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For: Kimelman A, Levy A, Sberro H, Kidron S, Leavitt A, Amitai G, Yoder-Himes DR, Wurtzel O, Zhu Y, Rubin EM, Sorek R. A vast collection of microbial genes that are toxic to bacteria. Genome Res 2012;22:802-9. [PMID: 22300632 PMCID: PMC3317161 DOI: 10.1101/gr.133850.111] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 01/25/2012] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Pu H, Chen Y, Zhao X, Dai L, Tong A, Tang D, Chen Q, Yu Y. A toxin-antitoxin system provides phage defense via DNA damage and repair. Nat Commun 2025;16:3141. [PMID: 40169592 PMCID: PMC11961720 DOI: 10.1038/s41467-025-58540-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 03/19/2025] [Indexed: 04/03/2025]  Open
2
Lee D, Gunamalai L, Kannan J, Vickery K, Yaacov O, Onuchic-Whitford AC, Chakravarti A, Kapoor A. Massively parallel reporter assays identify functional enhancer variants at QT interval GWAS loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.11.642686. [PMID: 40161821 PMCID: PMC11952420 DOI: 10.1101/2025.03.11.642686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
3
Sim M, Nguyen J, Škopová K, Yoo K, Tai CH, Knipling L, Chen Q, Kim D, Nolan S, Elaksher R, Majdalani N, Lorenzi H, Stibitz S, Moon K, Hinton DM. A highly conserved sRNA downregulates multiple genes, including a σ54 transcriptional activator, in the virulence mode of Bordetella pertussis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.19.624354. [PMID: 39803429 PMCID: PMC11722255 DOI: 10.1101/2024.11.19.624354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2025]
4
Nyerges A, Chiappino-Pepe A, Budnik B, Baas-Thomas M, Flynn R, Yan S, Ostrov N, Liu M, Wang M, Zheng Q, Hu F, Chen K, Rudolph A, Chen D, Ahn J, Spencer O, Ayalavarapu V, Tarver A, Harmon-Smith M, Hamilton M, Blaby I, Yoshikuni Y, Hajian B, Jin A, Kintses B, Szamel M, Seregi V, Shen Y, Li Z, Church GM. Synthetic genomes unveil the effects of synonymous recoding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.16.599206. [PMID: 38915524 PMCID: PMC11195188 DOI: 10.1101/2024.06.16.599206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
5
Schmitt DS, Siegel SD, Selle K. Applications of designer phage encoding recombinant gene payloads. Trends Biotechnol 2024;42:326-338. [PMID: 37833198 DOI: 10.1016/j.tibtech.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
6
Choi W, Maharjan A, Im HG, Park JY, Park JT, Park JH. Identification and Characterization of HEPN-MNT Type II TA System from Methanothermobacter thermautotrophicus ΔH. J Microbiol 2023;61:411-421. [PMID: 37071293 DOI: 10.1007/s12275-023-00041-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 04/19/2023]
7
Stokar-Avihail A, Fedorenko T, Hör J, Garb J, Leavitt A, Millman A, Shulman G, Wojtania N, Melamed S, Amitai G, Sorek R. Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell 2023;186:1863-1876.e16. [PMID: 37030292 DOI: 10.1016/j.cell.2023.02.029] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/09/2023] [Accepted: 02/20/2023] [Indexed: 04/10/2023]
8
Kelly A, Arrowsmith TJ, Went SC, Blower TR. Toxin-antitoxin systems as mediators of phage defence and the implications for abortive infection. Curr Opin Microbiol 2023;73:102293. [PMID: 36958122 DOI: 10.1016/j.mib.2023.102293] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/25/2023]
9
Malik T, Klenow L, Karyolaimos A, Gier JWD, Daniels R. Silencing Transcription from an Influenza Reverse Genetics Plasmid in E. coli Enhances Gene Stability. ACS Synth Biol 2023;12:432-445. [PMID: 36716395 PMCID: PMC9942234 DOI: 10.1021/acssynbio.2c00358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
10
Millman A, Melamed S, Leavitt A, Doron S, Bernheim A, Hör J, Garb J, Bechon N, Brandis A, Lopatina A, Ofir G, Hochhauser D, Stokar-Avihail A, Tal N, Sharir S, Voichek M, Erez Z, Ferrer JLM, Dar D, Kacen A, Amitai G, Sorek R. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 2022;30:1556-1569.e5. [DOI: 10.1016/j.chom.2022.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/15/2022] [Accepted: 09/28/2022] [Indexed: 01/16/2023]
11
