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Son H, Bae S, Lee S. A thermodynamic understanding of the salt-induced B-to-Z transition of DNA containing BZ junctions. Biochem Biophys Res Commun 2021; 583:142-145. [PMID: 34735876 DOI: 10.1016/j.bbrc.2021.10.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/17/2022]
Abstract
Z-DNA has attracted interest due to its distinctive left-handed helical structure. This non-canonical DNA structure is able to form transiently and plays an important role in cellular processes such as transcriptional regulation and DNA recombination. Alternating purine-pyrimidine sequences are well known to form Z-DNA under high-salt conditions, but the detailed mechanism of B-to-Z transition of DNA containing BZ junctions under these conditions is not well understood. Here, using single-molecule FRET and circular dichroism experiments, we studied the effect of BZ junctions on Z-DNA formation under high-salt conditions. Further thermodynamic analysis revealed that a discrepancy of different DNA substrates in the presence and absence of BZ junctions in Z-DNA formation can be attributed mainly to the competition between enthalpy and entropy. Salt-induced B-to-Z transition is entropically favored in the presence of BZ junctions and is enthalpically favored in their absence. This thermodynamic information provides a deeper understanding of Z-DNA formation of DNA containing BZ junctions.
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Hur JH, Kang CY, Lee S, Parveen N, Yu J, Shamim A, Yoo W, Ghosh A, Bae S, Park CJ, Kim KK. AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation. Nucleic Acids Res 2021; 49:10150-10165. [PMID: 34469538 PMCID: PMC8464069 DOI: 10.1093/nar/gkab728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/04/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022] Open
Abstract
I-motif or C4 is a four-stranded DNA structure with a protonated cytosine:cytosine base pair (C+:C) found in cytosine-rich sequences. We have found that oligodeoxynucleotides containing adenine and cytosine repeats form a stable secondary structure at a physiological pH with magnesium ion, which is similar to i-motif structure, and have named this structure ‘adenine:cytosine-motif (AC-motif)’. AC-motif contains C+:C base pairs intercalated with putative A+:C base pairs between protonated adenine and cytosine. By investigation of the AC-motif present in the CDKL3 promoter (AC-motifCDKL3), one of AC-motifs found in the genome, we confirmed that AC-motifCDKL3 has a key role in regulating CDKL3 gene expression in response to magnesium. This is further supported by confirming that genome-edited mutant cell lines, lacking the AC-motif formation, lost this regulation effect. Our results verify that adenine-cytosine repeats commonly present in the genome can form a stable non-canonical secondary structure with a non-Watson–Crick base pair and have regulatory roles in cells, which expand non-canonical DNA repertoires.
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Cecchin M, Jeong J, Son W, Kim M, Park S, Zuliani L, Cazzaniga S, Pompa A, Young Kang C, Bae S, Ballottari M, Jin E. LPA2 protein is involved in photosystem II assembly in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1648-1662. [PMID: 34218480 PMCID: PMC8518032 DOI: 10.1111/tpj.15405] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Photosynthetic eukaryotes require the proper assembly of photosystem II (PSII) in order to strip electrons from water and fuel carbon fixation reactions. In Arabidopsis thaliana, one of the PSII subunits (CP43/PsbC) was suggested to be assembled into the PSII complex via its interaction with an auxiliary protein called Low PSII Accumulation 2 (LPA2). However, the original articles describing the role of LPA2 in PSII assembly have been retracted. To investigate the function of LPA2 in the model organism for green algae, Chlamydomonas reinhardtii, we generated knockout lpa2 mutants by using the CRISPR-Cas9 target-specific genome editing system. Biochemical analyses revealed the thylakoidal localization of LPA2 protein in the wild type (WT), whereas lpa2 mutants were characterized by a drastic reduction in the levels of D1, D2, CP47 and CP43 proteins. Consequently, reduced PSII supercomplex accumulation, chlorophyll content per cell, PSII quantum yield and photosynthetic oxygen evolution were measured in the lpa2 mutants, leading to the almost complete impairment of photoautotrophic growth. Pulse-chase experiments demonstrated that the absence of LPA2 protein caused reduced PSII assembly and reduced PSII turnover. Taken together, our data indicate that, in C. reinhardtii, LPA2 is required for PSII assembly and proper function.
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Jung J, Lim SY, Lee J, Bae S, Lim YJ, Hong MJ, Kwak SH, Kim EO, Sung H, Kim MN, Bae JY, Park MS, Kim SH. Clustering and multiple-spreading events of nosocomial severe acute respiratory syndrome coronavirus 2 infection. J Hosp Infect 2021; 117:28-36. [PMID: 34453983 PMCID: PMC8384763 DOI: 10.1016/j.jhin.2021.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/04/2022]
Abstract
Background There is growing evidence that super-spreading events (SSEs) and multiple-spreading events (MSEs) are a characteristic feature of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, data regarding the possibility of SSEs or MSEs in healthcare settings are limited. Methods This study was performed at a tertiary-care hospital in Korea. We analysed the nosocomial COVID-19 cases that occurred in healthcare workers and inpatients and their caregivers between January and 20th December 2020. Cases with two to four secondary cases were defined as MSEs and those with five or more secondary cases as SSEs. Findings We identified 21 nosocomial events (single-case events, N = 12 (57%); MSE + SSE, N = 9 (43%)) involving 65 individuals with COVID-19. Of these 65 individuals, 21 (32%) were infectors. The infectors tended to have a longer duration between symptom onset and diagnostic confirmation than did the non-infectors (median two days vs zero days, P=0.08). Importantly, 12 (18%) individuals were responsible for MSEs and one (2%) for an SSE, which collectively generated 35 (54%) secondary cases. Conclusion In a hospital with thorough infection-control measures, approximately 70% of the nosocomial cases of COVID-19 did not generate secondary cases, and one-fifth of the infectors were responsible for SSEs and MSEs, which accounted for approximately half of the total cases. Early case identification, isolation, and extensive contact tracing are important for the prevention of transmission and SSEs.
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Jang HK, Jo DH, Lee SN, Cho CS, Jeong YK, Jung Y, Yu J, Kim JH, Woo JS, Bae S. High-purity production and precise editing of DNA base editing ribonucleoproteins. SCIENCE ADVANCES 2021; 7:7/35/eabg2661. [PMID: 34452911 PMCID: PMC8397273 DOI: 10.1126/sciadv.abg2661] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/07/2021] [Indexed: 05/05/2023]
Abstract
Ribonucleoprotein (RNP) complex-mediated base editing is expected to be greatly beneficial because of its reduced off-target effects compared to plasmid- or viral vector-mediated gene editing, especially in therapeutic applications. However, production of recombinant cytosine base editors (CBEs) or adenine base editors (ABEs) with ample yield and high purity in bacterial systems is challenging. Here, we obtained highly purified CBE/ABE proteins from a human cell expression system and showed that CBE/ABE RNPs exhibited different editing patterns (i.e., less conversion ratio of multiple bases to single base) compared to plasmid-encoded CBE/ABE, mainly because of the limited life span of RNPs in cells. Furthermore, we found that off-target effects in both DNA and RNA were greatly reduced for ABE RNPs compared to plasmid-encoded ABE. We ultimately applied NG PAM-targetable ABE RNPs to in vivo gene correction in retinal degeneration 12 (rd12) model mice.
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Hwang GH, Jeong YK, Habib O, Hong SA, Lim K, Kim JS, Bae S. PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing. Nucleic Acids Res 2021; 49:W499-W504. [PMID: 33939828 PMCID: PMC8265102 DOI: 10.1093/nar/gkab319] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/24/2021] [Accepted: 04/20/2021] [Indexed: 12/26/2022] Open
Abstract
Prime editing technology is capable of generating targeted insertions, deletions, and base conversions. However, the process of designing prime editing guide RNAs (pegRNAs), which contain a primer binding site and a reverse-transcription template at the 3′ end, is more complex than that for the single guide RNAs used with CRISPR nucleases or base editors. Furthermore, the assessment of high-throughput sequencing data after prime editors (PEs) have been employed should consider the unique feature of PEs; thus, pre-existing assessment tools cannot directly be adopted for PEs. Here, we present two user-friendly web-based tools for PEs, named PE-Designer and PE-Analyzer. PE-Designer, a dedicated tool for pegRNA selection, provides all possible target sequences, pegRNA extension sequences, and nicking guide RNA sequences together with useful information, and displays the results in an interactive image. PE-Analyzer, a dedicated tool for PE outcome analysis, accepts high-throughput sequencing data, summarizes mutation-related information in a table, and provides interactive graphs. PE-Analyzer was mainly written using JavaScript so that it can analyze several data sets without requiring that huge sequencing data (>100MB) be uploaded to the server, reducing analysis time and increasing personal security. PE-Designer and PE-Analyzer are freely available at http://www.rgenome.net/pe-designer/ and http://www.rgenome.net/pe-analyzer/ without a login process.
