Molecular Mechanisms Of Natural Genetic Engineering

(Hedges and Batzer 2005; Kelman and White 2005; Postberg, Heyse et al. 2008; Selmecki, Forche et al. 2010; Deem, Keszthelyi et al. 2011; Levin and Moran 2011)

DNA uptake from the environment

(Davey, Rech et al. 1989; Dubnau 1999; MacFadyen, Chen et al. 2001; Chen 2004; Meibom, Blokesch et al. 2005; Claverys, Prudhomme et al. 2006; Redfield, Findlay et al. 2006; Johnsen, Dubnau et al. 2009; Kovacs, Smits et al. 2009; Maughan and Redfield 2009; Weber-Lotfi, Ibrahim et al. 2009)

Sperm-mediated DNA transfer: (Gandolfi 1998; Chang, Qian et al. 2002; Smith and Spadafora 2005; Yanagimachi 2005; Lavitrano, Busnelli et al. 2006; Spadafora 2007; Navarro, Risco et al. 2008; Spadafora 2008; Garcia-Vazquez, Ruiz et al. 2010)

Intercellular DNA transfer

(Wolff, Malone et al. 1990; Heinemann and Sprague 1991; Sprague 1991; Wang, Goodman et al. 2002; Pappas and Winans 2003; Chung, Vaidya et al. 2006; Rocco and Churchward 2006; Simoes-Barbosa, Arganaraz et al. 2006; Richardson and Palmer 2007; Tsai, Huang et al. 2008; Lai and Lin 2009; Gillespie, Brayton et al. 2010; Hayes, Aoki et al. 2010; Hecht, Nitz et al. 2010; Snir and Trifonov 2010; Zhu and Mahato 2010; Ananiadou, Sullivan et al. 2011; Anderson and Seifert 2011; Babic, Berkmen et al. 2011; Fernandez-Gonzalez, de Paz et al. 2011; Ghinet, Bordeleau et al. 2011; Schroder, Schuelein et al. 2011)

Table III.1. Examples of intercellular and interkingdom DNA transfer

Horizontal transfer mode

Documented transfers

Uptake of environmental and liposomal DNA

Bacteria – bacteria: (Averhoff and Friedrich 2003; Claverys, Prudhomme et al. 2006; Averhoff 2009)

Archaea-archaea: (Bertani and Baresi 1987; Worrell, Nagle et al. 1988); (Cline, Schalkwyk et al. 1989; Patel, Nash et al. 1994; Metcalf, Zhang et al. 1997; Soppa 2006; Almeida, Leszczyniecka et al. 2008; Berkner and Lipps 2008; Soppa, Baumann et al. 2008)

Algal transfection: (Walker, Purton et al. 2005).

Plant – bacteria: (Kay, Vogel et al. 2002; de Vries, Herzfeld et al. 2004)

Plastid transfection: (O'Neill, Horvath et al. 1993)

Mammalian cell transfection: (Wolff and Budker 2005; Khalil, Kogure et al. 2006; Kim and Eberwine 2010) and lipofection: (Felgner 1987; Zuhorn, Kalicharan et al. 2002)

Plant protoplasts: (Potrykus 1990; Davey, Anthony et al. 2005)

Conjugal transfer

Bacteria – bacteria: (Hayes 1968)

Archaea – archaea: (Prangishvili, Albers et al. 1998)

Bacteria – archaea: (Dodsworth, Li et al. 2010)

Bacteria – yeast: (Heinemann and Sprague 1989; Heinemann and Sprague 1991)

Bacteria – plant: (Chilton 1983; Winans 1992; Broothaerts, Mitchell et al. 2005)

Bacteria – animal: (Schroder, Schuelein et al. 2011)

Viral transduction and GTAs (gene transfer agents)

 

Bacteria – bacteria: (Stanton 2007; McDaniel, Young et al. 2010)

Archaea-archaea: (Meile, Abendschein et al. 1990; Bertani 1999); (Zillig, Prangishvilli et al. 1996; Eiserling, Pushkin et al. 1999; Prangishvili 2003; Snyder, Stedman et al. 2003; Prangishvili and Garrett 2005; Prangishvili, Forterre et al. 2006; Prangishvili, Garrett et al. 2006)

Bacteria – plant: (Chung, Vaidya et al. 2006)

Animal cell – animal cell: (El-Aneed 2004)

Animal cell – virus: (Filee, Pouget et al. 2008)

direct fusion of cells or protoplasts that lack a rigid outer covering.

Bacteria-bacteria: (Schaeffer, Cami et al. 1976; Hopwood, Wright et al. 1977; Patnaik, Louie et al. 2002; Dai, Ziesman et al. 2005)

Mammal-mammal: (Ramos, Bonenfant et al. 2002; Trontelj, Usaj et al. 2010; Yamanaka and Blau 2010)

Plant-plant: (Gamborg and Holl 1977; Binding, Krumbiegel-Schroeren et al. 1986; Nehls, Krumbiegel-Schroeren et al. 1986; Potrykus 1990; Fahleson and Glimelius 1999; Davey, Anthony et al. 2005; Poma, Limongi et al. 2006; Savitha, Sadhasivam et al. 2010)

Parasitic or endosymbiotic association

Plant – fern: (Davis, Anderson et al. 2005)

Plant – plant: (Davis and Wurdack 2004) (Mower, Stefanovic et al. 2004)

Bacteria – invertebrate: (Hotopp, Clark et al. 2007; Nikoh, Tanaka et al. 2008; Nikoh and Nakabachi 2009)

Undetermined mechanism

Archaea – bacteria: (Koonin, Makarova et al. 2001)

Bacteria – fungus: (Belbahri, Calmin et al. 2008)

Bacteria – protist: (Huang, Mullapudi et al. 2004; Stechmann, Baumgartner et al. 2006; Whitaker, McConkey et al. 2009)

Archaea – protist: (Andersson, Sarchfield et al. 2005; Huang, Xu et al. 2005)