Rousset F, Depardieu F, Miele S, Dowding J, Laval AL, Lieberman E, Garry D, Rocha EPC, Bernheim A, Bikard D. Phages and their satellites encode hotspots of antiviral systems. Cell Host Microbe 2022;30:740-753.e5. [PMID: 35316646 PMCID: PMC9122126 DOI: 10.1016/j.chom.2022.02.018] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 01/27/2022] [Accepted: 02/23/2022] [Indexed: 11/18/2022]
12
Korniakova V, Devinck A, Groleau MC, Déziel E, Perreault J. Fluoride-Controlled Riboswitch-Based Dampening of Gene Expression for Cloning Potent Promoters. Front Genet 2022;12:591543. [PMID: 35126444 PMCID: PMC8814607 DOI: 10.3389/fgene.2021.591543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/15/2021] [Indexed: 11/29/2022]  Open
13
Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova NN, Levy A. Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes. Nucleic Acids Res 2021;50:e17. [PMID: 34871418 PMCID: PMC8860608 DOI: 10.1093/nar/gkab1115] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 10/11/2021] [Accepted: 10/23/2021] [Indexed: 11/13/2022]  Open
14
Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput Biol 2021;17:e1009461. [PMID: 34610008 PMCID: PMC8519471 DOI: 10.1371/journal.pcbi.1009461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/15/2021] [Accepted: 09/19/2021] [Indexed: 12/16/2022]  Open
15
Gu Q, He P, Wang D, Ma J, Zhong X, Zhu Y, Zhang Y, Bai Q, Pan Z, Yao H. An Auto-Regulating Type II Toxin-Antitoxin System Modulates Drug Resistance and Virulence in Streptococcus suis. Front Microbiol 2021;12:671706. [PMID: 34475853 PMCID: PMC8406773 DOI: 10.3389/fmicb.2021.671706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022]  Open
16
Wen X, Zhang Y, Cheng H, An J, Guo Y, Wang L, Wang M. A CRISPR/dCas9-assisted system to clone toxic genes in Escherichia coli. Biochim Biophys Acta Gen Subj 2021;1865:129994. [PMID: 34450195 DOI: 10.1016/j.bbagen.2021.129994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/26/2021] [Accepted: 08/22/2021] [Indexed: 11/19/2022]
17
Marques F, Luzhetskyy A, Mendes MV. Engineering Corynebacterium glutamicum with a comprehensive genomic library and phage-based vectors. Metab Eng 2020;62:221-234. [DOI: 10.1016/j.ymben.2020.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022]
18
Bhat S, Bialy D, Sealy JE, Sadeyen JR, Chang P, Iqbal M. A ligation and restriction enzyme independent cloning technique: an alternative to conventional methods for cloning hard-to-clone gene segments in the influenza reverse genetics system. Virol J 2020;17:82. [PMID: 32576218 PMCID: PMC7309217 DOI: 10.1186/s12985-020-01358-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/17/2020] [Indexed: 11/10/2022]  Open
19
Talukdar PK, Negretti NM, Turner KL, Konkel ME. Molecular Dissection of the Campylobacter jejuni CadF and FlpA Virulence Proteins in Binding to Host Cell Fibronectin. Microorganisms 2020;8:E389. [PMID: 32168837 PMCID: PMC7143056 DOI: 10.3390/microorganisms8030389] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/07/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023]  Open
20
Dobrzanski T, Pobre V, Moreno LF, Barbosa HCDS, Monteiro RA, de Oliveira Pedrosa F, de Souza EM, Arraiano CM, Steffens MBR. In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1. BMC Genomics 2020;21:134. [PMID: 32039705 PMCID: PMC7011215 DOI: 10.1186/s12864-019-6402-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/15/2019] [Indexed: 12/13/2022]  Open
21
Cataldo VF, Salgado V, Saa PA, Agosin E. Genomic integration of unclonable gene expression cassettes in Saccharomyces cerevisiae using rapid cloning-free workflows. Microbiologyopen 2020;9:e978. [PMID: 31944620 PMCID: PMC7066455 DOI: 10.1002/mbo3.978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 11/11/2022]  Open
22
Genome-Wide Screening for Identification of Novel Toxin-Antitoxin Systems in Staphylococcus aureus. Appl Environ Microbiol 2019;85:AEM.00915-19. [PMID: 31375497 DOI: 10.1128/aem.00915-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 07/11/2019] [Indexed: 01/24/2023]  Open
23
Sass AM, De Waele S, Daled S, Devreese B, Deforce D, Van Nieuwerburgh F, Coenye T. Small RNA NcS27 co-regulates utilization of carbon sources in Burkholderia cenocepacia J2315. MICROBIOLOGY-SGM 2019;165:1135-1150. [PMID: 31464662 DOI: 10.1099/mic.0.000848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
24