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Abbott R, Abbott TD, Abraham S, Acernese F, Ackley K, Adams A, Adams C, Adhikari RX, Adya VB, Affeldt C, Agarwal D, Agathos M, Agatsuma K, Aggarwal N, Aguiar OD, Aiello L, Ain A, Ajith P, Akutsu T, Aleman KM, Allen G, Allocca A, Altin PA, Amato A, Anand S, Ananyeva A, Anderson SB, Anderson WG, Ando M, Angelova SV, Ansoldi S, Antelis JM, Antier S, Appert S, Arai K, Arai K, Arai Y, Araki S, Araya A, Araya MC, Areeda JS, Arène M, Aritomi N, Arnaud N, Aronson SM, Asada H, Asali Y, Ashton G, Aso Y, Aston SM, Astone P, Aubin F, Auclair P, Aufmuth P, AultONeal K, Austin C, Babak S, Badaracco F, Bader MKM, Bae S, Bae Y, Baer AM, Bagnasco S, Bai Y, Baiotti L, Baird J, Bajpai R, Ball M, Ballardin G, Ballmer SW, Bals M, Balsamo A, Baltus G, Banagiri S, Bankar D, Bankar RS, Barayoga JC, Barbieri C, Barish BC, Barker D, Barneo P, Barnum S, Barone F, Barr B, Barsotti L, Barsuglia M, Barta D, Bartlett J, Barton MA, Bartos I, Bassiri R, Basti A, Bawaj M, Bayley JC, Baylor AC, Bazzan M, Bécsy B, Bedakihale VM, Bejger M, Belahcene I, Benedetto V, Beniwal D, Benjamin MG, Bennett TF, Bentley JD, BenYaala M, Bergamin F, Berger BK, Bernuzzi S, Bersanetti D, Bertolini A, Betzwieser J, Bhandare R, Bhandari AV, Bhattacharjee D, Bhaumik S, Bidler J, Bilenko IA, Billingsley G, Birney R, Birnholtz O, Biscans S, Bischi M, Biscoveanu S, Bisht A, Biswas B, Bitossi M, Bizouard MA, Blackburn JK, Blackman J, Blair CD, Blair DG, Blair RM, Bobba F, Bode N, Boer M, Bogaert G, Boldrini M, Bondu F, Bonilla E, Bonnand R, Booker P, Boom BA, Bork R, Boschi V, Bose N, Bose S, Bossilkov V, Boudart V, Bouffanais Y, Bozzi A, Bradaschia C, Brady PR, Bramley A, Branch A, Branchesi M, Breschi M, Briant T, Briggs JH, Brillet A, Brinkmann M, Brockill P, Brooks AF, Brooks J, Brown DD, Brunett S, Bruno G, Bruntz R, Bryant J, Buikema A, Bulik T, Bulten HJ, Buonanno A, Buscicchio R, Buskulic D, Cadonati L, Caesar M, Cagnoli G, Cahillane C, Cain HW, Calderón Bustillo J, Callaghan JD, Callister TA, Calloni E, Camp JB, Canepa M, Cannavacciuolo M, Cannon KC, Cao H, Cao J, Cao Z, Capocasa E, Capote E, Carapella G, Carbognani F, Carlin JB, Carney MF, Carpinelli M, Carullo G, Carver TL, Casanueva Diaz J, Casentini C, Castaldi G, Caudill S, Cavaglià M, Cavalier F, Cavalieri R, Cella G, Cerdá-Durán P, Cesarini E, Chaibi W, Chakravarti K, Champion B, Chan CH, Chan C, Chan CL, Chan M, Chandra K, Chanial P, Chao S, Charlton P, Chase EA, Chassande-Mottin E, Chatterjee D, Chaturvedi M, Chatziioannou K, Chen A, Chen C, Chen HY, Chen J, Chen K, Chen X, Chen YB, Chen YR, Chen Z, Cheng H, Cheong CK, Cheung HY, Chia HY, Chiadini F, Chiang CY, Chierici R, Chincarini A, Chiofalo ML, Chiummo A, Cho G, Cho HS, Choate S, Choudhary RK, Choudhary S, Christensen N, Chu H, Chu Q, Chu YK, Chua S, Chung KW, Ciani G, Ciecielag P, Cieślar M, Cifaldi M, Ciobanu AA, Ciolfi R, Cipriano F, Cirone A, Clara F, Clark EN, Clark JA, Clarke L, Clearwater P, Clesse S, Cleva F, Coccia E, Cohadon PF, Cohen DE, Cohen L, Colleoni M, Collette CG, Colpi M, Compton CM, Constancio M, Conti L, Cooper SJ, Corban P, Corbitt TR, Cordero-Carrión I, Corezzi S, Corley KR, Cornish N, Corre D, Corsi A, Cortese S, Costa CA, Cotesta R, Coughlin MW, Coughlin SB, Coulon JP, Countryman ST, Cousins B, Couvares P, Covas PB, Coward DM, Cowart MJ, Coyne DC, Coyne R, Creighton JDE, Creighton TD, Criswell AW, Croquette M, Crowder SG, Cudell JR, Cullen TJ, Cumming A, Cummings R, Cuoco E, Curyło M, Canton TD, Dálya G, Dana A, DaneshgaranBajastani LM, D'Angelo B, Danilishin SL, D'Antonio S, Danzmann K, Darsow-Fromm C, Dasgupta A, Datrier LEH, Dattilo V, Dave I, Davier M, Davies GS, Davis D, Daw EJ, Dean R, Deenadayalan M, Degallaix J, De Laurentis M, Deléglise S, Del Favero V, De Lillo F, De Lillo N, Del Pozzo W, DeMarchi LM, De Matteis F, D'Emilio V, Demos N, Dent T, Depasse A, De Pietri R, De Rosa R, De Rossi C, DeSalvo R, De Simone R, Dhurandhar S, Díaz MC, Diaz-Ortiz M, Didio NA, Dietrich T, Di Fiore L, Di Fronzo C, Di Giorgio C, Di Giovanni F, Di Girolamo T, Di Lieto A, Ding B, Di Pace S, Di Palma I, Di Renzo F, Divakarla AK, Dmitriev A, Doctor Z, D'Onofrio L, Donovan F, Dooley KL, Doravari S, Dorrington I, Drago M, Driggers JC, Drori Y, Du Z, Ducoin JG, Dupej P, Durante O, D'Urso D, Duverne PA, Dwyer SE, Easter PJ, Ebersold M, Eddolls G, Edelman B, Edo TB, Edy O, Effler A, Eguchi S, Eichholz J, Eikenberry SS, Eisenmann M, Eisenstein RA, Ejlli A, Enomoto Y, Errico L, Essick RC, Estellés H, Estevez D, Etienne Z, Etzel T, Evans M, Evans TM, Ewing BE, Fafone V, Fair H, Fairhurst S, Fan X, Farah AM, Farinon S, Farr B, Farr WM, Farrow NW, Fauchon-Jones EJ, Favata M, Fays M, Fazio M, Feicht J, Fejer MM, Feng F, Fenyvesi E, Ferguson DL, Fernandez-Galiana A, Ferrante I, Ferreira TA, Fidecaro F, Figura P, Fiori I, Fishbach M, Fisher RP, Fishner JM, Fittipaldi R, Fiumara V, Flaminio R, Floden E, Flynn E, Fong H, Font JA, Fornal B, Forsyth PWF, Franke A, Frasca S, Frasconi F, Frederick C, Frei Z, Freise A, Frey R, Fritschel P, Frolov VV, Fronzé GG, Fujii Y, Fujikawa Y, Fukunaga M, Fukushima M, Fulda P, Fyffe M, Gabbard HA, Gadre BU, Gaebel SM, Gair JR, Gais J, Galaudage S, Gamba R, Ganapathy D, Ganguly A, Gao D, Gaonkar SG, Garaventa B, García-Núñez C, García-Quirós C, Garufi F, Gateley B, Gaudio S, Gayathri V, Ge G, Gemme G, Gennai A, George J, Gergely L, Gewecke P, Ghonge S, Ghosh A, Ghosh A, Ghosh S, Ghosh S, Ghosh S, Giacomazzo B, Giacoppo L, Giaime JA, Giardina KD, Gibson DR, Gier C, Giesler M, Giri P, Gissi F, Glanzer J, Gleckl AE, Godwin P, Goetz E, Goetz R, Gohlke N, Goncharov B, González G, Gopakumar A, Gosselin M, Gouaty R, Grace B, Grado A, Granata M, Granata V, Grant A, Gras S, Grassia P, Gray C, Gray R, Greco G, Green AC, Green R, Gretarsson AM, Gretarsson EM, Griffith D, Griffiths W, Griggs HL, Grignani G, Grimaldi A, Grimes E, Grimm SJ, Grote H, Grunewald S, Gruning P, Guerrero JG, Guidi GM, Guimaraes AR, Guixé G, Gulati HK, Guo HK, Guo Y, Gupta A, Gupta A, Gupta P, Gustafson EK, Gustafson R, Guzman F, Ha S, Haegel L, Hagiwara A, Haino S, Halim O, Hall ED, Hamilton EZ, Hammond G, Han WB, Haney M, Hanks J, Hanna C, Hannam MD, Hannuksela OA, Hansen H, Hansen TJ, Hanson J, Harder T, Hardwick T, Haris K, Harms J, Harry GM, Harry IW, Hartwig D, Hasegawa K, Haskell B, Hasskew RK, Haster CJ, Hattori K, Haughian K, Hayakawa H, Hayama K, Hayes FJ, Healy J, Heidmann A, Heintze MC, Heinze J, Heinzel J, Heitmann H, Hellman F, Hello P, Helmling-Cornell AF, Hemming G, Hendry M, Heng IS, Hennes E, Hennig J, Hennig MH, Hernandez Vivanco F, Heurs M, Hild S, Hill P, Himemoto Y, Hines AS, Hiranuma Y, Hirata N, Hirose E, Hochheim S, Hofman D, Hohmann JN, Holgado AM, Holland NA, Hollows IJ, Holmes ZJ, Holt K, Holz DE, Hong Z, Hopkins P, Hough J, Howell EJ, Hoy CG, Hoyland D, Hreibi A, Hsieh B, Hsu Y, Huang GZ, Huang HY, Huang P, Huang YC, Huang YJ, Huang YW, Hübner MT, Huddart AD, Huerta EA, Hughey B, Hui DCY, Hui V, Husa S, Huttner SH, Huxford R, Huynh-Dinh T, Ide S, Idzkowski B, Iess A, Ikenoue B, Imam S, Inayoshi K, Inchauspe H, Ingram C, Inoue Y, Intini G, Ioka K, Isi M, Isleif K, Ito K, Itoh Y, Iyer BR, Izumi K, JaberianHamedan V, Jacqmin T, Jadhav SJ, Jadhav SP, James AL, Jan AZ, Jani K, Janssens K, Janthalur NN, Jaranowski P, Jariwala D, Jaume R, Jenkins AC, Jeon C, Jeunon M, Jia W, Jiang J, Jin HB, Johns GR, Jones AW, Jones DI, Jones JD, Jones P, Jones R, Jonker RJG, Ju L, Jung K, Jung P, Junker J, Kaihotsu K, Kajita T, Kakizaki M, Kalaghatgi CV, Kalogera V, Kamai B, Kamiizumi M, Kanda N, Kandhasamy S, Kang G, Kanner JB, Kao Y, Kapadia SJ, Kapasi DP, Karathanasis C, Karki S, Kashyap R, Kasprzack M, Kastaun W, Katsanevas S, Katsavounidis E, Katzman W, Kaur T, Kawabe K, Kawaguchi K, Kawai N, Kawasaki T, Kéfélian F, Keitel D, Key JS, Khadka S, Khalili FY, Khan I, Khan S, Khazanov EA, Khetan N, Khursheed M, Kijbunchoo N, Kim C, Kim JC, Kim J, Kim K, Kim WS, Kim YM, Kimball C, Kimura N, King PJ, Kinley-Hanlon M, Kirchhoff R, Kissel JS, Kita N, Kitazawa H, Kleybolte L, Klimenko S, Knee AM, Knowles TD, Knyazev E, Koch P, Koekoek G, Kojima Y, Kokeyama K, Koley S, Kolitsidou P, Kolstein M, Komori K, Kondrashov V, Kong AKH, Kontos A, Koper N, Korobko M, Kotake K, Kovalam M, Kozak DB, Kozakai C, Kozu R, Kringel V, Krishnendu NV, Królak A, Kuehn G, Kuei F, Kumar A, Kumar P, Kumar R, Kumar R, Kume J, Kuns K, Kuo C, Kuo HS, Kuromiya Y, Kuroyanagi S, Kusayanagi K, Kwak K, Kwang S, Laghi D, Lalande E, Lam TL, Lamberts A, Landry M, Lane BB, Lang RN, Lange J, Lantz B, La Rosa I, Lartaux-Vollard A, Lasky PD, Laxen M, Lazzarini A, Lazzaro C, Leaci P, Leavey S, Lecoeuche YK, Lee HK, Lee HM, Lee HW, Lee J, Lee K, Lee R, Lehmann J, Lemaître A, Leon E, Leonardi M, Leroy N, Letendre N, Levin Y, Leviton JN, Li AKY, Li B, Li J, Li KL, Li TGF, Li X, Lin CY, Lin FK, Lin FL, Lin HL, Lin LCC, Linde F, Linker SD, Linley JN, Littenberg TB, Liu GC, Liu J, Liu K, Liu X, Llorens-Monteagudo M, Lo RKL, Lockwood A, Lollie ML, London LT, Longo A, Lopez D, Lorenzini M, Loriette V, Lormand M, Losurdo G, Lough JD, Lousto CO, Lovelace G, Lück H, Lumaca D, Lundgren AP, Luo LW, Macas R, MacInnis M, Macleod DM, MacMillan IAO, Macquet A, Magaña Hernandez I, Magaña-Sandoval F, Magazzù C, Magee RM, Maggiore R, Majorana E, Maksimovic I, Maliakal S, Malik A, Man N, Mandic V, Mangano V, Mango JL, Mansell GL, Manske M, Mantovani M, Marchesoni F, Marchio M, Marion F, Mark Z, Márka S, Márka Z, Markakis C, Markosyan AS, Markowitz A, Maros E, Marquina A, Marsat S, Martelli F, Martin IW, Martin RM, Martinez M, Martinez