Protist – protist: (Andersson 2005; Andersson, Sarchfield et al. 2005; Andersson, Hirt et al. 2006; Andersson, Sjogren et al. 2007; Andersson 2009; Andersson 2009)

 

Intercellular RNA transfer

(Lotvall and Valadi 2007; Smalheiser 2007; Lai and Lin 2009; Westwood, Roney et al. 2009; Eldh, Ekstrom et al. 2010; Rudzinski and Aminabhavi 2010; Shim and Kwon 2010; Zhu and Mahato 2010; Zomer, Vendrig et al. 2010; Diken, Kreiter et al. 2011; Shegokar, Al Shaal et al. 2011; Yuan, Naguib et al. 2011)

            Exosomes: (Boss and Renne 2010; Mathivanan, Ji et al. 2010; Pegtel, Cosmopoulos et al. 2010; Pegtel, van de Garde et al. 2011; Ramachandran and Palanisamy 2011)

            Viral packaging of cell RNAs: (Jorgensen, Nielsen et al. 2009; Amen and Griffiths 2011)

Intercellular protein (and prion) transfer

(Maruyama and Hartl 1991; Hunter 2006; Smalheiser 2007; Eggenberger, Birtalan et al. 2009; Gousset, Schiff et al. 2009; Gousset and Zurzolo 2009; Chen, Bruce et al. 2010; Afanasieva, Kushnirov et al. 2011; Dubey and Ben-Yehuda 2011; Dupont, Prochiantz et al. 2011; Eggenberger, Mink et al. 2011; Lindgren and Langel 2011; Beringue, Herzog et al. 2012)

            Type I-VI and nanotube transfer/secretion systems: (Ball, Durand et al. 2002; Cascales and Christie 2003; Delepelaire 2004; Filloux 2004; Jacob-Dubuisson, Fernandez et al. 2004; Christie, Atmakuri et al. 2005; Cianciotto 2005; Angkawidjaja and Kanaya 2006; Buttner and Bonas 2006; Cornelis 2006; Desvaux, Cooper et al. 2006; Dautin and Bernstein 2007; Juhas, Crook et al. 2008; Krehenbrink and Downie 2008; Rossier, Dao et al. 2008; Senf, Tommassen et al. 2008; Alvarez-Martinez and Christie 2009; Boyer, Fichant et al. 2009; Deakin and Broughton 2009; Durand, Verger et al. 2009; Filloux 2009; Pukatzki, McAuley et al. 2009; Tseng, Tyler et al. 2009; Bleves, Viarre et al. 2010; Marlovits and Stebbins 2010; Masi and Wandersman 2010; Rego, Chandran et al. 2010; Salacha, Kovacic et al. 2010; Ananiadou, Sullivan et al. 2011; Dubey and Ben-Yehuda 2011; Ficht 2011; Filloux 2011)

Mutator trans-lesion polymerases and point mutations

(Maenhaut-Michel, Janel-Bintz et al. 1992; Wagner, Gruz et al. 1999; Godoy, Gizatullin et al. 2000; Napolitano, Janel-Bintz et al. 2000; Fuchs, Koffel-Schwartz et al. 2001; Pham, Rangarajan et al. 2001; Goodman 2002; Wagner, Etienne et al. 2002; Fuchs, Fujii et al. 2004; Tippin, Pham et al. 2004; Schlacher, Pham et al. 2006; Yamada, Nunoshiba et al. 2006; Fuchs and Fujii 2007; Fujii and Fuchs 2007; Godoy, Jarosz et al. 2007; Sundin and Weigand 2007; Cohen, Godoy et al. 2009; Jiang, Karata et al. 2009; Koskiniemi and Andersson 2009; Waters, Minesinger et al. 2009; Garcia-Villada and Drake 2010; Koskiniemi, Hughes et al. 2010; Patel, Jiang et al. 2010; Benson, Norton et al. 2011; Herr, Ogawa et al. 2011; Herr, Williams et al. 2011; Sladewski, Hetrick et al. 2011)

Homology-dependent recombination (HR)

(Myers and Stahl 1994; Takahashi and Norden 1994; Kuzminov 1999; Jakupciak and Wells 2000; Kowalczykowski 2000; Seitz, Haseltine et al. 2001; Lusetti and Cox 2002; Rong and Golic 2003; Miyazaki, Bressan et al. 2004; Nishant and Rao 2006; Pacher, Schmidt-Puchta et al. 2007; Argueso, Westmoreland et al. 2008; Dillingham and Kowalczykowski 2008; Frankenberg-Schwager, Becker et al. 2008; Karboul, Mazza et al. 2008; Naranjo and Corredor 2008; San Filippo, Sung et al. 2008; Wang and Maier 2008; Beucher, Birraux et al. 2009; Handa, Morimatsu et al. 2009; Lisby and Rothstein 2009; Hicks, Kim et al. 2010; Hoang, Tan et al. 2010; Manthey and Bailis 2010; Szekvolgyi and Nicolas 2010; Wahls and Davidson 2010; Daniel, Lange et al. 2011; Grey, Sommermeyer et al. 2011; Holloman 2011; Lange, Pan et al. 2011; Tang, Dominska et al. 2011)

Microhomology-dependent and single-strand annealing (SSA) break repair

(Wu, Sugiyama et al. 2006; Yamada-Inagawa, Klar et al. 2007; Frankenberg-Schwager, Becker et al. 2008; Hastings, Ira et al. 2009; Manthey, Naik et al. 2009; Letsolo, Rowson et al. 2010; Pannunzio, Manthey et al. 2010; Pannunzio, Manthey et al. 2010; Yu and McVey 2010; Chiarle, Zhang et al. 2011; Glover, Jun et al. 2011)

Non-homologous end-joining (NHEJ)

