DOCSLIB.ORG

(12) United States Patent (10) Patent No.: US 9,334,531 B2 Li Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) United States Patent (10) Patent No.: US 9,334,531 B2 Li Et Al USOO933.4531B2 (12) United States Patent (10) Patent No.: US 9,334,531 B2 Li et al. (45) Date of Patent: *May 10, 2016 (54) NUCLECACIDAMPLIFICATION (56) References Cited U.S. PATENT DOCUMENTS (71) Applicant: LIFE TECHNOLOGIES 5,223,414 A 6/1993 Zarling et al. CORPORATION, Carlsbad, CA (US) 5,616,478 A 4/1997 Chetverin et al. 5,670,325 A 9/1997 Lapidus et al. (72) Inventors: Chieh-Yuan Li, El Cerrito, CA (US); 5,928,870 A 7/1999 Lapidus et al. David Ruff, San Francisco, CA (US); 5,958,698 A 9, 1999 Chetverinet al. Shiaw-Min Chen, Fremont, CA (US); 6,001,568 A 12/1999 Chetverinet al. 6,033,881 A 3/2000 Himmler et al. Jennifer O'Neil, Wakefield, MA (US); 6,074,853. A 6/2000 Pati et al. Rachel Kasinskas, Amesbury, MA (US); 6,306,590 B1 10/2001 Mehta et al. Jonathan Rothberg, Guilford, CT (US); 6.432,360 B1 8, 2002 Church Bin Li, Palo Alto, CA (US); Kai Qin 6,440,706 B1 8/2002 Vogelstein et al. Lao, Pleasanton, CA (US) 6,511,803 B1 1/2003 Church et al. 6,929,915 B2 8, 2005 Benkovic et al. (73) Assignee: Life Technologies Corporation, 7,270,981 B2 9, 2007 Armes et al. 7,282,337 B1 10/2007 Harris Carlsbad, CA (US) 7,399,590 B2 7/2008 Piepenburg et al. 7.432,055 B2 * 10/2008 Pemov et al. ................ 435/6.11 (*) Notice: Subject to any disclaimer, the term of this 7,435,561 B2 10/2008 Piepenburg et al. patent is extended or adjusted under 35 7,485,428 B2 2/2009 Armes et al. U.S.C. 154(b) by 0 days. 7,604,940 B1 10/2009 Voss 7,666,598 B2 2/2010 Piepenburg et al. This patent is Subject to a terminal dis 7,723,031 B2 5, 2010 Benkovic et al. claimer. 7,763.427 B2 7/2010 Piepenburg et al. 7,785,790 B1 8, 2010 Church et al. (21) Appl. No.: 14/023,361 7,824,889 B2 11/2010 Vogelstein et al. 7,906,279 B2 3/2011 Benkovic et al. (22) Filed: Sep. 10, 2013 7,915,015 B2 3/2011 Vogelstein et al. 7,985,565 B2 7/2011 Mayer et al. 8,017,339 B2 9/2011 Piepenburg et al. (65) Prior Publication Data 8,030,000 B2 10/2011 Piepenburg et al. US 2014/O080717 A1 Mar. 20, 2014 8,062,850 B2 11/2011 Piepenburg et al. Related U.S. Application Data (Continued) (63) Continuation-in-part of application No. 13/923,232, FOREIGN PATENT DOCUMENTS filed on Jun. 20, 13, which is a continuation of CN 1489632 A2 4/2004 application No. 13/842.296, filed on Mar. 15, 2013, CN 1014 13034 B 2, 2011 which is a continuation-in-part of application No. (Continued) 13/328,844, filed on Dec. 16, 2011, now abandoned, OTHER PUBLICATIONS said application No. 13/842.296 is a Bentley et al. (Accurate Whole Human Genome Sequencing using continuation-in-part of application No. 13/828,049, Reversible Terminator Chemistry, Nature. Nov. 6, 2008; 4.56(7218): filed on Mar. 14, 2013, which is a continuation-in-part 53-59).