V, Martinovic K, Martynov DV, Marx EJ, Masalehdan H, Mason K, Massera E, Masserot A, Massinger TJ, Masso-Reid M, Mastrogiovanni S, Matas A, Mateu-Lucena M, Matichard F, Matiushechkina M, Mavalvala N, McCann JJ, McCarthy R, McClelland DE, McClincy P, McCormick S, McCuller L, McGhee GI, McGuire SC, McIsaac C, McIver J, McManus DJ, McRae T, McWilliams ST, Meacher D, Mehmet M, Mehta AK, Melatos A, Melchor DA, Mendell G, Menendez-Vazquez A, Menoni CS, Mercer RA, Mereni L, Merfeld K, Merilh EL, Merritt JD, Merzougui M, Meshkov S, Messenger C, Messick C, Meyers PM, Meylahn F, Mhaske A, Miani A, Miao H, Michaloliakos I, Michel C, Michimura Y, Middleton H, Milano L, Miller AL, Millhouse M, Mills JC, Milotti E, Milovich-Goff MC, Minazzoli O, Minenkov Y, Mio N, Mir LM, Mishkin A, Mishra C, Mishra T, Mistry T, Mitra S, Mitrofanov VP, Mitselmakher G, Mittleman R, Miyakawa O, Miyamoto A, Miyazaki Y, Miyo K, Miyoki S, Mo G, Mogushi K, Mohapatra SRP, Mohite SR, Molina I, Molina-Ruiz M, Mondin M, Montani M, Moore CJ, Moraru D, Morawski F, More A, Moreno C, Moreno G, Mori Y, Morisaki S, Moriwaki Y, Mours B, Mow-Lowry CM, Mozzon S, Muciaccia F, Mukherjee A, Mukherjee D, Mukherjee S, Mukherjee S, Mukund N, Mullavey A, Munch J, Muñiz EA, Murray PG, Musenich R, Nadji SL, Nagano K, Nagano S, Nakamura K, Nakano H, Nakano M, Nakashima R, Nakayama Y, Nardecchia I, Narikawa T, Naticchioni L, Nayak B, Nayak RK, Negishi R, Neil BF, Neilson J, Nelemans G, Nelson TJN, Nery M, Neunzert A, Ng KY, Ng SWS, Nguyen C, Nguyen P, Nguyen T, Nguyen Quynh L, Ni WT, Nichols SA, Nishizawa A, Nissanke S, Nocera F, Noh M, Norman M, North C, Nozaki S, Nuttall LK, Oberling J, O'Brien BD, Obuchi Y, O'Dell J, Ogaki W, Oganesyan G, Oh JJ, Oh K, Oh SH, Ohashi M, Ohishi N, Ohkawa M, Ohme F, Ohta H, Okada MA, Okutani Y, Okutomi K, Olivetto C, Oohara K, Ooi C, Oram R, O'Reilly B, Ormiston RG, Ormsby ND, Ortega LF, O'Shaughnessy R, O'Shea E, Oshino S, Ossokine S, Osthelder C, Otabe S, Ottaway DJ, Overmier H, Pace AE, Pagano G, Page MA, Pagliaroli G, Pai A, Pai SA, Palamos JR, Palashov O, Palomba C, Pan K, Panda PK, Pang H, Pang PTH, Pankow C, Pannarale F, Pant BC, Paoletti F, Paoli A, Paolone A, Parisi A, Park J, Parker W, Pascucci D, Pasqualetti A, Passaquieti R, Passuello D, Patel M, Patricelli B, Payne E, Pechsiri TC, Pedraza M, Pegoraro M, Pele A, Peña Arellano FE, Penn S, Perego A, Pereira A, Pereira T, Perez CJ, Périgois C, Perreca A, Perriès S, Petermann J, Petterson D, Pfeiffer HP, Pham KA, Phukon KS, Piccinni OJ, Pichot M, Piendibene M, Piergiovanni F, Pierini L, Pierro V, Pillant G, Pilo F, Pinard L, Pinto IM, Piotrzkowski BJ, Piotrzkowski K, Pirello M, Pitkin M, Placidi E, Plastino W, Pluchar C, Poggiani R, Polini E, Pong DYT, Ponrathnam S, Popolizio P, Porter EK, Powell J, Pracchia M, Pradier T, Prajapati AK, Prasai K, Prasanna R, Pratten G, Prestegard T, Principe M, Prodi GA, Prokhorov L, Prosposito P, Prudenzi L, Puecher A, Punturo M, Puosi F, Puppo P, Pürrer M, Qi H, Quetschke V, Quinonez PJ, Quitzow-James R, Raab FJ, Raaijmakers G, Radkins H, Radulesco N, Raffai P, Rail SX, Raja S, Rajan C, Ramirez KE, Ramirez TD, Ramos-Buades A, Rana J, Rapagnani P, Rapol UD, Ratto B, Raymond V, Raza N, Razzano M, Read J, Rees LA, Regimbau T, Rei L, Reid S, Reitze DH, Relton P, Rettegno P, Ricci F, Richardson CJ, Richardson JW, Richardson L, Ricker PM, Riemenschneider G, Riles K, Rizzo M, Robertson NA, Robie R, Robinet F, Rocchi A, Rocha JA, Rodriguez S, Rodriguez-Soto RD, Rolland L, Rollins JG, Roma VJ, Romanelli M, Romano R, Romel CL, Romero A, Romero-Shaw IM, Romie JH, Rose CA, Rosińska D, Rosofsky SG, Ross MP, Rowan S, Rowlinson SJ, Roy S, Roy S, Rozza D, Ruggi P, Ryan K, Sachdev S, Sadecki T, Sadiq J, Sago N, Saito S, Saito Y, Sakai K, Sakai Y, Sakellariadou M, Sakuno Y, Salafia OS, Salconi L, Saleem M, Salemi F, Samajdar A, Sanchez EJ, Sanchez JH, Sanchez LE, Sanchis-Gual N, Sanders JR, Sanuy A, Saravanan TR, Sarin N, Sassolas B, Satari H, Sato S, Sato T, Sauter O, Savage RL, Savant V, Sawada T, Sawant D, Sawant HL, Sayah S, Schaetzl D, Scheel M, Scheuer J, Schindler-Tyka A, Schmidt P, Schnabel R, Schneewind M, Schofield RMS, Schönbeck A, Schulte BW, Schutz BF, Schwartz E, Scott J, Scott SM, Seglar-Arroyo M, Seidel E, Sekiguchi T, Sekiguchi Y, Sellers D, Sengupta AS, Sennett N, Sentenac D, Seo EG, Sequino V, Setyawati Y, Shaffer T, Shahriar MS, Shams B, Shao L, Sharifi S, Sharma A, Sharma P, Shawhan P, Shcheblanov NS, Shen H, Shibagaki S, Shikauchi M, Shimizu R, Shimoda T, Shimode K, Shink R, Shinkai H, Shishido T, Shoda A, Shoemaker DH, Shoemaker DM, Shukla K, ShyamSundar S, Sieniawska M, Sigg D, Singer LP, Singh D, Singh N, Singha A, Sintes AM, Sipala V, Skliris V, Slagmolen BJJ, Slaven-Blair TJ, Smetana J, Smith JR, Smith RJE, Somala SN, Somiya K, Son EJ, Soni K, Soni S, Sorazu B, Sordini V, Sorrentino F, Sorrentino N, Sotani H, Soulard R, Souradeep T, Sowell E, Spagnuolo V, Spencer AP, Spera M, Srivastava AK, Srivastava V, Staats K, Stachie C, Steer DA, Steinlechner J, Steinlechner S, Stops DJ, Stover M, Strain KA, Strang LC, Stratta G, Strunk A, Sturani R, Stuver AL, Südbeck J, Sudhagar S, Sudhir V, Sugimoto R, Suh HG, Summerscales TZ, Sun H, Sun L, Sunil S, Sur A, Suresh J, Sutton PJ, Suzuki T, Suzuki T, Swinkels BL, Szczepańczyk MJ, Szewczyk P, Tacca M, Tagoshi H, Tait SC, Takahashi H, Takahashi R, Takamori A, Takano S, Takeda H, Takeda M, Talbot C, Tanaka H, Tanaka K, Tanaka K, Tanaka T, Tanaka T, Tanasijczuk AJ, Tanioka S, Tanner DB, Tao D, Tapia A, Tapia San Martin EN, Tapia San Martin EN, Tasson JD, Telada S, Tenorio R, Terkowski L, Test M, Thirugnanasambandam MP, Thomas M, Thomas P, Thompson JE, Thondapu SR, Thorne KA, Thrane E, Tiwari S, Tiwari S, Tiwari V, Toland K, Tolley AE, Tomaru T, Tomigami Y, Tomura T, Tonelli M, Torres-Forné A, Torrie CI, Tosta E Melo I, Töyrä D, Trapananti A, Travasso F, Traylor G, Tringali MC, Tripathee A, Troiano L, Trovato A, Trozzo L, Trudeau RJ, Tsai DS, Tsai D, Tsang KW, Tsang T, Tsao JS, Tse M, Tso R, Tsubono K, Tsuchida S, Tsukada L, Tsuna D, Tsutsui T, Tsuzuki T, Turconi M, Tuyenbayev D, Ubhi AS, Uchikata N, Uchiyama T, Udall RP, Ueda A, Uehara T, Ueno K, Ueshima G, Ugolini D, Unnikrishnan CS, Uraguchi F, Urban AL, Ushiba T, Usman SA, Utina AC, Vahlbruch H, Vajente G, Vajpeyi A, Valdes G, Valentini M, Valsan V, van Bakel N, van Beuzekom M, van den Brand JFJ, Van Den Broeck C, Vander-Hyde DC, van der Schaaf L, van Heijningen JV, van Putten MHPM, van Remortel N, Vardaro M, Vargas AF, Varma V, Vasúth M, Vecchio A, Vedovato G, Veitch J, Veitch PJ, Venkateswara K, Venneberg J, Venugopalan G, Verkindt D, Verma Y, Veske D, Vetrano F, Viceré A, Viets AD, Villa-Ortega V, Vinet JY, Vitale S, Vo T, Vocca H, von Reis ERG, Vorvick C, Vyatchanin SP, Wade LE, Wade M, Wagner KJ, Walet RC, Walker M, Wallace GS, Wallace L, Walsh S, Wang J, Wang JZ, Wang WH, Ward RL, Warner J, Was M, Washimi T, Washington NY, Watchi J, Weaver B, Wei L, Weinert M, Weinstein AJ, Weiss R, Weller CM, Wellmann F, Wen L, Weßels P, Westhouse JW, Wette K, Whelan JT, White DD, Whiting BF, Whittle C, Wilken D, Williams D, Williams MJ, Williamson AR, Willis JL, Willke B, Wilson DJ, Winkler W, Wipf CC, Wlodarczyk T, Woan G, Woehler J, Wofford JK, Wong ICF, Wrangel J, Wu C, Wu DS, Wu H, Wu S, Wysocki DM, Xiao L, Xu WR, Yamada T, Yamamoto H, Yamamoto K, Yamamoto K, Yamamoto T, Yamashita K, Yamazaki R, Yang FW, Yang L, Yang Y, Yang Y, Yang Z, Yap MJ, Yeeles DW, Yelikar AB, Ying M, Yokogawa K, Yokoyama J, Yokozawa T, Yoon A, Yoshioka T, Yu H, Yu H, Yuzurihara H, Zadrożny A, Zanolin M, Zeidler S, Zelenova T, Zendri JP, Zevin M, Zhan M, Zhang H, Zhang J, Zhang L, Zhang R, Zhang T, Zhao C, Zhao G, Zhao Y, Zhao Y, Zhou Z, Zhu XJ, Zhu ZH, Zucker ME, Zweizig J. Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run. PHYSICAL REVIEW LETTERS 2021; 126:241102. [PMID: 34213926 DOI: 10.1103/physrevd.97.102002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/31/2021] [Accepted: 05/23/2021] [Indexed: 05/21/2023]
Abstract
We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.
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Abbott R, Abbott TD, Abraham S, Acernese F, Ackley K, Adams A, Adams C, Adhikari RX, Adya VB, Affeldt C, Agarwal D, Agathos M, Agatsuma K, Aggarwal N, Aguiar OD, Aiello L, Ain A, Ajith P, Akutsu T, Aleman KM, Allen G, Allocca A, Altin PA, Amato A, Anand S, Ananyeva A, Anderson SB, Anderson WG, Ando M, Angelova SV, Ansoldi S, Antelis JM, Antier S, Appert S, Arai K, Arai K, Arai Y, Araki S, Araya A, Araya MC, Areeda JS, Arène M, Aritomi N, Arnaud N, Aronson SM, Asada H, Asali Y, Ashton G, Aso Y, Aston SM, Astone P, Aubin F, Auclair P, Aufmuth P, AultONeal K, Austin C, Babak S, Badaracco F, Bader MKM, Bae S, Bae Y, Baer AM, Bagnasco S, Bai Y, Baiotti L, Baird J, Bajpai R, Ball M, Ballardin G, Ballmer SW, Bals M, Balsamo A, Baltus G, Banagiri S, Bankar D, Bankar RS, Barayoga JC, Barbieri C, Barish BC, Barker D, Barneo P, Barnum S, Barone F, Barr B, Barsotti L, Barsuglia M, Barta D, Bartlett J, Barton MA, Bartos I, Bassiri R, Basti A, Bawaj M, Bayley JC, Baylor AC, Bazzan M, Bécsy B, Bedakihale VM, Bejger M, Belahcene I, Benedetto V, Beniwal D, Benjamin MG, Bennett TF, Bentley JD, BenYaala M, Bergamin F, Berger BK, Bernuzzi S, Bersanetti D, Bertolini A, Betzwieser J, Bhandare R, Bhandari AV, Bhattacharjee D, Bhaumik S, Bidler J, Bilenko IA, Billingsley G, Birney R, Birnholtz O, Biscans S, Bischi M, Biscoveanu S, Bisht A, Biswas B, Bitossi M, Bizouard MA, Blackburn JK, Blackman J, Blair CD, Blair DG, Blair RM, Bobba F, Bode N, Boer M, Bogaert G, Boldrini M, Bondu F, Bonilla E, Bonnand R, Booker P, Boom BA, Bork R, Boschi V, Bose N, Bose S, Bossilkov V, Boudart V, Bouffanais Y, Bozzi A, Bradaschia C, Brady