(Wilson and Lieber 1999; Dudasova, Dudas et al. 2004; Pitcher, Wilson et al. 2005; Bowater and Doherty 2006; Meaburn, Misteli et al. 2007; Pacher, Schmidt-Puchta et al. 2007; Pitcher, Brissett et al. 2007; Bennardo, Cheng et al. 2008; Chan, Galli et al. 2008; Frankenberg-Schwager, Becker et al. 2008; Malyarchuk, Castore et al. 2008; McVey and Lee 2008; Schulte-Uentrop, El-Awady et al. 2008; Wu, Topper et al. 2008; Yano and Chen 2008; Brissett and Doherty 2009; Mahaney, Meek et al. 2009; Mimitou and Symington 2009; Yano, Morotomi-Yano et al. 2009; Yano, Morotomi-Yano et al. 2009; Rupnik, Lowndes et al. 2010; Williams, Lees-Miller et al. 2010; Garcia, Phelps et al. 2011; Lowden, Flibotte et al. 2011; Mladenov and Iliakis 2011; Ogiwara and Kohno 2011; Stracker and Petrini 2011)

Site-specific recombination

(Murray 1987; Goodwin and Poulter 2001; Radman-Livaja, Shaw et al. 2003; Goodwin, Poulter et al. 2004; Groth and Calos 2004; Draper, Cesar et al. 2005; Kobryn and Chaconas 2005; Poulter and Goodwin 2005; Cesar and Llosa 2007; Piednoel and Bonnivard 2009; Rajeev, Malanowska et al. 2009; Rowe-Magnus 2009; Rice, Mouw et al. 2010; Smith, Brown et al. 2010; Vanhooff, Normand et al. 2010; Agundez, Machon et al. 2011; Kojima and Jurka 2011)

Integrons

(Hall and Stokes 1993; Vaisvila, Morgan et al. 2001; Fluit and Schmitz 2004; Gillings, Holley et al. 2005; Labbate, Case et al. 2009)

DNA Transpsosons

(McClintock 1987; Georgiev, Tikhomirova et al. 1997; Kempken and Kuck 1998; Haren, Ton-Hoang et al. 1999; Berger and Haas 2001; Duval-Valentin, Marty-Cointin et al. 2004; Gueguen, Rousseau et al. 2005; Liu, Crellin et al. 2005; Kapitonov and Jurka 2006; Menzel, Dechyeva et al. 2006; Pomerantseva, Biryukova et al. 2006; Brillet, Bigot et al. 2007; Wicker, Sabot et al. 2007; Brazelton and Baross 2009; Aziz, Breitbart et al. 2010; Claeys Bouuaert and Chalmers 2010; Ivics and Izsvak 2010; Ling and Cordaux 2010; Marquez and Pritham 2010; Momose, Abe et al. 2010; Munoz-Lopez and Garcia-Perez 2010; Pajunen, Rasila et al. 2010; Bardaji, Anorga et al. 2011; Demattei, Hedhili et al. 2011; Flutre, Duprat et al. 2011; Kojima and Jurka 2011; Montano and Rice 2011; Novick, Smith et al. 2011; Siddique, Buisine et al. 2011; Thomas, Sorourian et al. 2011)

LTR retrotransposons and retroviruses

(Errede, Company et al. 1985; Company and Errede 1987; Company and Errede 1988; Errede and Ammerer 1989; Haren, Ton-Hoang et al. 1999; Martin, Herniou et al. 1999; Goodwin and Poulter 2001; Tam, Hughes et al. 2002; Gifford and Tristem 2003; Goodwin, Poulter et al. 2004; Gifford, Kabat et al. 2005; Lewinski and Bushman 2005; Poulter and Goodwin 2005; Kejnovsky, Kubat et al. 2006; Katzourakis, Tristem et al. 2007; Morrish, Garcia-Perez et al. 2007; Delelis, Carayon et al. 2008; Eiden 2008; Faye, Arnaud et al. 2008; Gifford, Katzourakis et al. 2008; Hizi 2008; Zolotukhin, Schneider et al. 2008; Blomberg, Benachenhou et al. 2009; Cordaux and Batzer 2009; Gilbert, Maxfield et al. 2009; Jaratlerdsiri, Rodriguez-Zarate et al. 2009; Katzourakis, Gifford et al. 2009; Piednoel and Bonnivard 2009; Goldstone, Yap et al. 2010; Hou, Rajagopal et al. 2010; Kozak 2010; Silverman, Nguyen et al. 2010; van der Kuyl, Cornelissen et al. 2010; Yan, Liu et al. 2010; Dewannieux, Vernochet et al. 2011; Flutre, Duprat et al. 2011; Montano and Rice 2011; Neumann, Navratilova et al. 2011; Paprotka, Delviks-Frankenberry et al. 2011)

Non-LTR retrotransposons (SINEs, LINEs and retrotransposed RNAs)

(Bhattacharya, Bakre et al. 2002; Ohshima, Hattori et al. 2003; Dewannieux and Heidmann 2005; Ohshima and Okada 2005; Zingler, Willhoeft et al. 2005; Ding, Lin et al. 2006; Simoes-Barbosa, Arganaraz et al. 2006; Garcia-Perez, Doucet et al. 2007; Luo and Li 2007; Nishihara and Okada 2008; Dong, Poulter et al. 2009; Khazina and Weichenrieder 2009; Kroutter, Belancio et al. 2009; Fujii 2010; Konkel and Batzer 2010; Flutre, Duprat et al. 2011)