Kumar A, Kumar V, Kumar A. Functional characterization of host toxic EcdB transcription factor protein of echinocandin B biosynthetic gene cluster. Biotechnol Appl Biochem 2019;66:626-633. [PMID: 31069846 DOI: 10.1002/bab.1763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/07/2019] [Indexed: 11/09/2022]
25
Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. Proc Natl Acad Sci U S A 2019;116:8070-8079. [PMID: 30936302 PMCID: PMC6475421 DOI: 10.1073/pnas.1818259116] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
26
Induction of a Toxin-Antitoxin Gene Cassette under High Hydrostatic Pressure Enables Markerless Gene Disruption in the Hyperthermophilic Archaeon Pyrococcus yayanosii. Appl Environ Microbiol 2019;85:AEM.02662-18. [PMID: 30504216 DOI: 10.1128/aem.02662-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/28/2018] [Indexed: 11/20/2022]  Open
27
A novel method for cloning of coding sequences of highly toxic proteins. Biochim Biophys Acta Gen Subj 2018;1863:521-527. [PMID: 30578833 DOI: 10.1016/j.bbagen.2018.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/26/2018] [Accepted: 12/17/2018] [Indexed: 11/20/2022]
28
Avni E, Snir S. Reconstruction of real and simulated phylogenies based on quartet plurality inference. BMC Genomics 2018;19:570. [PMID: 30367577 PMCID: PMC6101080 DOI: 10.1186/s12864-018-4921-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
29
Leis B, Held C, Andreeßen B, Liebl W, Graubner S, Schulte LP, Schwarz WH, Zverlov VV. Optimizing the composition of a synthetic cellulosome complex for the hydrolysis of softwood pulp: identification of the enzymatic core functions and biochemical complex characterization. BIOTECHNOLOGY FOR BIOFUELS 2018;11:220. [PMID: 30116297 PMCID: PMC6083626 DOI: 10.1186/s13068-018-1220-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/31/2018] [Indexed: 05/30/2023]
30
Westmann CA, Alves LDF, Silva-Rocha R, Guazzaroni ME. Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli. Front Microbiol 2018;9:1344. [PMID: 29973927 PMCID: PMC6019500 DOI: 10.3389/fmicb.2018.01344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/31/2018] [Indexed: 11/13/2022]  Open
31
Jia X, Yao J, Gao Z, Liu G, Dong YH, Wang X, Zhang H. Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system. J Biol Chem 2018;293:6812-6823. [PMID: 29555683 PMCID: PMC5936836 DOI: 10.1074/jbc.ra118.002421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/13/2018] [Indexed: 11/06/2022]  Open
32
Wu J, Deng A, Sun Q, Bai H, Sun Z, Shang X, Zhang Y, Liu Q, Liang Y, Liu S, Che Y, Wen T. Bacterial Genome Editing via a Designed Toxin-Antitoxin Cassette. ACS Synth Biol 2018;7:822-831. [PMID: 28094982 DOI: 10.1021/acssynbio.6b00287] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
33
Sass A, Kiekens S, Coenye T. Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism. Sci Rep 2017;7:15665. [PMID: 29142288 PMCID: PMC5688073 DOI: 10.1038/s41598-017-15818-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/02/2017] [Indexed: 12/23/2022]  Open
34
Avni E, Snir S. Toxic genes present a unique phylogenetic signature. Mol Phylogenet Evol 2017;116:141-148. [PMID: 28842276 DOI: 10.1016/j.ympev.2017.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 08/17/2017] [Accepted: 08/17/2017] [Indexed: 10/19/2022]
35
Shidore T, Triplett LR. Toxin-Antitoxin Systems: Implications for Plant Disease. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017;55:161-179. [PMID: 28525308 DOI: 10.1146/annurev-phyto-080516-035559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
36
Koonin EV, Makarova KS, Wolf YI. Evolutionary Genomics of Defense Systems in Archaea and Bacteria. Annu Rev Microbiol 2017;71:233-261. [PMID: 28657885 DOI: 10.1146/annurev-micro-090816-093830] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
37
Burkholderia cepacia Complex Regulation of Virulence Gene Expression: A Review. Genes (Basel) 2017;8:genes8010043. [PMID: 28106859 PMCID: PMC5295037 DOI: 10.3390/genes8010043] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 12/31/2022]  Open
38
Benureau Y, Colin P, Staropoli I, Gonzalez N, Garcia-Perez J, Alcami J, Arenzana-Seisdedos F, Lagane B. Guidelines for cloning, expression, purification and functional characterization of primary HIV-1 envelope glycoproteins. J Virol Methods 2016;236:184-195. [PMID: 27451265 DOI: 10.1016/j.jviromet.2016.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/13/2016] [Accepted: 07/19/2016] [Indexed: 12/14/2022]