* of application No. 13/328,844, filed on Dec. 16, 2011, now abandoned, said application No. 13/842.296 is a (Continued) continuation-in-part of application No. Primary Examiner — Aaron Priest PCT/US2011/065535, filed on Dec. 16, 2011, application No. 14/023,361, which is a (57) ABSTRACT continuation-in-part of application No. In some embodiments, the present teachings provide methods PCT/US2013/037352, filed on Apr. 19, 2013. for nucleic acid amplification, comprising forming a reaction mixture, and Subjecting the reaction mixture to conditions (60) Provisional application No. 61/876,136, filed on Sep. Suitable for nucleic acid amplification. In some embodiments, 10, 2013, provisional application No. 61/859,000, methods for nucleic acid amplification include Subjecting the filed on Jul. 26, 2013, provisional application No. nucleic acid to be amplified to partially denaturing condi 61/858,977, filed on Jul. 26, 2013, provisional tions. In some embodiments, methods for nucleic acid ampli application No. 61/822,239, filed on May 10, 2013, fication include amplifying without fully denaturing the provisional application No. 61/822.226, filed on May nucleic acid that is amplified. In some embodiments, the 10, 2013, provisional application No. 61/792.247, methods for nucleic acid amplification employ an enzyme filed on Mar. 15, 2013, provisional application No. that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplifica (Continued) tion can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be (51) Int. C. conducted in a single continuous liquid phase of a reaction CI2O I/68 (2006.01) mixture, without need for compartmentalization of the reac (52) U.S. C. tion mixture or immobilization of reaction components. In CPC ............ CI2O I/6853 (2013.01): CI2O I/6846 Some embodiments, methods for nucleic acid amplification (2013.01); C12O 1/6855 (2013.01); C12O comprise a amplifying at least one polynucleotide onto a I/6874 (2013.01) Surface under isothermal amplification conditions, optionally (58) Field of Classification Search in the presence of a polymer. The polymer can include a None sieving agent and/or a diffusion-reducing agent. See application file for complete search history. 20 Claims, 20 Drawing Sheets US 9,334,531 B2 Page 2 Related U.S. Application Data WO WO-94,03624 2, 1994 WO WO-98.08975 3, 1998 61/781,016, filed on Mar. 14, 2013, provisional appli- WO WO-98. 44151 10, 1998 cation No. 61/767,766, filed on Feb. 21, 2013, provi- WO WO-OOf 18957 4/2000 sional application No. 61/692.830, filed on Aug. 24. W. W886. A2 858 2012, provisional application No. 61/699,810, filed on WO WO-01/81908 11, 2001 Sep. 11, 2012, provisional application No. 61/635,584, WO WOO181908 A1 * 11, 2001 filed on Apr. 19, 2012, provisional application No. WO WO-02/46456 A1 6, 2002 WO WO-O2/O72772 A2 9, 2002 61/424,599, filed on Dec. 17, 2010, provisional appli- WO WO-O3,O72805 9, 2003 cation No. 61/445,324, filed on Feb. 22, 2011, provi- WO WO-2005/007796 1, 2005 sional application No. 61/451,919, filed on Mar. 11, WO WO-2006/099579 A2 9, 2006 2011, provisional application No. 61/526,478, filed on WO WO-2007/O10252 1, 2007 Aug. 23, 2011, provisional application No. 61/552, W. W85886 338. 