            LINE: (Picard 1976; Fawcett, Lister et al. 1986; Sezutsu, Nitasaka et al. 1995; Pickeral, Makalowski et al. 2000; Yu, Zingler et al. 2001; Gilbert, Lutz-Prigge et al. 2002; Moran and Gilbert 2002; Morrish, Gilbert et al. 2002; Lutz, Vincent et al. 2003; Kale, Moore et al. 2005; Kulpa and Moran 2005; Martin, Cruceanu et al. 2005; Martin, Li et al. 2005; Zingler, Willhoeft et al. 2005; Babushok and Kazazian 2007; Garcia-Perez 2007; Garcia-Perez, Doucet et al. 2007; Gogvadze, Barbisan et al. 2007; Goodier, Zhang et al. 2007; Morrish, Garcia-Perez et al. 2007; Perrin, Ballestar et al. 2007; Perrin, Ballestar et al. 2007; Ramos, He et al. 2007; Repanas, Zingler et al. 2007; Yamamoto, Toyota et al. 2008; Dong, Poulter et al. 2009; Suzuki, Yamaguchi et al. 2009; Bao and Jurka 2010; Beck, Collier et al. 2010; Belancio, Roy-Engel et al. 2010; Doucet, Hulme et al. 2010; Doucet, Hulme et al. 2010; Han 2010; Kojima 2010; Rouchka, Montoya-Durango et al. 2010; Yoshitake, Aoyagi et al. 2010; Khazina, Truffault et al. 2011; Thompson and Christensen 2011)

            Alu: (Yu, Zingler et al. 2001; Kolomietz, Meyn et al. 2002; Ricci, Regis et al. 2003; Athanasiadis, Rich et al. 2004; McNeil 2004; Callinan, Wang et al. 2005; Zingler, Willhoeft et al. 2005; Chen, Ferec et al. 2007; Bennett, Keller et al. 2008; Wallace, Wagstaff et al. 2008; Srikanta, Sen et al. 2009; Srikanta, Sen et al. 2009)

            SVA: (Ostertag, Goodier et al. 2003; Wang, Xing et al. 2005; Bantysh and Buzdin 2009; Damert, Raiz et al. 2009; Hancks, Ewing et al. 2009; Hancks and Kazazian 2010; Hancks, Goodier et al. 2011; Raiz, Damert et al. 2011)

RNA processing and retroelements

(Merendino, Perron et al. 2006; Mougel, Houzet et al. 2009; Galligan, Marchetti et al. 2011)

            Diversity-generating retroelements (DGRs) (Doulatov, Hodes et al. 2004; Medhekar and Miller 2007; Guo, Tse et al. 2008; Miller, Le Coq et al. 2008; Guo, Tse et al. 2011)

Retroinserting group II introns

(Lazowska, Meunier et al. 1994; Zimmerly, Moran et al. 1999; Centron and Roy 2002; Dai and Zimmerly 2002; Podar, Mullineaux et al. 2002; Dai and Zimmerly 2003; Mohr and Lambowitz 2003; Munoz-Adelantado, San Filippo et al. 2003; Schafer, Gan et al. 2003; Odom, Shenkenberg et al. 2004; Noah, Park et al. 2006; Nisa-Martinez, Jimenez-Zurdo et al. 2007; Stabell, Tourasse et al. 2007; Simon, Clarke et al. 2008; Tourasse and Kolsto 2008; Valles, Halanych et al. 2008; Kroeger, Watkins et al. 2009; Zhuang, Mastroianni et al. 2009; Mullineux, Costa et al. 2010; Pyle 2010; Tourasse, Stabell et al. 2010; Chillon, Martinez-Abarca et al. 2011; Huang, Shaikh et al. 2011; Leclercq, Giraud et al. 2011)

Agrobacterium T-DNA insertion in plant chromosomes

(Zupan and Zambryski 1995; Zupan, Muth et al. 2000; Pelczar, Kalck et al. 2004; Tzfira and Citovsky 2006; Muller, Atkinson et al. 2007; Boyko, Matsuoka et al. 2009; Lacroix and Citovsky 2009)

Inteins, group I introns and homing endonucleases

(Gimble 2000; Pietrokovski 2001; Ko, Choi et al. 2002; Perler 2002; Stoddard 2005; Tourasse and Kolsto 2008; Bonocora and Shub 2009; Dassa, London et al. 2009; Edgell 2009; Nielsen and Johansen 2009; Singh, Tripathi et al. 2009; Marcaida, Munoz et al. 2010; Callahan, Topilina et al. 2011; Edgell, Chalamcharla et al. 2011)

Amplifications

(Von Hoff 1991; Hastings, Slack et al. 2004; Hersh, Ponder et al. 2004; Roth and Andersson 2004; Kejnovsky, Kubat et al. 2006; Slack, Thornton et al. 2006; Hastings 2007; Pritham and Feschotte 2007; Raman and Stopfer 2008; Andersson and Hughes 2009; Tanaka and Yao 2009; Brewer, Payen et al. 2011)

Fragile sites

(Le Beau 1986; Yunis 1987; Moriarty and Webster 2003; Ishii and Furukawa 2004; Arlt, Durkin et al. 2006; Glover 2006; O'Keefe and Richards 2006; Durkin and Glover 2007; Ruiz-Herrera and Robinson 2007; Pichiorri, Ishii et al. 2008; Burrow, Williams et al. 2009; Di Rienzi, Collingwood et al. 2009; Gericke 2010)

Topoisomerases and helicases

(Lippert, Kim et al. 2011; Mischo, Gomez-Gonzalez et al. 2011; Takahashi, Burguiere-Slezak et al. 2011)

Synthetic in vivo genetic engineering

(Aagaard, Leviev et al. 1996; Reilly and Silva 1996; Guo, Karberg et al. 2000; Kolkman and Stemmer 2001; Court, Sawitzke et al. 2002; Lyznik, Gordon-Kamm et al. 2003; Poteete, Fenton et al. 2004; Jones, Kierlin et al. 2005; Rawsthorne, Turner et al. 2006; Cui and Davis 2007; Yao and Lambowitz 2007; Abalakina, Tokmakova et al. 2008; Mueller, Coleman et al. 2009; Pedersen and Phillips 2009; Pennisi 2009; Arber 2010; Grabundzija, Irgang et al. 2010; Ivics and Izsvak 2010; Marton, Zuker et al. 2010; van Boxtel and Cuppen 2010; Wei, Shi et al. 2010; Akhverdyan, Gak et al. 2011; Carroll 2011; Cui, Ji et al. 2011; Esvelt, Carlson et al. 2011; Hockemeyer, Wang et al. 2011; Huang, Ashton et al. 2011; Miller, Tan et al. 2011; Nern, Pfeiffer et al. 2011; Turan, Galla et al. 2011; Venken, Schulze et al. 2011; Zhang, Cong et al. 2011)

