARY SEQUENCER: THE TWO MACHINES ARE EVALUATED FOR THEIR COMPLEXITY, ACCURACY, REPRODUCIBILITY, PRODUCTIVITY AND COST EFFECTIVENESS. by Jacques P. Thimote A Thesis Pres:ented to the Graduate--and Research Committee ofLehigh University in Candidacy for the Degree of Master ofScience III Chemistry Lehigh University September, 2008 Table of Contents Certificate ofapproval .ii Abstract. .1 Introduction '" 2 Materials Section 5 Experimental Section " " , 6 Discussion Section .Complexity 9 Accuracy 11 Productivity "" '" 13 Reproducibility : 13 Cost effectiveness 14 Conclusion 16 References , 17 Biography , '" , .1·8 iii Abstract The purpose of this research is to compare the ABI 3730xl sequencer to the Megabace 4500 sequencer by evaluating the sequence data obtained from both machines with DNA sample that were cloned into plasmid or M13 phase. -
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UNDERSTAND | Biology, Health A new method of genetic sequencing is making it easier than ever to decode DNA. Iaroslav Neliubov/Shutterstock.com Neliubov/Shutterstock.com Iaroslav Decoding DNA with a pocket-sized sequencer USB-powered sequencers smaller than your smartphone could revolutionise the way we decode DNA – in hospitals, in remote locations and even in space. By Kerstin Göpfrich and Kim Judge What were the biggest technological developments of the Now, another technology is being revolutionised in a 20th century? Computers may be the first thing that comes similar way: the DNA sequencer. to mind: early computers for military and commercial DNA stores the genetic information that is passed down use took up a whole room before they were transformed between generations. Similar to the way computers store into smaller, affordable consumer products in the 1980s. information as a string of zeros and ones, the information Computing power has advanced at such a rate that the in DNA is stored as a code of four bases: A, T, C and G smartphones we use today can perform tasks that even the (adenine, thymine, cytosine and guanine). most powerful computers could not achieve decades ago. www.scienceinschool.org I Science in School I Issue 43 : Spring 2018 I 17 Biology, Health | UNDERSTAND In 2003, the first human genome – the How does nanopore nanopore sequencer, which is plugged complete set of genetic information – sequencing work? into a laptop via a standard USB cable was sequenced. It took seven years, 150 (figure 1). scientists and 3 billion US dollars (2.5 Portable DNA sequencers have been on Inside the nanopore sequencer, an billion euros) to complete the mammoth the market since 2015. -
Whole-Genome Shotgun Assembly and Analysis of the Genome
R ESEARCH A RTICLE of the human genome, it contains a comparable complement of protein-coding genes, as in- Whole-Genome Shotgun ferred from random genomic sampling (3). Subsequently, more-targeted analyses (5–9) Assembly and Analysis of the showed that the Fugu genome has remarkable homologies to the human sequence. The intron- Genome of Fugu rubripes exon structure of most genes is preserved be- tween Fugu and human, in some cases with Samuel Aparicio,2,1* Jarrod Chapman,3 Elia Stupka,1* conserved alternative splicing (10). The relative Nik Putnam,3 Jer-ming Chia,1 Paramvir Dehal,3 compactness of the Fugu genome is accounted Alan Christoffels,1 Sam Rash,3 Shawn Hoon,1 Arian Smit,4 for by the proportional reduction in the size of introns and intergenic regions, in part owing to Maarten D. Sollewijn Gelpke,3 Jared Roach,4 Tania Oh,1 3 1 3 1 the relative scarcity of repeated sequences like Isaac Y. Ho, Marie Wong, Chris Detter, Frans Verhoef, those that litter the human genome. Conserva- 3 1 3 3 Paul Predki, Alice Tay, Susan Lucas, Paul Richardson, tion of synteny was discovered between hu- Sarah F. Smith,5 Melody S. Clark,5 Yvonne J. K. Edwards,5 mans and Fugu (5, 6), suggesting the possibil- Norman Doggett,6 Andrey Zharkikh,7 Sean V. Tavtigian,7 ity of identifying chromosomal elements from Dmitry Pruss,7 Mary Barnstead,8 Cheryl Evans,8 Holly Baden,8 the common ancestor. Noncoding sequence Justin Powell,9 Gustavo Glusman,4 Lee Rowen,4 Leroy Hood,4 comparisons detected core conserved regulato- ry elements in mice (11). -
Automated DNA Sequencing