660, filed on Oct. 28, 2011. WO WO-2009/102878 A2 8, 2009 WO WO-2011/106368 A2 9, 2011 (56) References Cited WO WO-2011/106368 A3 9, 2011 WO WO-2011 (106460 9, 2011 U.S. PATENT DOCUMENTS WO WO 2011 106368 A2 * 9, 2011 WO WO-2012,083189 A2 6, 2012 8,071.308 B2 12/2011 Piepenburg et al. WO WO-2012,083189 A3 6, 2012 8,124,342 B2 2/2012 Benkovic et al. WO WO-2012/106072 A2 8, 2012 8,129, 116 B2 3/2012 Benkovic et al. WO WO-2013/O19361 2, 2013 8,137,913 B2 3/2012 Benkovic et al. WO WO-2013,0457OO 4/2013 8,143,008 B2 3/2012 Kawashima et al. 8,241,851 B2 8/2012 Benkovic et al. OTHER PUBLICATIONS 8,361,718 B2 1/2013 Benkovic et al. 8,389,216 B2 3/2013 Benkovic et al. Pemov et al. (DNA analysis with multiplex microarray-enhanced 8,426,134 B2 4/2013 Piepenburg et al. PCR, Nucleic Acids Research, 2005, vol. 33, No. 2).* 8.460,875 B2 6/2013 Armes et al. Yershov et al. (DNA analysis and diagnostics on oligonucleotide E: 3. Rastal microchips, Proc. Natl. Acad. Sci. USA vol. 93, pp. 4913-4918, May 8,673,561 B2 3/2014 Benkovicetal. 1996). 8,759,000 B2 6/2014 Benkovic et al. Shigemori et al. (Multiplex PCR: use of heat-stable Thermus 8,765,374 B2 7/2014 Benkovic et al. thermophilus RecA protein to minimize non-specific PCR products, 8,895,249 B2 11/2014 Shen et al. Nucleic Acids Research, 2005, vol. 33, No. 14).* 2003, OOO3609 A1 1/2003 Sauer et al. Piepenburg et al. (DNA Detection Using Recombination Proteins, 2003/0143525 A1 7/2003 Benkovic et al. ................. 435/5 PLoS Biology, vol. 4, issue 7, Jul. 2006).* 2003/0219792 Al 11/2003 Armes et al. Pourmandet al. (Direct electrical detection of DNA synthesis, PNAS, 2004/0171060 A1 9, 2004 Benkovic et al. vol. 103, No. 17, Apr. 15, 2006, pp. 6466-6470).* 3881999 A. ck 58. SR .. 435/6 Rothberg et al. (An integrated semiconductor device enabling non 2007/0054296 A1* 3, 2007 E. al. t 435/6 optical genome Sequencing, Nature, vol. 475, Jul. 21, 2011, pp. 2008.0009420 A1 1/2008 Schroth et al. ........ 5061, 348-352). 2008/0166727 A1* 7/2008 Esfandyarpour et al. ......... 435/6 Shapero et al. (SNP Genotyping by Multiplexed Solid-Phase Ampli 2009/0093378 A1 4/2009 Bignell et al. fication and Fluorescent Miniseauencing, Genome Res. 2001 11: 2009/0127589 A1* 5/2009 Rothberg et al. ............. 257/253 1926-1934).* 2009/0171078 A1 7/2009 Lao et al. Adessi et al. (Solid phase DNA amplification: characterisation of 2009/0203531 A1* 8, 2009 Kurn ................................. 506.6 primer attachment and amplification mechanisms, Nucleic Acids 2009/0286286 A1* 11/2009 Lim et al. ..................... 435,912 Research, 2000, vol.