Genome Biology, Volume 8 Supplement 1, 2007, “Transposons in vertebrate functional genomics”: http://genomebiology.com/supplements/8/S1

 

Somatic cell diversification by movement of transposable elements

(Sheen, Sherry et al. 2000; Lutz, Vincent et al. 2003; Garcia-Perez 2007; Beck, Collier et al. 2010; Belancio, Roy-Engel et al. 2010; Singer, McConnell et al. 2010; St Laurent, Hammell et al. 2010; Baillie, Barnett et al. 2011)

 

REFERENCES

 

Aagaard, C., I. Leviev, et al. (1996). "General vectors for archaeal hyperthermophiles: strategies based on a mobile\ intron and a plasmid." FEMS Microbiol Rev\ 18\(2-3\): 93-104\. http://www.ncbi.nlm.nih.gov/pubmed/8639332\.

Abalakina, E. G., I. L. Tokmakova, et al. (2008). "Phage Mu-driven two-plasmid system for integration of recombinant DNA in the Methylophilus methylotrophus genome." Appl Microbiol Biotechnol 81(1): 191-200. http://www.ncbi.nlm.nih.gov/pubmed/18820908.

Afanasieva, E. G., V. V. Kushnirov, et al. (2011). "Molecular basis for transmission barrier and interference between closely related prion proteins in yeast." J Biol Chem 286(18): 15773-15780. http://www.ncbi.nlm.nih.gov/pubmed/21454674.

Agundez, L., C. Machon, et al. (2011). "Nuclear targeting of a bacterial integrase that mediates site-specific recombination between bacterial and human target sequences." Appl Environ Microbiol 77(1): 201-210. http://www.ncbi.nlm.nih.gov/pubmed/21037296.

Akhverdyan, V. Z., E. R. Gak, et al. (2011). "Application of the bacteriophage Mu-driven system for the integration/amplification of target genes in the chromosomes of engineered Gram-negative bacteria--mini review." Appl Microbiol Biotechnol 91(4): 857-871. http://www.ncbi.nlm.nih.gov/pubmed/21698377.

Almeida, F. C., M. Leszczyniecka, et al. (2008). "Examining Ancient Inter-domain Horizontal Gene Transfer." Evol Bioinform Online 4: 109-119. http://www.ncbi.nlm.nih.gov/pubmed/19204812.

Alvarez-Martinez, C. E. and P. J. Christie (2009). "Biological diversity of prokaryotic type IV secretion systems." Microbiol Mol Biol Rev 73(4): 775-808. http://www.ncbi.nlm.nih.gov/pubmed/19946141.

Amen, M. A. and A. Griffiths (2011). "Packaging of non-coding RNAs into herpesvirus virions: comparisons to coding RNAs." Front. Gene 2: 81. .

Ananiadou, S., D. Sullivan, et al. (2011). "Named entity recognition for bacterial Type IV secretion systems." PLoS One 6(3): e14780. http://www.ncbi.nlm.nih.gov/pubmed/21468321.

Anderson, M. T. and H. S. Seifert (2011). "Opportunity and means: horizontal gene transfer from the human host to a bacterial pathogen." MBio 2(1). http://www.ncbi.nlm.nih.gov/pubmed/21325040.

Andersson, D. I. and D. Hughes (2009). "Gene amplification and adaptive evolution in bacteria." Annu Rev Genet\ 43\: 167-195\. http://www.ncbi.nlm.nih.gov/pubmed/19686082\.

Andersson, J. O. (2005). "Lateral gene transfer in eukaryotes." Cell Mol Life Sci 62(11): 1182-1197. http://www.ncbi.nlm.nih.gov/pubmed/15761667.

Andersson, J. O. (2009). "Gene transfer and diversification of microbial eukaryotes." Annu Rev Microbiol 63: 177-193. http://www.ncbi.nlm.nih.gov/pubmed/19575565.

Andersson, J. O. (2009). "Horizontal gene transfer between microbial eukaryotes." Methods Mol Biol 532: 473-487. http://www.ncbi.nlm.nih.gov/pubmed/19271202.

Andersson, J. O., R. P. Hirt, et al. (2006). "Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes." BMC Evol Biol 6: 27. http://www.ncbi.nlm.nih.gov/pubmed/16551352.

Andersson, J. O., S. W. Sarchfield, et al. (2005). "Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids." Mol Biol Evol 22(1): 85-90. http://www.ncbi.nlm.nih.gov/pubmed/15356278.

Andersson, J. O., A. M. Sjogren, et al. (2007). "A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution." BMC Genomics 8: 51. http://www.ncbi.nlm.nih.gov/pubmed/17298675.

Angkawidjaja, C. and S. Kanaya (2006). "Family I.3 lipase: bacterial lipases secreted by the type I secretion system." Cell Mol Life Sci 63(23): 2804-2817. http://www.ncbi.nlm.nih.gov/pubmed/17103114.

Arber, W. (2010). "Genetic engineering compared to natural genetic variations." N Biotechnol 27(5): 517-521. http://www.ncbi.nlm.nih.gov/pubmed/20472106.

Argueso, J. L., J. Westmoreland, et al. (2008). "Double-strand breaks associated with repetitive DNA can reshape the genome." Proc Natl Acad Sci U S A 105(33): 11845-11850. http://www.ncbi.nlm.nih.gov/pubmed/18701715.

Arlt, M. F., S. G. Durkin, et al. (2006). "Common fragile sites as targets for chromosome rearrangements." DNA Repair (Amst) 5(9-10): 1126-1135. http://www.ncbi.nlm.nih.gov/pubmed/16807141.