PR, Bramley A, Branch A, Branchesi M, Breschi M, Briant T, Briggs JH, Brillet A, Brinkmann M, Brockill P, Brooks AF, Brooks J, Brown DD, Brunett S, Bruno G, Bruntz R, Bryant J, Buikema A, Bulik T, Bulten HJ, Buonanno A, Buscicchio R, Buskulic D, Cadonati L, Caesar M, Cagnoli G, Cahillane C, Cain HW, Calderón Bustillo J, Callaghan JD, Callister TA, Calloni E, Camp JB, Canepa M, Cannavacciuolo M, Cannon KC, Cao H, Cao J, Cao Z, Capocasa E, Capote E, Carapella G, Carbognani F, Carlin JB, Carney MF, Carpinelli M, Carullo G, Carver TL, Casanueva Diaz J, Casentini C, Castaldi G, Caudill S, Cavaglià M, Cavalier F, Cavalieri R, Cella G, Cerdá-Durán P, Cesarini E, Chaibi W, Chakravarti K, Champion B, Chan CH, Chan C, Chan CL, Chan M, Chandra K, Chanial P, Chao S, Charlton P, Chase EA, Chassande-Mottin E, Chatterjee D, Chaturvedi M, Chatziioannou K, Chen A, Chen C, Chen HY, Chen J, Chen K, Chen X, Chen YB, Chen YR, Chen Z, Cheng H, Cheong CK, Cheung HY, Chia HY, Chiadini F, Chiang CY, Chierici R, Chincarini A, Chiofalo ML, Chiummo A, Cho G, Cho HS, Choate S, Choudhary RK, Choudhary S, Christensen N, Chu H, Chu Q, Chu YK, Chua S, Chung KW, Ciani G, Ciecielag P, Cieślar M, Cifaldi M, Ciobanu AA, Ciolfi R, Cipriano F, Cirone A, Clara F, Clark EN, Clark JA, Clarke L, Clearwater P, Clesse S, Cleva F, Coccia E, Cohadon PF, Cohen DE, Cohen L, Colleoni M, Collette CG, Colpi M, Compton CM, Constancio M, Conti L, Cooper SJ, Corban P, Corbitt TR, Cordero-Carrión I, Corezzi S, Corley KR, Cornish N, Corre D, Corsi A, Cortese S, Costa CA, Cotesta R, Coughlin MW, Coughlin SB, Coulon JP, Countryman ST, Cousins B, Couvares P, Covas PB, Coward DM, Cowart MJ, Coyne DC, Coyne R, Creighton JDE, Creighton TD, Criswell AW, Croquette M, Crowder SG, Cudell JR, Cullen TJ, Cumming A, Cummings R, Cuoco E, Curyło M, Canton TD, Dálya G, Dana A, DaneshgaranBajastani LM, D'Angelo B, Danilishin SL, D'Antonio S, Danzmann K, Darsow-Fromm C, Dasgupta A, Datrier LEH, Dattilo V, Dave I, Davier M, Davies GS, Davis D, Daw EJ, Dean R, Deenadayalan M, Degallaix J, De Laurentis M, Deléglise S, Del Favero V, De Lillo F, De Lillo N, Del Pozzo W, DeMarchi LM, De Matteis F, D'Emilio V, Demos N, Dent T, Depasse A, De Pietri R, De Rosa R, De Rossi C, DeSalvo R, De Simone R, Dhurandhar S, Díaz MC, Diaz-Ortiz M, Didio NA, Dietrich T, Di Fiore L, Di Fronzo C, Di Giorgio C, Di Giovanni F, Di Girolamo T, Di Lieto A, Ding B, Di Pace S, Di Palma I, Di Renzo F, Divakarla AK, Dmitriev A, Doctor Z, D'Onofrio L, Donovan F, Dooley KL, Doravari S, Dorrington I, Drago M, Driggers JC, Drori Y, Du Z, Ducoin JG, Dupej P, Durante O, D'Urso D, Duverne PA, Dwyer SE, Easter PJ, Ebersold M, Eddolls G, Edelman B, Edo TB, Edy O, Effler A, Eguchi S, Eichholz J, Eikenberry SS, Eisenmann M, Eisenstein RA, Ejlli A, Enomoto Y, Errico L, Essick RC, Estellés H, Estevez D, Etienne Z, Etzel T, Evans M, Evans TM, Ewing BE, Fafone V, Fair H, Fairhurst S, Fan X, Farah AM, Farinon S, Farr B, Farr WM, Farrow NW, Fauchon-Jones EJ, Favata M, Fays M, Fazio M, Feicht J, Fejer MM, Feng F, Fenyvesi E, Ferguson DL, Fernandez-Galiana A, Ferrante I, Ferreira TA, Fidecaro F, Figura P, Fiori I, Fishbach M, Fisher RP, Fishner JM, Fittipaldi R, Fiumara V, Flaminio R, Floden E, Flynn E, Fong H, Font JA, Fornal B, Forsyth PWF, Franke A, Frasca S, Frasconi F, Frederick C, Frei Z, Freise A, Frey R, Fritschel P, Frolov VV, Fronzé GG, Fujii Y, Fujikawa Y, Fukunaga M, Fukushima M, Fulda P, Fyffe M, Gabbard HA, Gadre BU, Gaebel SM, Gair JR, Gais J, Galaudage S, Gamba R, Ganapathy D, Ganguly A, Gao D, Gaonkar SG, Garaventa B, García-Núñez C, García-Quirós C, Garufi F, Gateley B, Gaudio S, Gayathri V, Ge G, Gemme G, Gennai A, George J, Gergely L, Gewecke P, Ghonge S, Ghosh A, Ghosh A, Ghosh S, Ghosh S, Ghosh S, Giacomazzo B, Giacoppo L, Giaime JA, Giardina KD, Gibson DR, Gier C, Giesler M, Giri P, Gissi F, Glanzer J, Gleckl AE, Godwin P, Goetz E, Goetz R, Gohlke N, Goncharov B, González G, Gopakumar A, Gosselin M, Gouaty R, Grace B, Grado A, Granata M, Granata V, Grant A, Gras S, Grassia P, Gray C, Gray R, Greco G, Green AC, Green R, Gretarsson AM, Gretarsson EM, Griffith D, Griffiths W, Griggs HL, Grignani G, Grimaldi A, Grimes E, Grimm SJ, Grote H, Grunewald S, Gruning P, Guerrero JG, Guidi GM, Guimaraes AR, Guixé G, Gulati HK, Guo HK, Guo Y, Gupta A, Gupta A, Gupta P, Gustafson EK, Gustafson R, Guzman F, Ha S, Haegel L, Hagiwara A, Haino S, Halim O, Hall ED, Hamilton EZ, Hammond G, Han WB, Haney M, Hanks J, Hanna C, Hannam MD, Hannuksela OA, Hansen H, Hansen TJ, Hanson J, Harder T, Hardwick T, Haris K, Harms J, Harry GM, Harry IW, Hartwig D, Hasegawa K, Haskell B, Hasskew RK, Haster CJ, Hattori K, Haughian K, Hayakawa H, Hayama K, Hayes FJ, Healy J, Heidmann A, Heintze MC, Heinze J, Heinzel J, Heitmann H, Hellman F, Hello P, Helmling-Cornell AF, Hemming G, Hendry M, Heng IS, Hennes E, Hennig J, Hennig MH, Hernandez Vivanco F, Heurs M, Hild S, Hill P, Himemoto Y, Hines AS, Hiranuma Y, Hirata N, Hirose E, Hochheim S, Hofman D, Hohmann JN, Holgado AM, Holland NA, Hollows IJ, Holmes ZJ, Holt K, Holz DE, Hong Z, Hopkins P, Hough J, Howell EJ, Hoy CG, Hoyland D, Hreibi A, Hsieh B, Hsu Y, Huang GZ, Huang HY, Huang P, Huang YC, Huang YJ, Huang YW, Hübner MT, Huddart AD, Huerta EA, Hughey B, Hui DCY, Hui V, Husa S, Huttner SH, Huxford R, Huynh-Dinh T, Ide S, Idzkowski B, Iess A, Ikenoue B, Imam S, Inayoshi K, Inchauspe H, Ingram C, Inoue Y, Intini G, Ioka K, Isi M, Isleif K, Ito K, Itoh Y, Iyer BR, Izumi K, JaberianHamedan V, Jacqmin T, Jadhav SJ, Jadhav SP, James AL, Jan AZ, Jani K, Janssens K, Janthalur NN, Jaranowski P, Jariwala D, Jaume R, Jenkins AC, Jeon C, Jeunon M, Jia W, Jiang J, Jin HB, Johns GR, Jones AW, Jones DI, Jones JD, Jones P, Jones R, Jonker RJG, Ju L, Jung K, Jung P, Junker J, Kaihotsu K, Kajita T, Kakizaki M, Kalaghatgi CV, Kalogera V, Kamai B, Kamiizumi M, Kanda N, Kandhasamy S, Kang G, Kanner JB, Kao Y, Kapadia SJ, Kapasi DP, Karathanasis C, Karki S, Kashyap R, Kasprzack M, Kastaun W, Katsanevas S, Katsavounidis E, Katzman W, Kaur T, Kawabe K, Kawaguchi K, Kawai N, Kawasaki T, Kéfélian F, Keitel D, Key JS, Khadka S, Khalili FY, Khan I, Khan S, Khazanov EA, Khetan N, Khursheed M, Kijbunchoo N, Kim C, Kim JC, Kim J, Kim K, Kim WS, Kim YM, Kimball C, Kimura N, King PJ, Kinley-Hanlon M, Kirchhoff R, Kissel JS, Kita N, Kitazawa H, Kleybolte L, Klimenko S, Knee AM, Knowles TD, Knyazev E, Koch P, Koekoek G, Kojima Y, Kokeyama K, Koley S, Kolitsidou P, Kolstein M, Komori K, Kondrashov V, Kong AKH, Kontos A, Koper N, Korobko M, Kotake K, Kovalam M, Kozak DB, Kozakai C, Kozu R, Kringel V, Krishnendu NV, Królak A, Kuehn G, Kuei F, Kumar A, Kumar P, Kumar R, Kumar R, Kume J, Kuns K, Kuo C, Kuo HS, Kuromiya Y, Kuroyanagi S, Kusayanagi K, Kwak K, Kwang S, Laghi D, Lalande E, Lam TL, Lamberts A, Landry M, Lane BB, Lang RN, Lange J, Lantz B, La Rosa I, Lartaux-Vollard A, Lasky PD, Laxen M, Lazzarini A, Lazzaro C, Leaci P, Leavey S, Lecoeuche YK, Lee HK, Lee HM, Lee HW, Lee J, Lee K, Lee R, Lehmann J, Lemaître A, Leon E, Leonardi M, Leroy N, Letendre N, Levin Y, Leviton JN, Li AKY, Li B, Li J, Li KL, Li TGF, Li X, Lin CY, Lin FK, Lin FL, Lin HL, Lin LCC, Linde F, Linker SD, Linley JN, Littenberg TB, Liu GC, Liu J, Liu K, Liu X, Llorens-Monteagudo M, Lo RKL, Lockwood A, Lollie ML, London LT, Longo A, Lopez D, Lorenzini M, Loriette V, Lormand M, Losurdo G, Lough JD, Lousto CO, Lovelace G, Lück H, Lumaca D, Lundgren AP, Luo LW, Macas R, MacInnis M, Macleod DM, MacMillan IAO, Macquet A, Magaña Hernandez I, Magaña-Sandoval F, Magazzù C, Magee RM, Maggiore R, Majorana E, Maksimovic I, Maliakal S, Malik A, Man N, Mandic V, Mangano V, Mango JL, Mansell GL, Manske M, Mantovani M, Marchesoni F, Marchio M, Marion F, Mark Z, Márka S, Márka Z, Markakis C, Markosyan AS, Markowitz A, Maros E, Marquina A, Marsat S, Martelli F, Martin IW, Martin RM, Martinez M, Martinez V, Martinovic K, Martynov DV, Marx EJ, Masalehdan H, Mason K, Massera E, Masserot A, Massinger TJ, Masso-Reid M, Mastrogiovanni S, Matas A, Mateu-Lucena M, Matichard F, Matiushechkina M, Mavalvala N, McCann JJ, McCarthy R, McClelland DE, McClincy P, McCormick S, McCuller L, McGhee GI, McGuire SC, McIsaac C, McIver J, McManus DJ, McRae T, McWilliams ST, Meacher D, Mehmet M, Mehta AK, Melatos A, Melchor DA, Mendell G, Menendez-Vazquez A, Menoni CS, Mercer RA, Mereni L, Merfeld K, Merilh EL, Merritt JD, Merzougui M, Meshkov S, Messenger C, Messick C, Meyers PM, Meylahn F, Mhaske A, Miani A, Miao H, Michaloliakos I, Michel C, Michimura Y, Middleton H, Milano L, Miller AL, Millhouse M, Mills JC, Milotti E, Milovich-Goff MC, Minazzoli O, Minenkov Y, Mio N, Mir LM, Mishkin A, Mishra C, Mishra T, Mistry T, Mitra S, Mitrofanov VP, Mitselmakher G, Mittleman R, Miyakawa O, Miyamoto A, Miyazaki Y, Miyo K, Miyoki S, Mo G, Mogushi K, Mohapatra SRP, Mohite SR, Molina I, Molina-Ruiz M, Mondin M, Montani M, Moore CJ, Moraru D, Morawski F, More A, Moreno C, Moreno G, Mori Y, Morisaki S, Moriwaki Y, Mours B, Mow-Lowry CM, Mozzon S, Muciaccia F, Mukherjee A, Mukherjee D, Mukherjee S, Mukherjee S, Mukund N, Mullavey A, Munch J, Muñiz EA, Murray PG, Musenich R, Nadji SL, Nagano K, Nagano S, Nakamura K, Nakano H, Nakano M, Nakashima R, Nakayama Y, Nardecchia I, Narikawa T, Naticchioni L, Nayak B, Nayak RK, Negishi R, Neil BF, Neilson J, Nelemans G, Nelson TJN, Nery M, Neunzert A, Ng KY, Ng SWS, Nguyen C, Nguyen P, Nguyen T, Nguyen Quynh L, Ni WT, Nichols SA, Nishizawa A, Nissanke S, Nocera F, Noh M, Norman M, North C, Nozaki S, Nuttall LK, Oberling J, O'Brien BD, Obuchi Y, O'Dell J, Ogaki W, Oganesyan G, Oh JJ, Oh K, Oh SH, Ohashi M, Ohishi N, Ohkawa M, Ohme F, Ohta H, Okada MA, Okutani Y, Okutomi K, Olivetto C, Oohara K, Ooi C, Oram R, O'Reilly B, Ormiston