Load more

Recommended publications
  • CBIT Annual Report 2012
    Centre for Bio-Inspired Technology Annual Report 2012 Centre for Bio-Inspired Technology Institute of Biomedical Engineering Imperial College London South Kensington London SW7 2AZ T +44 (0)20 7594 0701 F +44 (0)20 7594 0704 [email protected] www.imperial.ac.uk/bioinspiredtechnology Centre for Bio-Inspired Technology Annual Report 2012 3 Director’s foreword 22 Medical science in the 21st century: a young engineer’s view 4 Founding Sponsor’s foreword 24 Clinical assessment of the 5 People bio-inspired artificial pancreas in 7 News subjects with type 1 diabetes 7 Honours and awards 26 Development of a genetic analysis 8 People and events platform to create innovative and 10 News from the interactive databases combining genotypic Centre’s ‘spin-out’ companies and phenotypic information for genetic detection devices 12 Research funding 29 Chip gallery 13 Research themes 33 Who we are 14 Metabolic technology 35 Academic staff profiles 15 Cardiovascular technology 40 Administrative staff profiles 16 Genetic technology 42 Staff research reports 17 Neural interfaces & neuroprosthetics 56 Research Students’ and 19 Research facilities Assistants’ reports 1 2 Centre for Bio-Inspired Technology | Annual Report 2012 Director’s foreword This Research Report for 2012 describes research institute, our collaborators include the research activities of The Centre for engineers, scientists, medical researchers and clinicians. We include here some brief reports of these Bio-Inspired Technology as it completes colleagues and how their current research has its third year of research. It is a privilege developed from their work in the Centre. to be Director of the Centre and to work One of the prime aims of the Institute of Biomedical with my colleagues at Imperial and Engineering, from which the Centre developed, was to around the world on a range of transfer technology from the laboratory into a innovative projects.
    [Show full text]
  • Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective
    Review Article Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective Cliff Meldrum,1,4† Maria A Doyle,2† *Richard W Tothill3 1Molecular Pathology, Hunter Area Pathology Service, Newcastle, NSW 2310; 2Bioinformatics and 3Next-generation DNA Sequencing Facility Research Department and 4Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Vic. 3002, Australia. †These authors contributed equally to this manuscript. *For correspondence: Dr Richard Tothill, [email protected] Abstract Next-generation sequencing (NGS) is arguably one of the most significant technological advances in the biological sciences of the last 30 years. The second generation sequencing platforms have advanced rapidly to the point that several genomes can now be sequenced simultaneously in a single instrument run in under two weeks. Targeted DNA enrichment methods allow even higher genome throughput at a reduced cost per sample. Medical research has embraced the technology and the cancer field is at the forefront of these efforts given the genetic aspects of the disease. World-wide efforts to catalogue mutations in multiple cancer types are underway and this is likely to lead to new discoveries that will be translated to new diagnostic, prognostic and therapeutic targets. NGS is now maturing to the point where it is being considered by many laboratories for routine diagnostic use. The sensitivity, speed and reduced cost per sample make it a highly attractive platform compared to other sequencing modalities. Moreover, as we identify more genetic determinants of cancer there is a greater need to adopt multi-gene assays that can quickly and reliably sequence complete genes from individual patient samples. Whilst widespread and routine use of whole genome sequencing is likely to be a few years away, there are immediate opportunities to implement NGS for clinical use.
    [Show full text]
  • Complete Thesis
    University of Groningen Omega transaminases: discovery, characterization and engineering Palacio, Cyntia Marcela IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2019 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Palacio, C. M. (2019). Omega transaminases: discovery, characterization and engineering. Rijksuniversiteit Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 01-10-2021 Omega transaminases: discovery, characterization and engineering Cyntia Marcela Palacio 2019 Cover design by Cyntia Palacio and Joris Goudsmits, adapted from a decorative mosaic artwork on the railway underpass on Moesstraat, Groningen.
    [Show full text]
  • Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor
    Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof.