Automated DNA Sequencing Chemistry Guide ©Copyright 1998, The Perkin-Elmer Corporation This product is for research purposes only. ABI PRISM, MicroAmp, and Perkin-Elmer are registered trademarks of The Perkin-Elmer Corporation. ABI, ABI PRISM, Applied Biosystems, BigDye, CATALYST, PE, PE Applied Biosystems, POP, POP-4, POP-6, and Primer Express are trademarks of The Perkin-Elmer Corporation. AmpliTaq, AmpliTaq Gold, and GeneAmp are registered trademarks of Roche Molecular Systems, Inc. Centricon is a registered trademark of W. R. Grace and Co. Centri-Sep is a trademark of Princeton Separations, Inc. Long Ranger is a trademark of The FMC Corporation. Macintosh and Power Macintosh are registered trademarks of Apple Computer, Inc. pGEM is a registered trademark of Promega Corporation. Contents 1 Introduction. 1-1 New DNA Sequencing Chemistry Guide . 1-1 Introduction to Automated DNA Sequencing . 1-2 ABI PRISM Sequencing Chemistries . 1-5 PE Applied Biosystems DNA Sequencing Instruments . 1-7 Data Collection and Analysis Settings . 1-12 2 ABI PRISM DNA Sequencing Chemistries . 2-1 Overview . 2-1 Dye Terminator Cycle Sequencing Kits . 2-2 Dye Primer Cycle Sequencing Kits . 2-8 Dye Spectra . 2-12 Chemistry/Instrument/Filter Set Compatibilities . 2-13 Dye/Base Relationships for Sequencing Chemistries . 2-14 Choosing a Sequencing Chemistry. 2-15 3 Performing DNA Sequencing Reactions . 3-1 Overview . 3-1 DNA Template Preparation . 3-2 Sequencing PCR Templates . 3-10 DNA Template Quality. 3-15 DNA Template Quantity. 3-17 Primer Design and Quantitation . 3-18 Reagent and Equipment Considerations. 3-20 Preparing Cycle Sequencing Reactions . 3-21 Cycle Sequencing . 3-27 Preparing Extension Products for Electrophoresis . -
2004 Albert Lasker Nomination Form
albert and mary lasker foundation 110 East 42nd Street Suite 1300 New York, ny 10017 November 3, 2003 tel 212 286-0222 fax 212 286-0924 Greetings: www.laskerfoundation.org james w. fordyce On behalf of the Albert and Mary Lasker Foundation, I invite you to submit a nomination Chairman neen hunt, ed.d. for the 2004 Albert Lasker Medical Research Awards. President mrs. anne b. fordyce The Awards will be offered in three categories: Basic Medical Research, Clinical Medical Vice President Research, and Special Achievement in Medical Science. This is the 59th year of these christopher w. brody Treasurer awards. Since the program was first established in 1944, 68 Lasker Laureates have later w. michael brown Secretary won Nobel Prizes. Additional information on previous Lasker Laureates can be found jordan u. gutterman, m.d. online at our web site http://www.laskerfoundation.org. Representative Albert Lasker Medical Research Awards Program Nominations that have been made in previous years may be updated and resubmitted in purnell w. choppin, m.d. accordance with the instructions on page 2 of this nomination booklet. daniel e. koshland, jr., ph.d. mrs. william mccormick blair, jr. the honorable mark o. hatfied Nominations should be received by the Foundation no later than February 2, 2004. Directors Emeritus A distinguished panel of jurors will select the scientists to be honored. The 2004 Albert Lasker Medical Research Awards will be presented at a luncheon ceremony given by the Foundation in New York City on Friday, October 1, 2004. Sincerely, Joseph L. Goldstein, M.D. Chairman, Awards Jury Albert Lasker Medical Research Awards ALBERT LASKER MEDICAL2004 RESEARCH AWARDS PURPOSE AND DESCRIPTION OF THE AWARDS The major purpose of these Awards is to recognize and honor individuals who have made signifi- cant contributions in basic or clinical research in diseases that are the main cause of death and disability. -
A Method for DNA Sequencing Using RNA Polymerase