Athanasiadis, A., A. Rich, et al. (2004). "Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome." PLoS Biol\ 2\(12\): e391\. http://www.ncbi.nlm.nih.gov/pubmed/15534692\.

Averhoff, B. (2009). "Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilus." FEMS Microbiol Rev 33(3): 611-626. http://www.ncbi.nlm.nih.gov/pubmed/19207744.

Averhoff, B. and A. Friedrich (2003). "Type IV pili-related natural transformation systems: DNA transport in mesophilic and thermophilic bacteria." Arch Microbiol 180(6): 385-393. http://www.ncbi.nlm.nih.gov/pubmed/14593449.

Aziz, R. K., M. Breitbart, et al. (2010). "Transposases are the most abundant, most ubiquitous genes in nature." Nucleic Acids Res 38(13): 4207-4217. http://www.ncbi.nlm.nih.gov/pubmed/20215432.

Babic, A., M. B. Berkmen, et al. (2011). "Efficient gene transfer in bacterial cell chains." MBio 2(2). http://www.ncbi.nlm.nih.gov/pubmed/21406598.

Babushok, D. V. and H. H. Kazazian, Jr. (2007). "Progress in understanding the biology of the human mutagen LINE-1." Hum Mutat 28(6): 527-539. http://www.ncbi.nlm.nih.gov/pubmed/17309057.

Baillie, J. K., M. W. Barnett, et al. (2011). "Somatic retrotransposition alters the genetic landscape of the human brain." Nature. http://www.ncbi.nlm.nih.gov/pubmed/22037309.

Ball, G., E. Durand, et al. (2002). "A novel type II secretion system in Pseudomonas aeruginosa." Mol Microbiol 43(2): 475-485. http://www.ncbi.nlm.nih.gov/pubmed/11985723.

Bantysh, O. B. and A. A. Buzdin (2009). "Novel Family of Human Transposable Elements Formed Due to Fusion of the First Exon of Gene MAST2 with Retrotransposon SVA." Biochemistry (Mosc) 74(12): 1393-1399. http://www.ncbi.nlm.nih.gov/pubmed/19961423.

Bao, W. and J. Jurka (2010). "Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1)." Gene 465(1-2): 9-16. http://www.ncbi.nlm.nih.gov/pubmed/20600705.

Bardaji, L., M. Anorga, et al. (2011). "Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola." PLoS One 6(10): e25773. http://www.ncbi.nlm.nih.gov/pubmed/22016774.

Beck, C. R., P. Collier, et al. (2010). "LINE-1 retrotransposition activity in human genomes." Cell\ 141\(7\): 1159-1170\. http://www.ncbi.nlm.nih.gov/pubmed/20602998\.

Belancio, V. P., A. M. Roy-Engel, et al. (2010). "Somatic expression of LINE-1 elements in human tissues." Nucleic Acids Res\ 38\(12\): 3909-3922\. http://www.ncbi.nlm.nih.gov/pubmed/20215437\.

Belbahri, L., G. Calmin, et al. (2008). "Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor." Gene 408(1-2): 1-8. http://www.ncbi.nlm.nih.gov/pubmed/18024004.

Bennardo, N., A. Cheng, et al. (2008). "Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair." PLoS Genet 4(6): e1000110. http://www.ncbi.nlm.nih.gov/pubmed/18584027.

Bennett, E. A., H. Keller, et al. (2008). "Active Alu retrotransposons in the human genome." Genome Res\ 18\(12\): 1875-1883\. http://www.ncbi.nlm.nih.gov/pubmed/18836035\.

Benson, R. W., M. D. Norton, et al. (2011). "An Active Site Aromatic Triad in Escherichia coli DNA Pol IV Coordinates Cell Survival and Mutagenesis in Different DNA Damaging Agents." PLoS One 6(5): e19944. http://www.ncbi.nlm.nih.gov/pubmed/21614131.

Berger, B. and D. Haas (2001). "Transposase and cointegrase: specialized transposition proteins of the bacterial insertion sequence IS21 and related elements." Cell Mol Life Sci 58(3): 403-419. http://www.ncbi.nlm.nih.gov/pubmed/11315188.

Beringue, V., L. Herzog, et al. (2012). "Facilitated cross-species transmission of prions in extraneural tissue." Science 335(6067): 472-475. http://www.ncbi.nlm.nih.gov/pubmed/22282814.

Berkner, S. and G. Lipps (2008). "Genetic tools for Sulfolobus spp.: vectors and first applications." Arch Microbiol 190(3): 217-230. http://www.ncbi.nlm.nih.gov/pubmed/18542925.

Bertani, G. (1999). "Transduction-like gene transfer in the methanogen Methanococcus voltae." J Bacteriol 181(10): 2992-3002. http://www.ncbi.nlm.nih.gov/pubmed/10321998.

Bertani, G. and L. Baresi (1987). "Genetic transformation in the methanogen Methanococcus voltae PS." J Bacteriol 169(6): 2730-2738. http://www.ncbi.nlm.nih.gov/pubmed/3034867.

Beucher, A., J. Birraux, et al. (2009). "ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2." Embo J 28(21): 3413-3427. http://www.ncbi.nlm.nih.gov/pubmed/19779458.

Bhattacharya, S., A. Bakre, et al. (2002). "Mobile genetic elements in protozoan parasites." J Genet 81(2): 73-86. http://www.ncbi.nlm.nih.gov/pubmed/12532039.

Binding, H., G. Krumbiegel-Schroeren, et al. (1986). "Protoplast fusion and early development of fusants." Results Probl Cell Differ 12: 37-66. http://www.ncbi.nlm.nih.gov/pubmed/3529271.

Bleves, S., V. Viarre, et al. (2010). "Protein secretion systems in Pseudomonas aeruginosa: A wealth of pathogenic weapons." Int J Med Microbiol 300(8): 534-543. http://www.ncbi.nlm.nih.gov/pubmed/20947426.