    [Show full text]
  • Human Genome Project
    Human Genome Project The Human Genome Project (HGP) was an international scientific research project with the goal of determining the sequence of nucleotide base pairs that make up human DNA, and of identifying and mapping all of the genes of the human genome from both a physical and a functional standpoint.[1] It remains the world's largest collaborative biological project.[2] After the idea was picked up in 1984 by the US government when the planning started, the project formally launched in 1990 and was declared complete in 2003[3]. Funding came from the US government through the National Institutes of Health (NIH) as well as numerous other groups from around the world. A parallel project was conducted outside government by the Celera Corporation, or Celera Genomics, which was formally launched in 1998. Most of the government-sponsored sequencing was performed in twenty universities and research centers in the United States, the United Kingdom, Japan, France, Logo HGP; Vitruvian Man, Leonardo Germany, Spain and China.[4] da Vinci The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome (more than three billion). The "genome" of any given individual is unique; mapping the "human genome" involved sequencing a small number of individuals and then assembling these together to get a complete sequence for each chromosome. Therefore, the finished human genome is a mosaic, not representing any one individual. Contents Human Genome Project History State of completion Applications and proposed
    [Show full text]
  • Genome Technology
    Contents | Zoom in | Zoom out For navigation instructions please click here Search Issue | Next Page This month in Genome Technology Also inside this month’s Genome Technology • STRUCTURAL VARIATION The latest findings and approaches to under- standing copy number variation regions and what they mean. • METABOLOMICS Work is underway to improve the technology and analytical tools needed to understand phenotype. • CASE STUDY Researchers aim for molecular diagnostics to decipher the mystery of metastatic carcinomas of unknown primary. • CLINICAL Q&A: Gurvaneet Randhawa The genomics advisor opines on evidence- based medicine. LOG ON NOW AT WWW.GENOME-TECHNOLOGY.COM RECENT RESULTS FROM GT POLLS Explore all of our exclusive new resources for molecular biologists: How do you keep up with research in your field? THE DAILY SCAN — Our editors’ daily picks of what’s worth reading on the Web I rely on PubMed. What else THE FORUM — Where scientists can inquire and comment on research, tools, is there? .............................................. 68% and other topics I go online, to community-based sites PODCASTS — Hear the full comments – in their own voices – of researchers like FriendFeed and blogs. ................. 10% interviewed in Genome Technology Magazine I use referrals from other scientists. ...... 4% POLLS — Make your opinions known on topics from the sublime to the ridiculous I stick to the basics: Nature and ARCHIVE — Magazine subscribers can read every word of every article we Science. ................................................ 18% have ever published Contents | Zoom in | Zoom out For navigation instructions please click here Search Issue | Next Page A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS 1000-Series Thermal Cyclers WE THINK YOU SHOULD BE ABLE TO OPTIMIZE ON THE FLY Convenience Is What Happens When You Rethink PCR Change the way you think about PCR with Bio-Rad’s new family of thermal cyclers.
    [Show full text]
  • Ca. P. Ectocarpi” Ec32 and the P
    Frontiers in Genetics - The “Ca. Phaeomarinobacter ectocarpi” genome – Data sheet 2 Page 1 Data sheet 2. Functional comparison of the “Ca. P. ectocarpi” Ec32 and the P. lavamentivorans DS- 1T genomes carried out using the RAST platform. Category Subcategory Subsystem Role “Ca. P. ectocarpi” only Amino Acids and Derivatives Alanine, serine, and glycine Alanine biosynthesis Valine--pyruvate aminotransferase (EC 2.6.1.66) Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system Sodium/glycine symporter GlyP Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine and Ornithine Degradation Ornithine cyclodeaminase (EC 4.3.1.12) Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1) Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Leucine-responsive regulatory protein, regulator for Biosynthesis leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system Amino Acids and Derivatives Glutamine, glutamate, aspartate, asparagine; Glutamate and Aspartate uptake in Glutamate Aspartate periplasmic binding protein ammonia assimilation Bacteria precursor GltI (TC 3.A.1.3.4) Amino Acids and Derivatives Glutamine, glutamate, aspartate, asparagine; Glutamate and Aspartate uptake in Glutamate Aspartate transport system permease protein ammonia assimilation Bacteria GltJ (TC 3.A.1.3.4) Amino Acids and Derivatives Glutamine, glutamate, aspartate, asparagine; Glutamate and Aspartate
    [Show full text]
  • Next-Generation Sequencing