RG, Ormsby ND, Ortega LF, O'Shaughnessy R, O'Shea E, Oshino S, Ossokine S, Osthelder C, Otabe S, Ottaway DJ, Overmier H, Pace AE, Pagano G, Page MA, Pagliaroli G, Pai A, Pai SA, Palamos JR, Palashov O, Palomba C, Pan K, Panda PK, Pang H, Pang PTH, Pankow C, Pannarale F, Pant BC, Paoletti F, Paoli A, Paolone A, Parisi A, Park J, Parker W, Pascucci D, Pasqualetti A, Passaquieti R, Passuello D, Patel M, Patricelli B, Payne E, Pechsiri TC, Pedraza M, Pegoraro M, Pele A, Peña Arellano FE, Penn S, Perego A, Pereira A, Pereira T, Perez CJ, Périgois C, Perreca A, Perriès S, Petermann J, Petterson D, Pfeiffer HP, Pham KA, Phukon KS, Piccinni OJ, Pichot M, Piendibene M, Piergiovanni F, Pierini L, Pierro V, Pillant G, Pilo F, Pinard L, Pinto IM, Piotrzkowski BJ, Piotrzkowski K, Pirello M, Pitkin M, Placidi E, Plastino W, Pluchar C, Poggiani R, Polini E, Pong DYT, Ponrathnam S, Popolizio P, Porter EK, Powell J, Pracchia M, Pradier T, Prajapati AK, Prasai K, Prasanna R, Pratten G, Prestegard T, Principe M, Prodi GA, Prokhorov L, Prosposito P, Prudenzi L, Puecher A, Punturo M, Puosi F, Puppo P, Pürrer M, Qi H, Quetschke V, Quinonez PJ, Quitzow-James R, Raab FJ, Raaijmakers G, Radkins H, Radulesco N, Raffai P, Rail SX, Raja S, Rajan C, Ramirez KE, Ramirez TD, Ramos-Buades A, Rana J, Rapagnani P, Rapol UD, Ratto B, Raymond V, Raza N, Razzano M, Read J, Rees LA, Regimbau T, Rei L, Reid S, Reitze DH, Relton P, Rettegno P, Ricci F, Richardson CJ, Richardson JW, Richardson L, Ricker PM, Riemenschneider G, Riles K, Rizzo M, Robertson NA, Robie R, Robinet F, Rocchi A, Rocha JA, Rodriguez S, Rodriguez-Soto RD, Rolland L, Rollins JG, Roma VJ, Romanelli M, Romano R, Romel CL, Romero A, Romero-Shaw IM, Romie JH, Rose CA, Rosińska D, Rosofsky SG, Ross MP, Rowan S, Rowlinson SJ, Roy S, Roy S, Rozza D, Ruggi P, Ryan K, Sachdev S, Sadecki T, Sadiq J, Sago N, Saito S, Saito Y, Sakai K, Sakai Y, Sakellariadou M, Sakuno Y, Salafia OS, Salconi L, Saleem M, Salemi F, Samajdar A, Sanchez EJ, Sanchez JH, Sanchez LE, Sanchis-Gual N, Sanders JR, Sanuy A, Saravanan TR, Sarin N, Sassolas B, Satari H, Sato S, Sato T, Sauter O, Savage RL, Savant V, Sawada T, Sawant D, Sawant HL, Sayah S, Schaetzl D, Scheel M, Scheuer J, Schindler-Tyka A, Schmidt P, Schnabel R, Schneewind M, Schofield RMS, Schönbeck A, Schulte BW, Schutz BF, Schwartz E, Scott J, Scott SM, Seglar-Arroyo M, Seidel E, Sekiguchi T, Sekiguchi Y, Sellers D, Sengupta AS, Sennett N, Sentenac D, Seo EG, Sequino V, Setyawati Y, Shaffer T, Shahriar MS, Shams B, Shao L, Sharifi S, Sharma A, Sharma P, Shawhan P, Shcheblanov NS, Shen H, Shibagaki S, Shikauchi M, Shimizu R, Shimoda T, Shimode K, Shink R, Shinkai H, Shishido T, Shoda A, Shoemaker DH, Shoemaker DM, Shukla K, ShyamSundar S, Sieniawska M, Sigg D, Singer LP, Singh D, Singh N, Singha A, Sintes AM, Sipala V, Skliris V, Slagmolen BJJ, Slaven-Blair TJ, Smetana J, Smith JR, Smith RJE, Somala SN, Somiya K, Son EJ, Soni K, Soni S, Sorazu B, Sordini V, Sorrentino F, Sorrentino N, Sotani H, Soulard R, Souradeep T, Sowell E, Spagnuolo V, Spencer AP, Spera M, Srivastava AK, Srivastava V, Staats K, Stachie C, Steer DA, Steinlechner J, Steinlechner S, Stops DJ, Stover M, Strain KA, Strang LC, Stratta G, Strunk A, Sturani R, Stuver AL, Südbeck J, Sudhagar S, Sudhir V, Sugimoto R, Suh HG, Summerscales TZ, Sun H, Sun L, Sunil S, Sur A, Suresh J, Sutton PJ, Suzuki T, Suzuki T, Swinkels BL, Szczepańczyk MJ, Szewczyk P, Tacca M, Tagoshi H, Tait SC, Takahashi H, Takahashi R, Takamori A, Takano S, Takeda H, Takeda M, Talbot C, Tanaka H, Tanaka K, Tanaka K, Tanaka T, Tanaka T, Tanasijczuk AJ, Tanioka S, Tanner DB, Tao D, Tapia A, Tapia San Martin EN, Tapia San Martin EN, Tasson JD, Telada S, Tenorio R, Terkowski L, Test M, Thirugnanasambandam MP, Thomas M, Thomas P, Thompson JE, Thondapu SR, Thorne KA, Thrane E, Tiwari S, Tiwari S, Tiwari V, Toland K, Tolley AE, Tomaru T, Tomigami Y, Tomura T, Tonelli M, Torres-Forné A, Torrie CI, Tosta E Melo I, Töyrä D, Trapananti A, Travasso F, Traylor G, Tringali MC, Tripathee A, Troiano L, Trovato A, Trozzo L, Trudeau RJ, Tsai DS, Tsai D, Tsang KW, Tsang T, Tsao JS, Tse M, Tso R, Tsubono K, Tsuchida S, Tsukada L, Tsuna D, Tsutsui T, Tsuzuki T, Turconi M, Tuyenbayev D, Ubhi AS, Uchikata N, Uchiyama T, Udall RP, Ueda A, Uehara T, Ueno K, Ueshima G, Ugolini D, Unnikrishnan CS, Uraguchi F, Urban AL, Ushiba T, Usman SA, Utina AC, Vahlbruch H, Vajente G, Vajpeyi A, Valdes G, Valentini M, Valsan V, van Bakel N, van Beuzekom M, van den Brand JFJ, Van Den Broeck C, Vander-Hyde DC, van der Schaaf L, van Heijningen JV, van Putten MHPM, van Remortel N, Vardaro M, Vargas AF, Varma V, Vasúth M, Vecchio A, Vedovato G, Veitch J, Veitch PJ, Venkateswara K, Venneberg J, Venugopalan G, Verkindt D, Verma Y, Veske D, Vetrano F, Viceré A, Viets AD, Villa-Ortega V, Vinet JY, Vitale S, Vo T, Vocca H, von Reis ERG, Vorvick C, Vyatchanin SP, Wade LE, Wade M, Wagner KJ, Walet RC, Walker M, Wallace GS, Wallace L, Walsh S, Wang J, Wang JZ, Wang WH, Ward RL, Warner J, Was M, Washimi T, Washington NY, Watchi J, Weaver B, Wei L, Weinert M, Weinstein AJ, Weiss R, Weller CM, Wellmann F, Wen L, Weßels P, Westhouse JW, Wette K, Whelan JT, White DD, Whiting BF, Whittle C, Wilken D, Williams D, Williams MJ, Williamson AR, Willis JL, Willke B, Wilson DJ, Winkler W, Wipf CC, Wlodarczyk T, Woan G, Woehler J, Wofford JK, Wong ICF, Wrangel J, Wu C, Wu DS, Wu H, Wu S, Wysocki DM, Xiao L, Xu WR, Yamada T, Yamamoto H, Yamamoto K, Yamamoto K, Yamamoto T, Yamashita K, Yamazaki R, Yang FW, Yang L, Yang Y, Yang Y, Yang Z, Yap MJ, Yeeles DW, Yelikar AB, Ying M, Yokogawa K, Yokoyama J, Yokozawa T, Yoon A, Yoshioka T, Yu H, Yu H, Yuzurihara H, Zadrożny A, Zanolin M, Zeidler S, Zelenova T, Zendri JP, Zevin M, Zhan M, Zhang H, Zhang J, Zhang L, Zhang R, Zhang T, Zhao C, Zhao G, Zhao Y, Zhao Y, Zhou Z, Zhu XJ, Zhu ZH, Zucker ME, Zweizig J. Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run. PHYSICAL REVIEW LETTERS 2021; 126:241102. [PMID: 34213926 DOI: 10.1103/physrevlett.126.241102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/31/2021] [Accepted: 05/23/2021] [Indexed: 06/13/2023]
Abstract
We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.
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Song B, Yang S, Hwang GH, Yu J, Bae S. Analysis of NHEJ-Based DNA Repair after CRISPR-Mediated DNA Cleavage. Int J Mol Sci 2021; 22:6397. [PMID: 34203807 PMCID: PMC8232687 DOI: 10.3390/ijms22126397] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/26/2022] Open
Abstract
Genome editing using CRISPR-Cas9 nucleases is based on the repair of the DNA double-strand break (DSB). In eukaryotic cells, DSBs are rejoined through homology-directed repair (HDR), non-homologous end joining (NHEJ) or microhomology-mediated end joining (MMEJ) pathways. Among these, it is thought that the NHEJ pathway is dominant and occurs throughout a cell cycle. NHEJ-based DSB repair is known to be error-prone; however, there are few studies that delve into it deeply in endogenous genes. Here, we quantify the degree of NHEJ-based DSB repair accuracy (termed NHEJ accuracy) in human-originated cells by incorporating exogenous DNA oligonucleotides. Through an analysis of joined sequences between the exogenous DNA and the endogenous target after DSBs occur, we determined that the average value of NHEJ accuracy is approximately 75% in maximum in HEK 293T cells. In a deep analysis, we found that NHEJ accuracy is sequence-dependent and the value at the DSB end proximal to a protospacer adjacent motif (PAM) is relatively lower than that at the DSB end distal to the PAM. In addition, we observed a negative correlation between the insertion mutation ratio and the degree of NHEJ accuracy. Our findings would broaden the understanding of Cas9-mediated genome editing.
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Jung YJ, Lee HJ, Yu J, Bae S, Cho YG, Kang KK. Transcriptomic and physiological analysis of OsCAO1 knockout lines using the CRISPR/Cas9 system in rice. PLANT CELL REPORTS 2021; 40:1013-1024. [PMID: 32980909 DOI: 10.1007/s00299-020-02607-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
The altered rice leaf color based on the knockout of CAO1 gene generated using CRISPR/Cas9 technology plays important roles in chlorophyll degradation and ROS scavenging to regulate both natural and induced senescence in rice. Rice chlorophyllide a oxygenase (OsCAO1), identified as the chlorophyll b synthesis under light condition, plays a critical role in regulating rice plant photosynthesis. In this study, the development of edited lines with pale green leaves by knockout of OsCAO1 gene known as a chlorophyll synthesis process is reported. Eighty-one genetically edited lines out of 181 T0 plants were generated through CRISPR/Cas9 system. The edited lines have short narrow flag leaves and pale green leaves compared with wild-type 'Dongjin' plants (WT). Additionally, edited lines have lower chlorophyll b and carotenoid contents both at seedling and mature stages. A transcriptome analysis identified 580 up-regulated and 206 downregulated genes in the edited lines. The differentially expressed genes (DEGs) involved in chlorophyll biosynthesis, magnesium chelatase subunit (CHLH), and glutamate-1-semialdehyde2, 1-aminomutase (GSA) metabolism decreased significantly. Meanwhile, the gel consistency (GC) levels of rice grains, chalkiness ratios and chalkiness degrees (CD) decreased in the edited lines. Thus, knockout of OsCAO1 influenced growth period, leaf development and grain quality characters of rice. Overall, the result suggests that OsCAO1 also plays important roles in chlorophyll degradation and ROS scavenging to regulate both natural and induced rice senescence.