Blomberg, J., F. Benachenhou, et al. (2009). "Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations." Gene 448(2): 115-123. http://www.ncbi.nlm.nih.gov/pubmed/19540319.

Bonocora, R. P. and D. A. Shub (2009). "A likely pathway for formation of mobile group I introns." Curr Biol 19(3): 223-228. http://www.ncbi.nlm.nih.gov/pubmed/19200727.

Boss, I. W. and R. Renne (2010). "Viral miRNAs: tools for immune evasion." Curr Opin Microbiol 13(4): 540-545. http://www.ncbi.nlm.nih.gov/pubmed/20580307.

Bowater, R. and A. J. Doherty (2006). "Making ends meet: repairing breaks in bacterial DNA by non-homologous end-joining." PLoS Genet 2(2): e8. http://www.ncbi.nlm.nih.gov/pubmed/16518468.

Boyer, F., G. Fichant, et al. (2009). "Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?" BMC Genomics 10: 104. http://www.ncbi.nlm.nih.gov/pubmed/19284603.

Boyko, A., A. Matsuoka, et al. (2009). "High frequency Agrobacterium tumefaciens-mediated plant transformation induced by ammonium nitrate." Plant Cell Rep 28(5): 737-757. http://www.ncbi.nlm.nih.gov/pubmed/19221758.

Brazelton, W. J. and J. A. Baross (2009). "Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm." Isme J 3(12): 1420-1424. http://www.ncbi.nlm.nih.gov/pubmed/19571895.

Brewer, B. J., C. Payen, et al. (2011). "Origin-Dependent Inverted-Repeat Amplification: A Replication-Based Model for Generating Palindromic Amplicons." PLoS Genet 7(3): e1002016. http://www.ncbi.nlm.nih.gov/pubmed/21437266.

Brillet, B., Y. Bigot, et al. (2007). "Assembly of the Tc1 and mariner transposition initiation complexes depends on the origins of their transposase DNA binding domains." Genetica 130(2): 105-120. http://www.ncbi.nlm.nih.gov/pubmed/16912840.

Brissett, N. C. and A. J. Doherty (2009). "Repairing DNA double-strand breaks by the prokaryotic non-homologous end-joining pathway." Biochem Soc Trans 37(Pt 3): 539-545. http://www.ncbi.nlm.nih.gov/pubmed/19442248.

Broothaerts, W., H. J. Mitchell, et al. (2005). "Gene transfer to plants by diverse species of bacteria." Nature 433(7026): 629-633. http://www.ncbi.nlm.nih.gov/pubmed/15703747.

Burrow, A. A., L. E. Williams, et al. (2009). "Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites." BMC Genomics 10: 59. http://www.ncbi.nlm.nih.gov/pubmed/19183484.

Buttner, D. and U. Bonas (2006). "Who comes first? How plant pathogenic bacteria orchestrate type III secretion." Curr Opin Microbiol 9(2): 193-200. http://www.ncbi.nlm.nih.gov/pubmed/16529983.

Callahan, B. P., N. I. Topilina, et al. (2011). "Structure of catalytically competent intein caught in a redox trap with functional and evolutionary implications." Nat Struct Mol Biol 18(5): 630-633. http://www.ncbi.nlm.nih.gov/pubmed/21460844.

Callinan, P. A., J. Wang, et al. (2005). "Alu retrotransposition-mediated deletion." J Mol Biol\ 348\(4\): 791-800\. http://www.ncbi.nlm.nih.gov/pubmed/15843013\.

Carroll, D. (2011). "Genome engineering with zinc-finger nucleases." Genetics 188(4): 773-782. http://www.ncbi.nlm.nih.gov/pubmed/21828278.

Cascales, E. and P. J. Christie (2003). "The versatile bacterial type IV secretion systems." Nat Rev Microbiol 1(2): 137-149. http://www.ncbi.nlm.nih.gov/pubmed/15035043.

Centron, D. and P. H. Roy (2002). "Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion." Antimicrob Agents Chemother 46(5): 1402-1409. http://www.ncbi.nlm.nih.gov/pubmed/11959575.

Cesar, C. E. and M. Llosa (2007). "TrwC-mediated site-specific recombination is controlled by host factors altering local DNA topology." J Bacteriol 189(24): 9037-9043. http://www.ncbi.nlm.nih.gov/pubmed/17921309.

Chan, C. Y., A. Galli, et al. (2008). "Pol3 is involved in nonhomologous end-joining in Saccharomyces cerevisiae." DNA Repair (Amst) 7(9): 1531-1541. http://www.ncbi.nlm.nih.gov/pubmed/18606574.

Chang, K., J. Qian, et al. (2002). "Effective generation of transgenic pigs and mice by linker based sperm-mediated gene transfer." BMC Biotechnol 2: 5. http://www.ncbi.nlm.nih.gov/pubmed/11964188.

Chen, B., K. L. Bruce, et al. (2010). "Genetic and epigenetic control of the efficiency and fidelity of cross-species prion transmission." Mol Microbiol 76(6): 1483-1499. http://www.ncbi.nlm.nih.gov/pubmed/20444092.

Chen, I., Dubnau, D (2004). "DNA uptake during bacterial transformation." Nat Rev Microbiol 2: 241-249. .

Chen, J. M., C. Ferec, et al. (2007). "Mechanism of Alu integration into the human genome." Genomic Med 1(1-2): 9-17. http://www.ncbi.nlm.nih.gov/pubmed/18923924.

Chiarle, R., Y. Zhang, et al. (2011). "Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells." Cell 147(1): 107-119. http://www.ncbi.nlm.nih.gov/pubmed/21962511.

Chillon, I., F. Martinez-Abarca, et al. (2011). "Splicing of the Sinorhizobium meliloti RmInt1 group II intron provides evidence of retroelement behavior." Nucleic Acids Res 39(3): 1095-1104. http://www.ncbi.nlm.nih.gov/pubmed/20876688.