    CAREER SNAPSHOTS Next-generation sequencing The speed, cost and accessibility of DNA sequencing has been transformed in recent years by new technologies, opening up exciting possibilities for disease diagnosis and therapeutic intervention. This month, we interview two of the pioneers in the field. Since then, Branton and Deamer (who is a Branton’s proposal that freeze-etching methods Daniel Branton, Ph.D. professor at the University of California, Irvine, for electron microscopy could reveal the internal Emeritus Professor USA) have continued their research in trying to structure of biological membranes (Science 158, of Biology, Harvard derive sequence information from nanopores, 655; 1967), much to the surprise of experts in University, Boston, and have been joined by many of their students the techniques. “Indeed, following a lecture on Massachusetts, USA. and other investigators. “Although early these results, one expert asked what specialized nanopore experiments disappointed naive facilities I had used,” Branton says. “On hearing expectations of an easy path to inexpensive that we had only some makeshift equipment on In 1991, a conversation with a friend and DNA sequencing, much progress has been a bench-top, he laughed and said: ‘Dan, if you collaborator, David Deamer, about the push to made,” says Branton (see Nature Biotech. had known more about what you were doing, sequence the human genome catalysed Daniel 26, 1146–1153; 2008). “And the advantages you would have realized that you cannot get any Branton’s entry into the field
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 9,353,390 B2 Yan Et Al
    US009353390B2 (12) United States Patent (10) Patent No.: US 9,353,390 B2 Yan et al. (45) Date of Patent: May 31, 2016 (54) GENETICALLY ENGINEERED MICROBES National Center for Biotechnology Information, National Library of AND METHODS FOR PRODUCING Medicine, National Institutes of Health, GenBank Locus 4-HYDROXYCOUMARIN NP 252920. Accession No. NP 252920, "isochorismate-pyruvate lyase IPseudomonas aeruginosa PAO1),” online). Bethesda, MD (71) Applicant: University of Georgia Research retrieved on Aug. 3, 2015. Retrieved from the Internet: <URL: Foundation, Inc., Athens, GA (US) http://www.ncbi.nlm.nih.gov/protein/NP 252920. 1; 3 pgs. National Center for Biotechnology Information, National Library of (72) Inventors: Yajun Yan, Athens, GA (US); Yuheng Medicine, National Institutes of Health, GenBank Locus Lin, Marietta, GA (US) NP 415125. Accession No. NP 415125. "isochorismate synthase 1 Escherichia coli str. K-12 substr. MG 1655, online. Bethesda, (73) Assignee: University of Georgia Research MD retrieved on Aug. 3, 2015). Retrieved from the Internet: <URL: http://www.ncbi.nlm.nih.gov/protein/NP 415125.1.>; 3 pgs. Foundation, Inc., Athens, GA (US) Ajikumar et al. “Isoprenoid Pathway Optimization for Taxol Precur (*) Notice: Subject to any disclaimer, the term of this sor Overproduction in Escherichia coli" Science, Oct. 1, 2010; 330(6000):70-4. patent is extended or adjusted under 35 Anthony et al. “Optimization of the mevalonate-based isoprenoid U.S.C. 154(b) by 0 days. biosynthetic pathway in Escherichia coli for production of the anti malarial drug precursor amorpha-4,11-diene' Metab. Eng. Jan. 2009; (21) Appl. No.: 14/304,105 11(1): 13-9.
    [Show full text]
  • Meyer Cornellgrad 0058F 10073
    METHODS FOR FUNCTIONAL INFERENCE IN THE PROTEOME AND INTERACTOME A Dissertation Presented to the Faculty of the Graduate School of Cornell University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Michael Joseph Meyer January 2017 © 2017 Michael Joseph Meyer ALL RIGHTS RESERVED METHODS FOR FUNCTIONAL INFERENCE IN THE PROTEOME AND INTERACTOME Michael Meyer Cornell University 2017 Over the past several decades, biology has become an increasingly data-driven science. Due in large part to new techniques that allow massive collection of biological data, including next-generation sequencing and high-throughput experimental screening, many of the limitations currently facing the field are in the organization and interpretation of these data. In this dissertation, I present several computational methods and resources designed to organize and perform functional inference on these systems-level biological data sources. In Chapters 2 and 3, I describe the construction of a database and web tool to aid in foundational genomics research by providing predictions of interacting protein domains in interactomes and all-by-all conversions of popular variant identification formats. In Chapter 4, I describe the construction of the first whole-interactome protein interaction network in the fission yeast S. pombe, and, through comparisons with other complete networks in human and the budding yeast S. cerevisiae, demonstrate principles of functional evolution. Finally, in Chapters 5 and 6, I propose two new methods for functional genomic inference—an algorithm to predict cancer driver genes and mutations through 3D atomic clustering of somatic mutations and an ensemble machine learning method to predict the 3D interfaces of protein interactions by taking into account the evolutionary relationships and biophysical properties of proteins.