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Yu J, Tu L, Subburaj S, Bae S, Lee GJ. Simultaneous targeting of duplicated genes in Petunia protoplasts for flower color modification via CRISPR-Cas9 ribonucleoproteins. PLANT CELL REPORTS 2021; 40:1037-1045. [PMID: 32959126 DOI: 10.1007/s00299-020-02593-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/26/2020] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE We obtained a complete mutant line of Petunia having mutations in both F3H genes via Cas9-ribonucleoproteins delivery, which exhibited a pale purplish pink flower color. The CRISPR-Cas system is now revolutionizing agriculture by allowing researchers to generate various desired mutations in plants at will. In particular, DNA-free genome editing via Cas9-ribonucleoproteins (RNPs) delivery has many advantages in plants; it does not require codon optimization or specific promoters for expression in plant cells; furthermore, it can bypass GMO regulations in some countries. Here, we have performed site-specific mutagenesis in Petunia to engineer flower color modifications. We determined that the commercial Petunia cultivar 'Madness Midnight' has two F3H coding genes and designed one guide RNA that targets both F3H genes at once. Among 67 T0 plants regenerated from Cas9-RNP transfected protoplasts, we obtained seven mutant lines that contain mutations in either F3HA or F3HB gene and one complete mutant line having mutations in both F3H genes without any selectable markers. It is noteworthy that only the f3ha f3hb exhibited a clearly modified, pale purplish pink flower color (RHS 69D), whereas the others, including the single copy gene knock-out plants, displayed purple violet (RHS 93A) flowers similar to the wild-type Petunia. To the best of our knowledge, we demonstrated a precedent of ornamental crop engineering by DNA-free CRISPR method for the first time, which will greatly accelerate a transition from a laboratory to a farmer's field.
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Song B, Kang CY, Han JH, Kano M, Konnerth A, Bae S. In vivo genome editing in single mammalian brain neurons through CRISPR-Cas9 and cytosine base editors. Comput Struct Biotechnol J 2021; 19:2477-2485. [PMID: 34025938 PMCID: PMC8113754 DOI: 10.1016/j.csbj.2021.04.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 10/31/2022] Open
Abstract
Gene manipulation is a useful approach for understanding functions of genes and is important for investigating basic mechanisms of brain function on the level of single neurons and circuits. Despite the development and the wide range of applications of CRISPR-Cas9 and base editors (BEs), their implementation for an analysis of individual neurons in vivo remained limited. In fact, conventional gene manipulations are generally achieved only on the population level. Here, we combined either CRISPR-Cas9 or BEs with the targeted single-cell electroporation technique as a proof-of-concept test for gene manipulation in single neurons in vivo. Our assay consisted of CRISPR-Cas9- or BEs-induced gene knockout in single Purkinje cells in the cerebellum. Our results demonstrate the feasibility of both gene editing and base editing in single cells in the intact brain, providing a tool through which molecular perturbations of individual neurons can be used for analysis of circuits and, ultimately, behaviors.
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Shin I, Kim H, Ahn SS, Sohn B, Bae S, Park JE, Kim HS, Lee SK. Development and Validation of a Deep Learning-Based Model to Distinguish Glioblastoma from Solitary Brain Metastasis Using Conventional MR Images. AJNR Am J Neuroradiol 2021; 42:838-844. [PMID: 33737268 DOI: 10.3174/ajnr.a7003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND PURPOSE Differentiating glioblastoma from solitary brain metastasis preoperatively using conventional MR images is challenging. Deep learning models have shown promise in performing classification tasks. The diagnostic performance of a deep learning-based model in discriminating glioblastoma from solitary brain metastasis using preoperative conventional MR images was evaluated. MATERIALS AND METHODS Records of 598 patients with histologically confirmed glioblastoma or solitary brain metastasis at our institution between February 2006 and December 2017 were retrospectively reviewed. Preoperative contrast-enhanced T1WI and T2WI were preprocessed and roughly segmented with rectangular regions of interest. A deep neural network was trained and validated using MR images from 498 patients. The MR images of the remaining 100 were used as an internal test set. An additional 143 patients from another tertiary hospital were used as an external test set. The classifications of ResNet-50 and 2 neuroradiologists were compared for their accuracy, precision, recall, F1 score, and area under the curve. RESULTS The areas under the curve of ResNet-50 were 0.889 and 0.835 in the internal and external test sets, respectively. The area under the curve of neuroradiologists 1 and 2 were 0.889 and 0.768 in the internal test set and 0.857 and 0.708 in the external test set, respectively. CONCLUSIONS A deep learning-based model may be a supportive tool for preoperative discrimination between glioblastoma and solitary brain metastasis using conventional MR images.
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Kim C, Jeong YK, Yu J, Shin HJ, Ku KB, Cha HJ, Han JH, Hong SA, Kim BT, Kim SJ, Woo JS, Bae S. Efficient Human Cell Coexpression System and Its Application to the Production of Multiple Coronavirus Antigens. Adv Biol (Weinh) 2021; 5:e2000154. [PMID: 33852178 DOI: 10.1002/adbi.202000154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 01/08/2021] [Indexed: 01/14/2023]
Abstract
Coproduction of multiple proteins at high levels in a single human cell line would be extremely useful for basic research and medical applications. Here, a novel strategy for the stable expression of multiple proteins by integrating the genes into defined transcriptional hotspots in the human genome is presented. As a proof-of-concept, it is shown that EYFP is expressed at similar levels from hotspots and that the EYFP expression increases proportionally with the copy number. It is confirmed that three different fluorescent proteins, encoded by genes integrated at different loci, can be coexpressed at high levels. Further, a stable cell line is generated, producing antigens from different human coronaviruses: MERS-CoV and HCoV-OC43. Antibodies raised against these antigens, which contain human N-glycosylation, show neutralizing activities against both viruses, suggesting that the coexpression system provides a quick and predictable way to produce multiple coronavirus antigens, such as the recent 2019 novel human coronavirus.
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Bae S, Lim D, Kim D, Jeon J, Oh T. In vitro antibacterial effects of non-thermal atmospheric plasma irradiation on Staphylococcus pseudintermedius and Pseudomonas aeruginosa. Pol J Vet Sci 2021; 23:13-19. [PMID: 32233288 DOI: 10.24425/pjvs.2019.131414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the last decade, atmospheric plasma has been used to treating bacterial infections in humans due to its bactericidal effects; however, its efficacy in dogs is unclear. This study evaluated the in vitro bactericidal efficacy of atmospheric plasma on Staphylococcus pseudinter- medius and Pseudomonas aeruginosa, two of the most important bacterial agents isolated from canine pyodermas. Three isolates each of S. pseudintermedius and P. aeruginosa obtained from dogs with pyoderma were subjected to atmospheric plasma. The isolates from the control group were not exposed to plasma, while those from the treatment groups were exposed to plasma for 15 (7.5 J/cm2), 30 (15 J/cm2), 60 (30 J/cm2), or 90 (45 J/cm2) seconds. After each treatment, a reduction in colony formation was observed. Bacterial viability was evaluated using the LIVE/ DEAD® BacLight™ Bacterial Viability Kit. The antibacterial effects were evaluated with Image J software and significance was assessed statistically in comparison to the control group. The bactericidal effect of atmospheric plasma against both bacteria increased significantly in a time-dependent manner. These results demonstrate the bactericidal capacity of atmospheric plasma, and suggest that it could serve as an alternative treatment method for canine pyoderma. Further studies are needed to evaluate the safety and efficacy of atmospheric plasma in dogs.
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Kim HS, Hwang GH, Lee HK, Bae T, Park SH, Kim YJ, Lee S, Park JH, Bae S, Hur JK. CReVIS-Seq: A highly accurate and multiplexable method for genome-wide mapping of lentiviral integration sites. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 20:792-800. [PMID: 33768124 PMCID: PMC7961857 DOI: 10.1016/j.omtm.2020.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/17/2020] [Indexed: 12/16/2022]
Abstract
Lentiviruses have been widely used as a means of transferring exogenous DNAs into human cells to treat various genetic diseases. Lentiviral vectors are fundamentally integrated into the host genome, but their integration sites are generally unpredictable, which may increase the uncertainty for their use in therapeutics. To determine the viral integration sites in the host genome, several PCR-based methods have been developed. However, the sensitivities of the PCR-based methods are highly dependent on the primer sequences, and optimized primer design is required for individual target sites. In order to address this issue, we developed an alternative method for genome-wide mapping of viral insertion sites, named CReVIS-seq (CRISPR-enhanced Viral Integration Site Sequencing). The method is based on the sequential steps: fragmentation of genomic DNAs, in vitro circularization, cleavage of target sequence in a CRISPR guide RNA-specific manner, high-throughput sequencing of the linearized DNA fragments in an unbiased manner, and identification of viral insertion sites via sequence analysis. By design, CReVIS-seq is not affected by biases that could be introduced during the target enrichment step via PCR amplification using site specific primers. Furthermore, we found that multiplexed CReVIS-seq, using collections of different single-guide RNAs (sgRNAs), enables simultaneous identification of multiple target sites and structural variations (i.e., circularized viral genome), in both single cell clones and heterogeneous cell populations.
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Abstract
The CRISPR-Cas system is broadly used for genome editing because of its convenience and relatively low cost. However, the use of CRISPR nucleases to induce specific nucleotide changes in target DNA requires complex procedures and additional donor DNAs. Furthermore, CRISPR nuclease-mediated DNA cleavage at target sites frequently causes large deletions or genomic rearrangements. In contrast, base editors that consist of catalytically dead Cas9 (dCas9) or Cas9 nickase (nCas9) connected to a cytidine or a guanine deaminase can correct point mutations in the absence of additional donor DNA and without generating double-strand breaks (DSBs) in the target region. To design target sites and assess mutation ratios for cytosine and adenine base editors (CBEs and ABEs), we have developed web tools, named BE-Designer and BE-Analyzer. These tools are easy to use (such that tasks are accomplished by clicking on relevant buttons) and do not require a deep knowledge of bioinformatics.
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Abstract
The CRISPR-Cas system facilitates highly efficient genome editing; thus, it has been applied in many research fields such as biological science, medicine, and gene therapy. However, CRISPR nucleases can cleave off-target sites as well as on-target sites, causing unwanted mutations. Furthermore, after CRISPR treatments are delivered into cells or organisms, it is important to estimate the resulting mutation rates and to determine the patterns of mutations, but these tasks can be difficult. To address these issues, we have developed a tool for identifying potential off-target sites (Cas-OFFinder), a tool for designing CRISPR targets (Cas-Designer), and an assessment tool (Cas-Analyzer). These programs are all implemented on our website so that researchers can easily design CRISPR guide RNAs and assess the resulting mutations by simply clicking on the appropriate buttons; no login process is required.
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Chen X, Xie R, Li H, Jaber F, Musharavati F, Zalnezhad E, Bae S, Hui KS, Hui KN. Supercapacitor performance of porous nickel cobaltite nanosheets. Sci Rep 2020; 10:18956. [PMID: 33144659 PMCID: PMC7642284 DOI: 10.1038/s41598-020-75946-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 09/10/2020] [Indexed: 11/19/2022] Open
Abstract
In this work, nickel cobaltite (NiCo2O4) nanosheets with a porous structure were fabricated on nickel foam as a working electrode for supercapacitor applications. The nanosheets were fabricated by electrochemical deposition of nickel-cobalt hydroxide on the nickel foam substrate at ambient temperature in a three-electrode cell followed by annealing at 300 °C to transform the coating into a porous NiCo2O4 nanosheet. Field emission scanning electron microscopy and transmission electron microscopy revealed a three-dimensional mesoporous structure, which facilitates ion transport and electronic conduction for fast redox reactions. For one cycle, the NiCo2O4 electrodeposited nickel foam has a high specific capacitance (1734.9 F g-1) at a current density (CD) of 2 A g-1. The electrode capacitance decreased by only approximately 12.7% after 3500 cycles at a CD of 30 A g-1. Moreover, a solid-state asymmetric supercapacitor (ASC) was built utilising the NiCo2O4 nanosheets, carbon nanotubes, and a polyvinyl alcohol-potassium hydroxide gel as the anode, cathode, and solid-state electrolyte, respectively. The ASC displayed great electrochemical properties with a 42.25 W h kg-1 energy density at a power density of 298.79 W kg-1.
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Rebesco G, Ramachandran R, Bae S, Dobelbower M, McDonald A, Spencer S, Willey C, Bonner J, Keene K. A Pilot Study Investigating the Opioid Prescribing Patterns in an Academic Radiation Oncology Clinic. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Odei B, Gawu P, Bae S, Fabian D, Pan J, Arnett A, Pardo DAD, Mitchell D. Women and Leadership in Radiation Oncology: How are we doing? Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bae S, Ahn SS, Kim BM, Kim DJ, Kim YD, Nam HS, Heo JH, Lee SK. Hyperattenuating lesions after mechanical thrombectomy in acute ischaemic stroke: factors predicting symptomatic haemorrhage and clinical outcomes. Clin Radiol 2020; 76:80.e15-80.e23. [PMID: 32950255 DOI: 10.1016/j.crad.2020.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 08/19/2020] [Indexed: 11/26/2022]
Abstract
AIM To evaluate the clinical significance of hyperattenuating lesions on CT after mechanical thrombectomy for acute ischaemic stroke, and to identify imaging factors that predict symptomatic haemorrhage and unfavourable outcomes. MATERIALS AND METHODS Seventy-eight patients with acute ischaemic stroke in the anterior circulation who underwent mechanical thrombectomy were evaluated. All patients underwent post-interventional unenhanced computed tomography (CT) within 24 h and follow-up CT or magnetic resonance imaging (MRI) within 7 days. Baseline characteristics and clinical outcomes were compared between patients with and without hyperattenuating lesions. In patients with hyperattenuating lesions, clinical and imaging factors that predict symptomatic haemorrhage and unfavourable outcomes were determined. RESULTS Fifty-six of 78 patients (71.8%) demonstrated hyperattenuating lesions on post-interventional CT. Patients with hyperattenuating lesions showed lower Alberta Stroke Program Early CT score (ASPECTS), persistent/symptomatic haemorrhage, and unfavourable outcomes than those without. In patients with hyperattenuating lesions, larger hyperattenuating lesion volume (>21.3 ml; OR, 55.60, p<0.001) and perilesional oedema (OR, 46.04, p=0.015) were independent factors predicting symptomatic haemorrhage. Older age (OR, 1.2, p=0.006) and lower ASPECTS (OR, 0.45, p=0.046) were independent factors predicting unfavourable outcomes in patients with hyperattenuating lesions. Adding the volume of the hyperattenuating lesion to age and ASPECTS increased the predictive performance of unfavourable outcomes (area under the curve 0.874 versus 0.934, p=0.043). CONCLUSIONS Hyperattenuating lesions on post-interventional CT are associated with increased risk of symptomatic haemorrhage and unfavourable outcomes. Larger hyperattenuating lesion volume is an independent factor of symptomatic haemorrhage and it has added predictive value for unfavourable outcomes.
