DNA signatures for detecting genetic engineering in bacteria

Genome Biology

Volumn 9, Issue 3, 2008, Pages

  Allen, Jonathan E ^a   Gardner, Shea N ^a   Slezak, Tom R ^a  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PLASMID DNA; PLASMID VECTOR;

ARTICLE; BACTERIAL GENOME; DNA DETERMINATION; DNA SEQUENCE; GENETIC ENGINEERING; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; NONHUMAN; SENSITIVITY AND SPECIFICITY; SPECIES DIFFERENCE; BACTERIUM; BIOLOGY; GENE VECTOR; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PLASMID;

BACTERIA (MICROORGANISMS);

BACTERIA; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; GENETIC ENGINEERING; GENETIC VECTORS; PLASMIDS; SEQUENCE ANALYSIS, DNA;

EID: 45549107061     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-3-r56     Document Type: Article

References (39)

1. Verma R Boleti E George AJT Antibody engineering: Comparison of bacterial, yeast, insect and mammalian expression systems. J Immunol Methods 1998, 216:165-181. 10.1016/S0022-1759(98)00077-5 9760222
2. Benner SA Sismour AM Synthetic biology. Nat Rev Genet 2005, 6:533-543. 10.1038/nrg1637 15995697
3. Smith HO Hutchinson CA 3rd Pfannkoch C Venter JC Generating a synthetic genome by whole genome assembly:pHiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci USA 2003, 100:15440-15445. 14657399 10.1073/pnas.2237126100 307586
4. Sturino JM Klaenhammer TR Engineered bacteriophage-defence systems in bioprocessing. Nat Rev Microbiol 2006, 4:395-404. 10.1038/nrmicro1393 16715051
5. Khosla C Keasling JD Metabolic engineering for drug discovery and development. Nat Rev Drug Discov 2003, 2:1019-1025. 10.1038/nrd1256 14654799
6. Bugl H Danner JP Molinari RJ Mullligan JT Park HO Reichert B Roth DA Wagner R Budowle B Scripp RM Smith JAL Steele SJ Church G Endy D DNA synthesis and biological security. Nat Biotechnol 2007, 25:627-629. 10.1038/nbt0607-627 17557094
7. Budowle B Schutzer SE Ascher MS Atlas RM Burans JP Chakraborty R Dunn JJ Fraser CM Franz DR Leighton TJ Morse SA Murch RS Ravel J Rock DL Slezak TR Velsko SP Walsh AC Walters RA Toward a system of microbial forensics: from sample collection to interpretation of evidence. Appl Environ Microbiol 2005, 71:2209-2213. 1087589 15870301 10.1128/ AEM.71.5.2209-2213.2005
8. Gardner SN Kuczmarski TA Vitalis EA Slezak TR Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis A, B, C, and E viruses and human immunodeficiency virus. J Clin Microbiol 2003, 41:2417-2427. 156483 12791858 10.1128/JCM.41.6.2417-2427.2003
9. Slezak T Kuczmarski T Ott L Torres C Medeiros D Smith J Truitt B Mulakken N Lam M Vitalis B Zemla A Zhou C Gardner S Comparative genomics tools applied to bioterrorism defence. Brief Bioinform 2003, 4:133-149. 10.1093/bib/4.2.133 12846395
10. Fitch JP Gardner SN Kuczmarski TA Kurtz S Myers R Ott LL Slezak TR Vitalis EA Zemla AT Mccready PM Rapid development of nucleic acid diagnostics. Proc IEEE Inst Electr Electron Eng 2002, 90:1708-1720.
11. Vora GJ Meador CE Stenger DA Andreadis JD Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol 2004, 70:3047-3054. 404398 15128566 10.1128/ AEM.70.5.3047-3054.2004
12. Tembe W Zavaljevski N Bode E Chase C Geyer J Wasieloski L Benson G Reifman J Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics 2007, 23:5-13. 10.1093/bioinformatics/btl549 17068088
13. Phillippy AM Mason JA Ayanbule K Sommer DD Taviani E Huq A Colwell RR Knight IT Salzberg SL Comprehensive DNA signature discovery and validation. PLoS Comput Biol 2007, 3:e98. 1868776 17511514 10.1371/ journal.pcbi.0030098
14. Primrose SB Twyman RM Principles of Gene Manipulation and Genomics Oxford: Blackwell 7 2006.
15. Vinga S Almeida J Alignment-free sequence comparison - a review. Bioinformatics 2003, 19:513-523. 10.1093/bioinformatics/btg005 12611807