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 3455–3460, March 1998 Biochemistry Transcriptional sequencing: A method for DNA sequencing using RNA polymerase NOBUYA SASAKI*, MASAKI IZAWA*†,MASANORI WATAHIKI†,KAORI OZAWA‡,TAKUMI TANAKA‡,YUKO YONEDA†, SHUJI MATSUURA‡,PIERO CARNINCI*, MASAMI MURAMATSU*, YASUSHI OKAZAKI*, AND YOSHIHIDE HAYASHIZAKI*§ *Genome Science Laboratory, Tsukuba Life Science Center, The Institute of Physical and Chemical Research, 3-1-1 Koyadai, Tsukuba, Ibaraki 305, Japan; †Research and Development, Nippon Gene Co., Ltd., 1-29, Tonya-machi, Toyama, 930 Japan; and ‡Osaka Research Laboratories, Wako Pure Chemical Industries, Ltd., 6-1, Takada-cho, Amagasaki, Hyogo 661, Japan Communicated by Webster K. Cavenee, University of California, San Diego, La Jolla, CA, December 24, 1997 (received for review November 20, 1997) ABSTRACT We have developed a sequencing method direct sequencing of PCR products by using Dye-terminator based on the RNA polymerase chain termination reaction with chemistry, unreacted 29-dNTP and primers must be eliminated rhodamine dye attached to 3*-deoxynucleoside triphosphate to avoid interference with the subsequent sequencing reaction. (3*-dNTP). This method enables us to conduct a rapid iso- Although efforts have been made to quickly purify the PCR thermal sequencing reaction in <30 min, to reduce the amount product such as enzymatic degradation using exonuclease I of template required, and to do PCR direct sequencing without and shrimp alkaline phosphatase, most protocols are time- the elimination of primers and 2*-dNTP, which disturbs the consuming, laborious, and expensive (7, 8). Sanger sequencing reaction. An accurate and longer read To overcome the above problems, we pursued a completely length was made possible by newly designed four-color dye- different approach. -
Biological Organization and Pathology: Three Views on the Normativity of Medicine
Chapter 8 Biological Organization and Pathology: Three Views on the Normativity of Medicine Arantza Etxeberria A b s t r a c t Medical knowledge aims to identify different diseases as wrong conditions of biological organization. One main issue within the fi eld of the phi- losophy of medicine is the question of just how confi dent we can be that what we know about biological organization will help us to identify diseases and propose cures or treatments for them. The concept of biological organization is a complex abstraction which requires the coexistence of constitutive, interactive and experien- tial aspects; while the main attempts at naturalist descriptions of the concept (functional, mechanistic and systemic) fail to be fully comprehensive. Different arguments have supported a naturalist normativity in medicine; the strongest such perspective contrasts the normal or typical state of organizational elements with their “broken” versions. However, the complexity of biological organization sug- gests that there are multiple ways of being healthy or diseased. Thus, the normative goal of medicine of identifying diseases encounters two fundamental questions: (1) Is biology itself normative and can it defi ne the “natural” state? (2) Can medi- cine rely on knowledge other than biological knowledge to identify what goes wrong? As a normative discipline, medicine comes into confl ict with the multiplicity in the very ontology of diseases, which needs to be complemented with epistemic pluralism. Philosophy of medicine therefore needs to explore the sources of that normativity. Keywords Naturalism • Constructivism • Normative and descriptive • Functional approach • Normal–broken framework A. Etxeberria (*) Department of Logic and Philosophy of Science , University of the Basque Country UPV- EHU , Tolosa Hiribidea 70 , 20018 Donostia-San Sebastián , Spain e-mail: [email protected] © Springer International Publishing Switzerland 2016 121 É. -
The Road from Systems Biology to Systems Medicine
nature publishing group Review The road from systems biology to systems medicine Olaf Wolkenhauer1,2, Charles Auffray3, Robert Jaster4, Gustav Steinhoff5 and Olaf Dammann6,7 As research institutions prepare roadmaps for “systems datasets, requiring not only new computational platforms to medicine,” we ask how this differs from applications of systems manage data but most importantly, requiring new ways of biology approaches in medicine and what we (should) have thinking, including the application and development of meth- learned from about one decade of funding in systems biology. odologies from the mathematical sciences; and (iv) to address After surveying the area, we conclude that systems medicine clinical questions with statistical, mathematical, computational, is the logical next step