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Kim KT, Park JC, Jang HK, Lee H, Park S, Kim J, Kwon OS, Go YH, Jin Y, Kim W, Lee J, Bae S, Cha HJ. Safe scarless cassette-free selection of genome-edited human pluripotent stem cells using temporary drug resistance. Biomaterials 2020; 262:120295. [PMID: 32916603 DOI: 10.1016/j.biomaterials.2020.120295] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 07/26/2020] [Accepted: 08/01/2020] [Indexed: 02/07/2023]
Abstract
An efficient gene-editing technique for use in human pluripotent stem cells (hPSCs) has great potential value in regenerative medicine, as well as in drug discovery based on isogenic human disease models. However, the extremely low efficiency of gene editing in hPSCs remains as a major technical hurdle. Previously, we demonstrated that YM155, a survivin inhibitor developed as an anti-cancer drug, induces highly selective cell death in undifferentiated hPSCs. In this study, we demonstrated that the high cytotoxicity of YM155 in hPSCs, which is mediated by selective cellular uptake of the drug, is due to the high expression of SLC35F2 in these cells. Knockout of SLC35F2 with CRISPR-Cas9, or depletion with siRNAs, made the hPSCs highly resistant to YM155. Simultaneous editing of a gene of interest and transient knockdown of SLC35F2 following YM155 treatment enabled the survival of genome-edited hPSCs as a result of temporary YM155 resistance, thereby achieving an enriched selection of clonal populations with gene knockout or knock-in. This precise and efficient genome editing approach took as little as 3 weeks and required no cell sorting or the introduction of additional genes, to be a more feasible approach for gene editing in hPSCs due to its simplicity.
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Abbott R, Abbott TD, Abraham S, Acernese F, Ackley K, Adams C, Adhikari RX, Adya VB, Affeldt C, Agathos M, Agatsuma K, Aggarwal N, Aguiar OD, Aich A, Aiello L, Ain A, Ajith P, Akcay S, Allen G, Allocca A, Altin PA, Amato A, Anand S, Ananyeva A, Anderson SB, Anderson WG, Angelova SV, Ansoldi S, Antier S, Appert S, Arai K, Araya MC, Areeda JS, Arène M, Arnaud N, Aronson SM, Arun KG, Asali Y, Ascenzi S, Ashton G, Aston SM, Astone P, Aubin F, Aufmuth P, AultONeal K, Austin C, Avendano V, Babak S, Bacon P, Badaracco F, Bader MKM, Bae S, Baer AM, Baird J, Baldaccini F, Ballardin G, Ballmer SW, Bals A, Balsamo A, Baltus G, Banagiri S, Bankar D, Bankar RS, Barayoga JC, Barbieri C, Barish BC, Barker D, Barkett K, Barneo P, Barone F, Barr B, Barsotti L, Barsuglia M, Barta D, Bartlett J, Bartos I, Bassiri R, Basti A, Bawaj M, Bayley JC, Bazzan M, Bécsy B, Bejger M, Belahcene I, Bell AS, Beniwal D, Benjamin MG, Bentley JD, Bergamin F, Berger BK, Bergmann G, Bernuzzi S, Berry CPL, Bersanetti D, Bertolini A, Betzwieser J, Bhandare R, Bhandari AV, Bidler J, Biggs E, Bilenko IA, Billingsley G, Birney R, Birnholtz O, Biscans S, Bischi M, Biscoveanu S, Bisht A, Bissenbayeva G, Bitossi M, Bizouard MA, Blackburn JK, Blackman J, Blair CD, Blair DG, Blair RM, Bobba F, Bode N, Boer M, Boetzel Y, Bogaert G, Bondu F, Bonilla E, Bonnand R, Booker P, Boom BA, Bork R, Boschi V, Bose S, Bossilkov V, Bosveld J, Bouffanais Y, Bozzi A, Bradaschia C, Brady PR, Bramley A, Branchesi M, Brau JE, Breschi M, Briant T, Briggs JH, Brighenti F, Brillet A, Brinkmann M, Brockill P, Brooks AF, Brooks J, Brown DD, Brunett S, Bruno G, Bruntz R, Buikema A, Bulik T, Bulten HJ, Buonanno A, Buscicchio R, Buskulic D, Byer RL, Cabero M, Cadonati L, Cagnoli G, Cahillane C, Calderón Bustillo J, Callaghan JD, Callister TA, Calloni E, Camp JB, Canepa M, Cannon KC, Cao H, Cao J, Carapella G, Carbognani F, Caride S, Carney MF, Carullo G, Casanueva Diaz J, Casentini C, Castañeda J, Caudill S, Cavaglià M, Cavalier F, Cavalieri R, Cella G, Cerdá-Durán P, Cesarini E, Chaibi O, Chakravarti K, Chan C, Chan M, Chandra K, Chao S, Charlton P, Chase EA, Chassande-Mottin E, Chatterjee D, Chaturvedi M, Chatziioannou K, Chen HY, Chen X, Chen Y, Cheng HP, Cheong CK, Chia HY, Chiadini F, Chierici R, Chincarini A, Chiummo A, Cho G, Cho HS, Cho M, Christensen N, Chu Q, Chua S, Chung KW, Chung S, Ciani G, Ciecielag P, Cieślar M, Ciobanu AA, Ciolfi R, Cipriano F, Cirone A, Clara F, Clark JA, Clearwater P, Clesse S, Cleva F, Coccia E, Cohadon PF, Cohen D, Colleoni M, Collette CG, Collins C, Colpi M, Constancio M, Conti L, Cooper SJ, Corban P, Corbitt TR, Cordero-Carrión I, Corezzi S, Corley KR, Cornish N, Corre D, Corsi A, Cortese S, Costa CA, Cotesta R, Coughlin MW, Coughlin SB, Coulon JP, Countryman ST, Couvares P, Covas PB, Coward DM, Cowart MJ, Coyne DC, Coyne R, Creighton JDE, Creighton TD, Cripe J, Croquette M, Crowder SG, Cudell JR, Cullen TJ, Cumming A, Cummings R, Cunningham L, Cuoco E, Curylo M, Canton TD, Dálya G, Dana A, Daneshgaran-Bajastani LM, D'Angelo B, Danilishin SL, D'Antonio S, Danzmann K, Darsow-Fromm C, Dasgupta A, Datrier LEH, Dattilo V, Dave I, Davier M, Davies GS, Davis D, Daw EJ, DeBra D, Deenadayalan M, Degallaix J, De Laurentis M, Deléglise S, Delfavero M, De Lillo N, Del Pozzo W, DeMarchi LM, D'Emilio V, Demos N, Dent T, De Pietri R, De Rosa R, De Rossi C, DeSalvo R, de Varona O, Dhurandhar S, Díaz MC, Diaz-Ortiz M, Dietrich T, Di Fiore L, Di Fronzo C, Di Giorgio C, Di Giovanni F, Di Giovanni M, Di Girolamo T, Di Lieto A, Ding B, Di Pace S, Di Palma I, Di Renzo F, Divakarla AK, Dmitriev A, Doctor Z, Donovan F, Dooley KL, Doravari S, Dorrington I, Downes TP, Drago M, Driggers JC, Du Z, Ducoin JG, Dupej P, Durante O, D'Urso D, Dwyer SE, Easter PJ, Eddolls G, Edelman B, Edo TB, Edy O, Effler A, Ehrens P, Eichholz J, Eikenberry SS, Eisenmann M, Eisenstein RA, Ejlli A, Errico L, Essick RC, Estelles H, Estevez D, Etienne ZB, Etzel T, Evans M, Evans TM, Ewing BE, Fafone V, Fairhurst S, Fan X, Farinon S, Farr B, Farr WM, Fauchon-Jones EJ, Favata M, Fays M, Fazio M, Feicht J, Fejer MM, Feng F, Fenyvesi E, Ferguson DL, Fernandez-Galiana A, Ferrante I, Ferreira EC, Ferreira TA, Fidecaro F, Fiori I, Fiorucci D, Fishbach M, Fisher RP, Fittipaldi R, Fitz-Axen M, Fiumara V, Flaminio R, Floden E, Flynn E, Fong H, Font JA, Forsyth PWF, Fournier JD, Frasca S, Frasconi F, Frei Z, Freise A, Frey R, Frey V, Fritschel P, Frolov VV, Fronzè G, Fulda P, Fyffe M, Gabbard HA, Gadre BU, Gaebel SM, Gair JR, Galaudage S, Ganapathy D, Ganguly A, Gaonkar SG, García-Quirós C, Garufi F, Gateley B, Gaudio S, Gayathri V, Gemme G, Genin E, Gennai A, George D, George J, Gergely L, Ghonge S, Ghosh A, Ghosh A, Ghosh S, Giacomazzo B, Giaime JA, Giardina KD, Gibson DR, Gier C, Gill K, Glanzer J, Gniesmer J, Godwin P, Goetz E, Goetz R, Gohlke N, Goncharov B, González G, Gopakumar A, Gossan SE, Gosselin M, Gouaty R, Grace B, Grado A, Granata M, Grant A, Gras S, Grassia P, Gray C, Gray R, Greco G, Green AC, Green R, Gretarsson EM, Griggs HL, Grignani G, Grimaldi A, Grimm SJ, Grote H, Grunewald S, Gruning P, Guidi GM, Guimaraes AR, Guixé G, Gulati HK, Guo Y, Gupta A, Gupta A, Gupta P, Gustafson EK, Gustafson R, Haegel L, Halim O, Hall ED, Hamilton EZ, Hammond G, Haney M, Hanke MM, Hanks J, Hanna C, Hannam MD, Hannuksela OA, Hansen TJ, Hanson J, Harder T, Hardwick T, Haris K, Harms J, Harry GM, Harry IW, Hasskew RK, Haster CJ, Haughian K, Hayes FJ, Healy J, Heidmann A, Heintze MC, Heinze J, Heitmann H, Hellman F, Hello P, Hemming G, Hendry M, Heng IS, Hennes E, Hennig J, Heurs M, Hild S, Hinderer T, Hoback SY, Hochheim S, Hofgard E, Hofman D, Holgado AM, Holland NA, Holt K, Holz DE, Hopkins P, Horst C, Hough J, Howell EJ, Hoy CG, Huang Y, Hübner MT, Huerta EA, Huet D, Hughey B, Hui V, Husa S, Huttner SH, Huxford R, Huynh-Dinh T, Idzkowski B, Iess A, Inchauspe H, Ingram C, Intini G, Isac JM, Isi M, Iyer BR, Jacqmin T, Jadhav SJ, Jadhav SP, James AL, Jani K, Janthalur NN, Jaranowski P, Jariwala D, Jaume R, Jenkins AC, Jiang J, Johns GR, Johnson-McDaniel NK, Jones AW, Jones DI, Jones JD, Jones P, Jones R, Jonker RJG, Ju L, Junker J, Kalaghatgi CV, Kalogera V, Kamai B, Kandhasamy S, Kang G, Kanner JB, Kapadia SJ, Karki S, Kashyap R, Kasprzack M, Kastaun W, Katsanevas S, Katsavounidis E, Katzman W, Kaufer S, Kawabe K, Kéfélian F, Keitel D, Keivani A, Kennedy R, Key JS, Khadka S, Khalili FY, Khan I, Khan S, Khan ZA, Khazanov EA, Khetan N, Khursheed M, Kijbunchoo N, Kim C, Kim GJ, Kim JC, Kim K, Kim W, Kim WS, Kim YM, Kimball C, King PJ, Kinley-Hanlon M, Kirchhoff R, Kissel JS, Kleybolte L, Klimenko S, Knowles TD, Knyazev E, Koch P, Koehlenbeck SM, Koekoek G, Koley S, Kondrashov V, Kontos A, Koper N, Korobko M, Korth WZ, Kovalam M, Kozak DB, Kringel V, Krishnendu NV, Królak A, Krupinski N, Kuehn G, Kumar A, Kumar P, Kumar R, Kumar R, Kumar S, Kuo L, Kutynia A, Lackey BD, Laghi D, Lalande E, Lam TL, Lamberts A, Landry M, Lane BB, Lang RN, Lange J, Lantz B, Lanza RK, La Rosa I, Lartaux-Vollard A, Lasky PD, Laxen M, Lazzarini A, Lazzaro C, Leaci P, Leavey S, Lecoeuche YK, Lee CH, Lee HM, Lee HW, Lee J, Lee K, Lehmann J, Leroy N, Letendre N, Levin Y, Li AKY, Li J, Li K, Li TGF, Li X, Linde F, Linker SD, Linley JN, Littenberg TB, Liu J, Liu X, Llorens-Monteagudo M, Lo RKL, Lockwood A, London LT, Longo A, Lorenzini M, Loriette V, Lormand M, Losurdo G, Lough JD, Lousto