39
Young REB, Purton S. Codon reassignment to facilitate genetic engineering and biocontainment in the chloroplast of Chlamydomonas reinhardtii. PLANT BIOTECHNOLOGY JOURNAL 2016;14:1251-60. [PMID: 26471875 PMCID: PMC5102678 DOI: 10.1111/pbi.12490] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/08/2015] [Accepted: 09/13/2015] [Indexed: 05/18/2023]
40
Zhang C, Tsoi R, You L. Addressing biological uncertainties in engineering gene circuits. Integr Biol (Camb) 2015;8:456-64. [PMID: 26674800 DOI: 10.1039/c5ib00275c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
41
Designing overall stoichiometric conversions and intervening metabolic reactions. Sci Rep 2015;5:16009. [PMID: 26530953 PMCID: PMC4632160 DOI: 10.1038/srep16009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/07/2015] [Indexed: 02/07/2023]  Open
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Sass AM, Van Acker H, Förstner KU, Van Nieuwerburgh F, Deforce D, Vogel J, Coenye T. Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315. BMC Genomics 2015;16:775. [PMID: 26462475 PMCID: PMC4603805 DOI: 10.1186/s12864-015-1993-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/06/2015] [Indexed: 12/20/2022]  Open
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Yao J, Guo Y, Zeng Z, Liu X, Shi F, Wang X. Identification and characterization of a HEPN-MNT family type II toxin-antitoxin in Shewanella oneidensis. Microb Biotechnol 2015;8:961-73. [PMID: 26112399 PMCID: PMC4621449 DOI: 10.1111/1751-7915.12294] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/20/2015] [Accepted: 05/02/2015] [Indexed: 11/30/2022]  Open
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Antimicrobial compounds from seaweeds-associated bacteria and fungi. Appl Microbiol Biotechnol 2014;99:1571-86. [PMID: 25549621 DOI: 10.1007/s00253-014-6334-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/14/2014] [Accepted: 12/15/2014] [Indexed: 12/22/2022]
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Nielsen AAK, Voigt CA. Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks. Mol Syst Biol 2014;10:763. [PMID: 25422271 PMCID: PMC4299604 DOI: 10.15252/msb.20145735] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/26/2014] [Accepted: 10/29/2014] [Indexed: 12/24/2022]  Open
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Chaisson MJP, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE. Resolving the complexity of the human genome using single-molecule sequencing. Nature 2014;517:608-11. [PMID: 25383537 DOI: 10.1038/nature13907] [Citation(s) in RCA: 538] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/30/2014] [Indexed: 12/11/2022]
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High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1. Biochem Biophys Res Commun 2014;453:826-32. [PMID: 25450355 DOI: 10.1016/j.bbrc.2014.10.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/09/2014] [Indexed: 11/21/2022]
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Lu S, Le S, Tan Y, Li M, Liu C, Zhang K, Huang J, Chen H, Rao X, Zhu J, Zou L, Ni Q, Li S, Wang J, Jin X, Hu Q, Yao X, Zhao X, Zhang L, Huang G, Hu F. Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity. BMC Genomics 2014;15:803. [PMID: 25233860 PMCID: PMC4177049 DOI: 10.1186/1471-2164-15-803] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 09/16/2014] [Indexed: 12/02/2022]  Open
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Sagy O, Shamir R, Rechavi O. Examination of exhaustive cloning attempts reveals that C. elegans piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria. Front Genet 2014;5:275. [PMID: 25221566 PMCID: PMC4148067 DOI: 10.3389/fgene.2014.00275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/26/2014] [Indexed: 11/13/2022]  Open
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Renda BA, Hammerling MJ, Barrick JE. Engineering reduced evolutionary potential for synthetic biology. MOLECULAR BIOSYSTEMS 2014;10:1668-78. [PMID: 24556867 DOI: 10.1039/c3mb70606k] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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