and necessary extension of systems molecular, and cell-biological methodologies requires strategic biology, and we focus on clinically relevant applications. We efforts to motivate and sustain cross-disciplinary collaborations. specifically discuss three related notions. First, more interdis- Applying systems approaches in a clinical setting, practical, ciplinary collaborations are needed to face the challenges of i.e., formal/legal and computational issues of data collection and integrating basic research and clinical practice: integration, sharing are the most immediate challenge and potential threat analysis, and interpretation of clinical and nonclinical data for to progress. Although these issues are crucial and most press- diagnosis, prognosis, and therapy require advanced statistical, ing, we shall here emphasize the role of mathematical modeling computational, and mathematical tools. Second, strategies are as one aspect that is easily forgotten when it comes to setting required to (i) develop and maintain computational platforms priorities. -
A Review of J. Craig Venter's a Life Decoded
A peer-reviewed electronic journal published by the Institute for Ethics and Emerging Technologies ISSN 1541-0099 17(1) – March 2008 A review of J. Craig Venter’s A Life Decoded Randy Mayes, Duke University Journal of Evolution and Technology - Vol. 17 Issue 1 – March 2008 - pgs 71-72 http://jetpress.org/v17/mayes.htm In the early 1980s, a number of researchers suggested sequencing and mapping the human genome to help the science community better understand diseases and evolution. Following the announcement that the human genome had been sequenced, scientists wrote in peer-reviewed journals that we are not as hardwired as was once believed, and that the sequencing of the genome was just the beginning. Today, researchers have a new set of goals. In popular journalism, however, the science was lost in the shuffle. The media focused more on the dynamics of the conflicting philosophies of the private and public projects. This emphasis is also clear in the titles of several books chronicling the Human Genome Project, all appearing prior to the recent release of Craig Venter’s autobiography, A Life Decoded: My Genome: My Life (2007). Readers will find that Robert Cook-Deegan’s The Gene Wars (1995) and The Common Thread by Sir John Sulston and Georgina Ferry (2002), both written by insiders, are biased towards the philosophy of the public project, a commons approach. Sulston is a socialist who grows runner beans and drives a second hand car. By contrast, Venter travels in Lear jets and conducts business from his yacht. Three other books are more objective. -
Award Recipients Award Consists of a Plaque and a Cash Stipend
SOT HONOR AND AWARD DESCRIPTIONS AND HISTORY In recognition of distinguished toxicologists and students, Nominations for many awards must be submitted by a sponsor SOT presents Honorary Membership and Awards each year. and a seconder who are Full members of SOT using the online In addition to receiving a plaque, recipients are honored Award Nomination form. The supporting documentation at a special Awards Ceremony at the SOT Annual Meeting must indicate the candidate’s achievements in toxicology and and their names are listed in SOT publications. The deadline is critical in the review of each application. See the award for 2013 Honorary Membership and Award nominations is description for the additional requirements and details. There October 9, 2012. are specific applications for Fellowships and Graduate Student Travel Support. SOT Council reviews nominations for Honorary Membership and the Awards Committee reviews applications for SOT Other graduate student and postdoctoral fellow awards are Awards and most Sponsored Awards. Awards Committee available through Regional Chapters, Special Interest Groups, members are not eligible to receive any awards conferred by and Specialty Sections (many of these awards are funded the Committee while serving on the Committee and for one through the various Named Endowment Funds). A student or subsequent year. postdoctoral scholar may apply for any award for which he or she is eligible and may apply for and receive multiple awards, The Best Paper Awards in Toxicological Sciences are reviewed whether SOT, Regional Chapters, Special Interest Groups, or by the Board of Publications. The Education Committee selects Specialty Sections administrators the awards. Policies related the recipients of the Pfizer Undergraduate Travel Award and to travel support are determined by the sponsor (SOT, the Committee on Diversity Initiatives selects the recipients Regional Chapter, Special Interest Group, or Specialty Section). -