CO, Lovelace G, Lück H, Lumaca D, Lundgren AP, Ma Y, Macas R, Macfoy S, MacInnis M, Macleod DM, MacMillan IAO, Macquet A, Magaña Hernandez I, Magaña-Sandoval F, Magee RM, Majorana E, Maksimovic I, Malik A, Man N, Mandic V, Mangano V, Mansell GL, Manske M, Mantovani M, Mapelli M, Marchesoni F, Marion F, Márka S, Márka Z, Markakis C, Markosyan AS, Markowitz A, Maros E, Marquina A, Marsat S, Martelli F, Martin IW, Martin RM, Martinez V, Martynov DV, Masalehdan H, Mason K, Massera E, Masserot A, Massinger TJ, Masso-Reid M, Mastrogiovanni S, Matas A, Matichard F, Mavalvala N, Maynard E, McCann JJ, McCarthy R, McClelland DE, McCormick S, McCuller L, McGuire SC, McIsaac C, McIver J, McManus DJ, McRae T, McWilliams ST, Meacher D, Meadors GD, Mehmet M, Mehta AK, Mejuto Villa E, Melatos A, Mendell G, Mercer RA, Mereni L, Merfeld K, Merilh EL, Merritt JD, Merzougui M, Meshkov S, Messenger C, Messick C, Metzdorff R, Meyers PM, Meylahn F, Mhaske A, Miani A, Miao H, Michaloliakos I, Michel C, Middleton H, Milano L, Miller AL, Millhouse M, Mills JC, Milotti E, Milovich-Goff MC, Minazzoli O, Minenkov Y, Mishkin A, Mishra C, Mistry T, Mitra S, Mitrofanov VP, Mitselmakher G, Mittleman R, Mo G, Mogushi K, Mohapatra SRP, Mohite SR, Molina-Ruiz M, Mondin M, Montani M, Moore CJ, Moraru D, Morawski F, Moreno G, Morisaki S, Mours B, Mow-Lowry CM, Mozzon S, Muciaccia F, Mukherjee A, Mukherjee D, Mukherjee S, Mukherjee S, Mukund N, Mullavey A, Munch J, Muñiz EA, Murray PG, Nagar A, Nardecchia I, Naticchioni L, Nayak RK, Neil BF, Neilson J, Nelemans G, Nelson TJN, Nery M, Neunzert A, Ng KY, Ng S, Nguyen C, Nguyen P, Nichols D, Nichols SA, Nissanke S, Nitz A, Nocera F, Noh M, North C, Nothard D, Nuttall LK, Oberling J, O'Brien BD, Oganesyan G, Ogin GH, Oh JJ, Oh SH, Ohme F, Ohta H, Okada MA, Oliver M, Olivetto C, Oppermann P, Oram RJ, O'Reilly B, Ormiston RG, Ortega LF, O'Shaughnessy R, Ossokine S, Osthelder C, Ottaway DJ, Overmier H, Owen BJ, Pace AE, Pagano G, Page MA, Pagliaroli G, Pai A, Pai SA, Palamos JR, Palashov O, Palomba C, Pan H, Panda PK, Pang PTH, Pankow C, Pannarale F, Pant BC, Paoletti F, Paoli A, Parida A, Parker W, Pascucci D, Pasqualetti A, Passaquieti R, Passuello D, Patricelli B, Payne E, Pearlstone BL, Pechsiri TC, Pedersen AJ, Pedraza M, Pele A, Penn S, Perego A, Perez CJ, Périgois C, Perreca A, Perriès S, Petermann J, Pfeiffer HP, Phelps M, Phukon KS, Piccinni OJ, Pichot M, Piendibene M, Piergiovanni F, Pierro V, Pillant G, Pinard L, Pinto IM, Piotrzkowski K, Pirello M, Pitkin M, Plastino W, Poggiani R, Pong DYT, Ponrathnam S, Popolizio P, Porter EK, Powell J, Prajapati AK, Prasai K, Prasanna R, Pratten G, Prestegard T, Principe M, Prodi GA, Prokhorov L, Punturo M, Puppo P, Pürrer M, Qi H, Quetschke V, Quinonez PJ, Raab FJ, Raaijmakers G, Radkins H, Radulesco N, Raffai P, Rafferty H, Raja S, Rajan C, Rajbhandari B, Rakhmanov M, Ramirez KE, Ramos-Buades A, Rana J, Rao K, Rapagnani P, Raymond V, Razzano M, Read J, Regimbau T, Rei L, Reid S, Reitze DH, Rettegno P, Ricci F, Richardson CJ, Richardson JW, Ricker PM, Riemenschneider G, Riles K, Rizzo M, Robertson NA, Robinet F, Rocchi A, Rodriguez-Soto RD, Rolland L, Rollins JG, Roma VJ, Romanelli M, Romano R, Romel CL, Romero-Shaw IM, Romie JH, Rose CA, Rose D, Rose K, Rosińska D, Rosofsky SG, Ross MP, Rowan S, Rowlinson SJ, Roy PK, Roy S, Roy S, Ruggi P, Rutins G, Ryan K, Sachdev S, Sadecki T, Sakellariadou M, Salafia OS, Salconi L, Saleem M, Salemi F, Samajdar A, Sanchez EJ, Sanchez LE, Sanchis-Gual N, Sanders JR, Santiago KA, Santos E, Sarin N, Sassolas B, Sathyaprakash BS, Sauter O, Savage RL, Savant V, Sawant D, Sayah S, Schaetzl D, Schale P, Scheel M, Scheuer J, Schmidt P, Schnabel R, Schofield RMS, Schönbeck A, Schreiber E, Schulte BW, Schutz BF, Schwarm O, Schwartz E, Scott J, Scott SM, Seidel E, Sellers D, Sengupta AS, Sennett N, Sentenac D, Sequino V, Sergeev A, Setyawati Y, Shaddock DA, Shaffer T, Sharifi S, Shahriar MS, Sharma A, Sharma P, Shawhan P, Shen H, Shikauchi M, Shink R, Shoemaker DH, Shoemaker DM, Shukla K, ShyamSundar S, Siellez K, Sieniawska M, Sigg D, Singer LP, Singh D, Singh N, Singha A, Singhal A, Sintes AM, Sipala V, Skliris V, Slagmolen BJJ, Slaven-Blair TJ, Smetana J, Smith JR, Smith RJE, Somala S, Son EJ, Soni S, Sorazu B, Sordini V, Sorrentino F, Souradeep T, Sowell E, Spencer AP, Spera M, Srivastava AK, Srivastava V, Staats K, Stachie C, Standke M, Steer DA, Steinke M, Steinlechner J, Steinlechner S, Steinmeyer D, Stevenson S, Stocks D, Stops DJ, Stover M, Strain KA, Stratta G, Strunk A, Sturani R, Stuver AL, Sudhagar S, Sudhir V, Summerscales TZ, Sun L, Sunil S, Sur A, Suresh J, Sutton PJ, Swinkels BL, Szczepańczyk MJ, Tacca M, Tait SC, Talbot C, Tanasijczuk AJ, Tanner DB, Tao D, Tápai M, Tapia A, Tapia San Martin EN, Tasson JD, Taylor R, Tenorio R, Terkowski L, Thirugnanasambandam MP, Thomas M, Thomas P, Thompson JE, Thondapu SR, Thorne KA, Thrane E, Tinsman CL, Saravanan TR, Tiwari S, Tiwari S, Tiwari V, Toland K, Tonelli M, Tornasi Z, Torres-Forné A, Torrie CI, Tosta E Melo I, Töyrä D, Travasso F, Traylor G, Tringali MC, Tripathee A, Trovato A, Trudeau RJ, Tsang KW, Tse M, Tso R, Tsukada L, Tsuna D, Tsutsui T, Turconi M, Ubhi AS, Udall R, Ueno K, Ugolini D, Unnikrishnan CS, Urban AL, Usman SA, Utina AC, Vahlbruch H, Vajente G, Valdes G, Valentini M, van Bakel N, van Beuzekom M, van den Brand JFJ, Van Den Broeck C, Vander-Hyde DC, van der Schaaf L, Van Heijningen JV, van Veggel AA, Vardaro M, Varma V, Vass S, Vasúth M, Vecchio A, Vedovato G, Veitch J, Veitch PJ, Venkateswara K, Venugopalan G, Verkindt D, Veske D, Vetrano F, Viceré A, Viets AD, Vinciguerra S, Vine DJ, Vinet JY, Vitale S, Vivanco FH, Vo T, Vocca H, Vorvick C, Vyatchanin SP, Wade AR, Wade LE, Wade M, Walet R, Walker M, Wallace GS, Wallace L, Walsh S, Wang JZ, Wang S, Wang WH, Ward RL, Warden ZA, Warner J, Was M, Watchi J, Weaver B, Wei LW, Weinert M, Weinstein AJ, Weiss R, Wellmann F, Wen L, Weßels P, Westhouse JW, Wette K, Whelan JT, Whiting BF, Whittle C, Wilken DM, Williams D, Willis JL, Willke B, Winkler W, Wipf CC, Wittel H, Woan G, Woehler J, Wofford JK, Wong ICF, Wright JL, Wu DS, Wysocki DM, Xiao L, Yamamoto H, Yang L, Yang Y, Yang Z, Yap MJ, Yazback M, Yeeles DW, Yu H, Yu H, Yuen SHR, Zadrożny AK, Zadrożny A, Zanolin M, Zelenova T, Zendri JP, Zevin M, Zhang J, Zhang L, Zhang T, Zhao C, Zhao G, Zhou M, Zhou Z, Zhu XJ, Zimmerman AB, Zucker ME, Zweizig J. GW190521: A Binary Black Hole Merger with a Total Mass of 150 M_{⊙}. PHYSICAL REVIEW LETTERS 2020; 125:101102. [PMID: 32955328 DOI: 10.1103/physrevlett.125.101102] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/19/2020] [Accepted: 07/09/2020] [Indexed: 06/08/2023]
Abstract
On May 21, 2019 at 03:02:29 UTC Advanced LIGO and Advanced Virgo observed a short duration gravitational-wave signal, GW190521, with a three-detector network signal-to-noise ratio of 14.7, and an estimated false-alarm rate of 1 in 4900 yr using a search sensitive to generic transients. If GW190521 is from a quasicircular binary inspiral, then the detected signal is consistent with the merger of two black holes with masses of 85_{-14}^{+21} M_{⊙} and 66_{-18}^{+17} M_{⊙} (90% credible intervals). We infer that the primary black hole mass lies within the gap produced by (pulsational) pair-instability supernova processes, with only a 0.32% probability of being below 65 M_{⊙}. We calculate the mass of the remnant to be 142_{-16}^{+28} M_{⊙}, which can be considered an intermediate mass black hole (IMBH). The luminosity distance of the source is 5.3_{-2.6}^{+2.4} Gpc, corresponding to a redshift of 0.82_{-0.34}^{+0.28}. The inferred rate of mergers similar to GW190521 is 0.13_{-0.11}^{+0.30} Gpc^{-3} yr^{-1}.
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Jeong YK, Song B, Bae S. Current Status and Challenges of DNA Base Editing Tools. Mol Ther 2020; 28:1938-1952. [PMID: 32763143 PMCID: PMC7474268 DOI: 10.1016/j.ymthe.2020.07.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/01/2020] [Accepted: 07/18/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-mediated DNA base editors, which include cytosine base editors (CBEs) and adenine base editors (ABEs), are promising tools that can induce point mutations at desired sites in a targeted manner to correct or disrupt gene expression. Their high editing efficiency, coupled with their ability to generate a targeted mutation without generating a DNA double-strand break (DSB) or requiring a donor DNA template, suggests that DNA base editors will be useful for treating genetic diseases, among other applications. However, this hope has recently been challenged by the discovery of DNA base editor shortcomings, including off-target DNA editing, the generation of bystander mutations, and promiscuous deamination effects in both DNA and RNA, which arise from the main DNA base editor constituents, a Cas nuclease variant and a deaminase. In this review, we summarize information about the DNA base editors that have been developed to date, introduce their associated potential challenges, and describe current efforts to minimize or mitigate those issues of DNA base editors.
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