    [Show full text]
  • Your Human Genome
    the Candid Conversations series is a collaboration between Scientifi c American’s Custom Media Division and its selected sponsors YOUR HUMAN GENOME THE GENE SEERS: Q&A WITH GREG LUCIER & JONATHAN ROTHBERG OF DNA & THE DAWN OF DIGITAL MEDICINE MEDIA DIRECTOR: JEREMY ABBATE ART DIRECTOR & ILLUSTRATOR: JOELLE BOLT Q&A WITH GREG LUCIER & and it’s what allows you to have a camera caught up somewhere around 2014, and help a doctor to access and interpret ge- in there. We made a chip that saw chem- then the progress and cost of sequencing netic information with more expertise. THE JONATHAN ROTHBERG istry instead of light! That was the key will progress along with all other costs The other reason is because the more se- “aha!” moment. that are driven by Moore’s Law. quencing we do of individuals and the GENE erhaps the most exciting frontier in medicine today We’re leveraging that trillion dollar more we correlate gene sequences with is the emerging fi eld of personal genomics: the use investment over the past 40 years in Q: As you know, one of the concerns of- their medical records, the more we of detailed knowledge about a patient’s individual those chips, and the same supply chain, ten voiced is that sequencing technology know. If I sequence one person, I don’t SEERS: genetics as a guide to better prevention and treat- and of course, the same Moore’s Law. may start pumping out genomic informa- know anything. But if I sequence ment. Much of what makes it possible are the rapid That’s why it was inevitable that we’d tion faster than we know what to do with it.
    [Show full text]
  • Next-Generation Sequencing and Its Potential Impact on Food Microbial Genomics
    Ann Microbiol (2013) 63:21–37 DOI 10.1007/s13213-012-0478-8 REVIEW ARTICLE Next-generation sequencing and its potential impact on food microbial genomics Lisa Solieri & Tikam Chand Dakal & Paolo Giudici Received: 23 January 2012 /Accepted: 24 April 2012 /Published online: 31 May 2012 # Springer-Verlag and the University of Milan 2012 Abstract Recent efforts of researchers to elucidate the Sanger dideoxy chain-termination sequencing method has molecular mechanisms of biological systems have been been relied on for determining gene/DNA sequences. This revolutionized greatly with the use of high throughput and technology reached its zenith in the development of single cost-effective techniques such as next generation sequenc- tube chemistry with fluorescently marked termination bases, ing (NGS). Application of NGS to microbial genomics is heat stable polymerases, and automated capillary electro- not just limited to predict the prevalence of microorganisms in phoresis; but then reached a plateau in terms of technical food samples but also to elucidate the molecular basis of how development. With the ultimate goal of deciphering complete microorganisms respond to different food-associated condi- genomes, the requirement for high-throughput sequencing tions, which in turn offers tremendous opportunities to predict grew by an unpredicted extent. Several novel approaches and control the growth and survival of desirable or undesirable evolved to replace the Sanger method as the dominant pro- microorganisms in food. Concurrently, NGS has facilitated vider of sequencing data. These approaches fall under a broad the development of new genome-assisted approaches for cor- definition of “next generation sequencing” (NGS) and provide relating genotype and phenotype.
    [Show full text]