Applying Systems Biology to Biomedical Research and Health Care
Schleidgen et al. BMC Health Services Research (2017) 17:761 DOI 10.1186/s12913-017-2688-z RESEARCH ARTICLE Open Access Applying systems biology to biomedical research and health care: a précising definition of systems medicine Sebastian Schleidgen1*† , Sandra Fernau2†, Henrike Fleischer3†, Christoph Schickhardt4†, Ann-Kristin Oßa4 and Eva C. Winkler4 Abstract Background: Systems medicine has become a key word in biomedical research. Although it is often referred to as P4-(predictive, preventive, personalized and participatory)-medicine, it still lacks a clear definition and is open to interpretation. This conceptual lack of clarity complicates the scientific and public discourse on chances, risks and limits of Systems Medicine and may lead to unfounded hopes. Against this background, our goal was to develop a sufficiently precise and widely acceptable definition of Systems Medicine. Methods: In a first step, PubMed was searched using the keyword “systems medicine”. A data extraction tabloid was developed putting forward a means/ends-division. Full-texts of articles containing Systems Medicine in title or abstract were screened for definitions. Definitions were extracted; their semantic elements were assigned as either means or ends. To reduce complexity of the resulting list, summary categories were developed inductively. In a second step, we applied six criteria for adequate definitions (necessity, non-circularity, non-redundancy, consistency, non-vagueness, and coherence) to these categories to derive a so-called précising definition of Systems Medicine. Results: We identified 185 articles containing the term Systems Medicine in title or abstract. 67 contained at least one definition of Systems Medicine. In 98 definitions, we found 114 means and 132 ends. -
28Th Course in Medical Genetics
European School of Genetic Medicine th 28 Course in Medical Genetics Bertinoro University Residential Centre Via Frangipane, 6 – Bertinoro Course Directors: H. Brunner (Nijmegen, The Netherlands), G.Romeo (Bologna, Italy), B.Wirth (Cologne, Germany) 1 28th Course in Medical Genetics CONTENTS PROGRAMME 3 ABSTRACTS OF LECTURES 7 ABSTRACTS OF STUDENTS POSTERS 37 STUDENTS WHO IS WHO 40 FACULTY WHO IS WHO 51 2 Arrival: Saturday May 16 Sunday, May 17 Morning Session: Introduction to Human Genome Analysis 8.30 – 9.00 Registration to the course 9.00 – 9.30 Introduction to the course G. Romeo 9.30 – 10.15 Medical Genetics Today D. Donnai 10.15 – 11.00 Genotypes & phenotypes H. Brunner 11.00 – 11.30 Coffee Break 11.30 – 12.15 Introduction in Next Generation Sequencing technologies and applications J. Veltman 12.15 – 13.00 How to deal with next generation sequencing output. C. Gilissen 13.10 – 14.00 Lunch Break Afternoon Session: 14.30 – 16.00 Concurrent Workshops 16.00-16.30 Coffee Break 16.30 – 18.00 Concurrent Workshops 3 Monday, May 18 Morning Session: Approaches to Clinical and Molecular Genetics 9.00 – 9.50 Linkage and association (in a conceptual and historic perspective) A. Read 9.50- 10.40 Arrays and CNVs E. Klopocki 10.40 – 11.10 Coffee Break 11.10 – 12.00 Molecular syndromology in the NGS-era: which phenotype, which family, which strategy? Applications to aging research B. Wollnik 12.00 – 12.50 Bottlenecks in understanding mitochondrial diseases P. Chinnery 13.10 – 14.00 Lunch Break Afternoon Session: 14.30 – 16.00 Concurrent Workshops – including Ethics by Andrew Read 16.00-16.30 Coffee Break 16.30 – 18.00 Concurrent Workshops 18.30 – 19.30 Poster Viewing Session 4 Tuesday, May 19 Morning Session: Gene regulation and complex genetic disorders 9.00 - 9.50 Preventing and treating mitochondrial diseases Patrick Chinnery 9.50 – 10.40 Epigenetics and disease K.