16. Haubold B Pierstorff N Möller F Wiehe T Genome comparison without alignment using shortest unique substrings. BMC Bioinformatics 2005, 6:123. 1166540 15910684 10.1186/1471-2105-6-123
17. Batzoglou S The many faces of sequence alignment. Brief Bioinform 2005, 6:6-22. 10.1093/bib/6.1.6 15826353
18. Kurtz S Phillippy A Delcher AL Smoot M Shumway M Antonescu C Salzberg SL Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12. 395750 14759262 10.1186/gb-2004-5-2-r12
19. Nordberg EK YODA: Selecting signature oligonucleotides. Bioinformatics 2005, 21:1365-1370. 10.1093/bioinformatics/bti182 15572465
20. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool. J Mol Biol 1990, 215:403-410. 2231712
21. Muyrers JP Zhang Y Steward AF Techniques: Recombinogenic engineering - new options for cloning and manipulating DNA. Trends Biochem Sci 2001, 26:325-331. 10.1016/S0968-0004(00)01757-6 11343926
22. Wessner DR Techview software. Planning plasmids. Science 1999, 286:1495-1496. 10.1126/science.286.5444.1495 10610552
23. Walton DK Gendel SM Atherly AG DNA sequence and shuttle vector construction of plasmid pGL3 from Plectonema boryanum PCC 6306. Nucleic Acids Res 1993, 21:746. 309182 8441688 10.1093/nar/21.3.746
24. Nieto C Fernandes de Palencia P Lopez P Espinosa M Construction of a tightly regulated plasmid vector for Streptococcus pneumoniae: controlled expression of the green flourescent protein. Plasmid 2000, 43:205-213. 10.1006/plas.2000.1465 10783299
25. Okamura Y Takeyama H Sekine T Sakaguchi T Wahyudi AT Sato R Kamiya S Matsunaga T Design and application of a new cryptic-plasmid-based shuttle vector for Magnetospirillum magneticum. Appl Environ Microbiol 2003, 69:4274-4277. 165158 12839813 10.1128/AEM.69.7.4274-4277.2003
26. Lee JH Halgerson JS Kim JH O'Sullivan DJ Comparative sequence analysis of plasmids from Lactobacillus delbrueckii and construction of a shuttle cloning vector. Appl Environ Microbiol 2007, 73:4417-4424. 1932812 17526779 10.1128/AEM.00099-07
27. Welch TJ Fricke WF McDermott PF White DG Rosso ML Rasko DA Mammel MK Eppinger M Rosovitz M Wagner D Rahalison L LeClerc JE Hinshaw JM Lindler LE Cebula TA Carniel E Ravel J Multiple antimicrobial resistance in plague: An emerging public health risk. PLoS ONE 2007, 2:e309. 1819562 17375195 10.1371/journal.pone.0000309
28. Schweizer HP Hoang TT Propst KL Ornelas HR Karhoff-Schweizer RR Vector design and development of host systems for Pseudomonas Doredrecht: Kluwer 2001, 23:69-82.
29. Inui M Nakata K Roh JH Vertes AA Yukawa H Isolation and molecular characterization of pMG160, a mobilizable cryptic plasmid from Rhodobacter blasticus. Appl Environ Microbiol 2003, 69:725-733. 143669 12570988 10.1128/AEM.69.2.725-733.2003
30. Lee JH O'Sullivan DJ Sequence analysis of two cryptic plasmids from Bifidobacterium longum DJO10A and construction of a shuttle cloning vector. Appl Environ Microbiol 2006, 72:527-535. 1352255 16391088 10.1128/AEM.72.1.527-535.2006
31. Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Wheeler DL GenBank. Nucleic Acids Res 2007, 35: (Database issue) D21-D25. 10.1093/nar/gkl986
32. Molbak L Tett A Ussery DW Wall K Turner S Bailey M Field D The plasmid genome database. Microbiology 2003, 149:3043-3045. 10.1099/mic.0.C0123-0 14600215
33. Vector subset of GenBank ftp://ncbi.nlm.nih.gov/blast/db
34. ATCC Vectors ftp://ftp.atcc.org/pub/vector_seqs
35. Virmatics vector database http://www.virmatics.com/vcs/index.php
36. Choi JH Cho HG Analysis of common k -mers for whole genome sequences using SSB-Tree. Genome Inform 2002, 13:30-41. 14571372
37. Höhl M Kurtz S Ohlebusch E Efficient multiple genome alignment. Bioinformatics 2002, 18:S312-S320. 12169561
38. Google Sparse Hash Table http://code.google.com/p/google-sparsehash/
39. Bomze I Budinich M Pardalos P Pelillo M The maximum clique problem. Handbook of Combinatorial Optimization Dordrecht: Kluwer 1999, 4.