Chilton, M. D. (1983). "A Vector for Introducing New Genes into Plants." Scientific American 248: 50-59. .

Christie, P. J., K. Atmakuri, et al. (2005). "Biogenesis, architecture, and function of bacterial type IV secretion systems." Annu Rev Microbiol 59: 451-485. http://www.ncbi.nlm.nih.gov/pubmed/16153176.

Chung, S. M., M. Vaidya, et al. (2006). "Agrobacterium is not alone: gene transfer to plants by viruses and other bacteria." Trends Plant Sci 11(1): 1-4. http://www.ncbi.nlm.nih.gov/pubmed/16297655.

Cianciotto, N. P. (2005). "Type II secretion: a protein secretion system for all seasons." Trends Microbiol 13(12): 581-588. http://www.ncbi.nlm.nih.gov/pubmed/16216510.

Claeys Bouuaert, C. and R. Chalmers (2010). "Transposition of the human Hsmar1 transposon: rate-limiting steps and the importance of the flanking TA dinucleotide in second strand cleavage." Nucleic Acids Res 38(1): 190-202. http://www.ncbi.nlm.nih.gov/pubmed/19858101.

Claverys, J. P., M. Prudhomme, et al. (2006). "Induction of competence regulons as a general response to stress in gram-positive bacteria." Annu Rev Microbiol 60: 451-475. http://www.ncbi.nlm.nih.gov/pubmed/16771651.

Cline, S. W., L. C. Schalkwyk, et al. (1989). "Transformation of the archaebacterium Halobacterium volcanii with genomic DNA." J Bacteriol 171(9): 4987-4991. http://www.ncbi.nlm.nih.gov/pubmed/2768194.

Cohen, S. E., V. G. Godoy, et al. (2009). "Transcriptional modulator NusA interacts with translesion DNA polymerases in Escherichia coli." J Bacteriol 191(2): 665-672. http://www.ncbi.nlm.nih.gov/pubmed/18996995.

Company, M. and B. Errede (1987). "Cell-type-dependent gene activation by yeast transposon Ty1 involves multiple regulatory determinants." Mol Cell Biol 7(9): 3205-3211. http://www.ncbi.nlm.nih.gov/pubmed/2823122.

Company, M. and B. Errede (1988). "A Ty1 cell-type-specific regulatory sequence is a recognition element for a constitutive binding factor." Mol Cell Biol 8(12): 5299-5309. http://www.ncbi.nlm.nih.gov/pubmed/2854195.

Cordaux, R. and M. A. Batzer (2009). "The impact of retrotransposons on human genome evolution." Nat Rev Genet 10(10): 691-703. http://www.ncbi.nlm.nih.gov/pubmed/19763152.

Cornelis, G. R. (2006). "The type III secretion injectisome." Nat Rev Microbiol 4(11): 811-825. http://www.ncbi.nlm.nih.gov/pubmed/17041629.

Court, D. L., J. A. Sawitzke, et al. (2002). "Genetic engineering using homologous recombination." Annu Rev Genet 36: 361-388. http://www.ncbi.nlm.nih.gov/pubmed/12429697.

Cui, X. and G. Davis (2007). "Mobile group II intron targeting: applications in prokaryotes and perspectives in\ eukaryotes." Front Biosci\ 12\: 4972-4985\. http://www.ncbi.nlm.nih.gov/pubmed/17569624\.

Cui, X., D. Ji, et al. (2011). "Targeted integration in rat and mouse embryos with zinc-finger nucleases." Nat Biotechnol 29(1): 64-67. http://www.ncbi.nlm.nih.gov/pubmed/21151125.

Dai, L. and S. Zimmerly (2002). "Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior." Nucleic Acids Res 30(5): 1091-1102. http://www.ncbi.nlm.nih.gov/pubmed/11861899.

Dai, L. and S. Zimmerly (2003). "ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs." RNA 9(1): 14-19. http://www.ncbi.nlm.nih.gov/pubmed/12554871.

Dai, M., S. Ziesman, et al. (2005). "Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli." Metab Eng 7(1): 45-52. http://www.ncbi.nlm.nih.gov/pubmed/15974564.

Damert, A., J. Raiz, et al. (2009). "5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome." Genome Res 19(11): 1992-2008. http://www.ncbi.nlm.nih.gov/pubmed/19652014.

Daniel, K., J. Lange, et al. (2011). "Meiotic homologue alignment and its quality surveillance are controlled by mouse HORMAD1." Nat Cell Biol 13(5): 599-610. http://www.ncbi.nlm.nih.gov/pubmed/21478856.

Dassa, B., N. London, et al. (2009). "Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family." Nucleic Acids Res 37(8): 2560-2573. http://www.ncbi.nlm.nih.gov/pubmed/19264795.

Dautin, N. and H. D. Bernstein (2007). "Protein secretion in gram-negative bacteria via the autotransporter pathway." Annu Rev Microbiol 61: 89-112. http://www.ncbi.nlm.nih.gov/pubmed/17506669.

Davey, M. R., P. Anthony, et al. (2005). "Plant protoplasts: status and biotechnological perspectives." Biotechnol Adv 23(2): 131-171. http://www.ncbi.nlm.nih.gov/pubmed/15694124.

Davey, M. R., E. L. Rech, et al. (1989). "Direct DNA transfer to plant cells." Plant Mol Biol 13(3): 273-285. http://www.ncbi.nlm.nih.gov/pubmed/2491654.

Davis, C. C., W. R. Anderson, et al. (2005). "Gene transfer from a parasitic flowering plant to a fern." Proc Biol Sci 272(1578): 2237-2242. http://www.ncbi.nlm.nih.gov/pubmed/16191635.

Davis, C. C. and K. J. Wurdack (2004). "Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales." Science 305(5684): 676-678. http://www.ncbi.nlm.nih.gov/pubmed/15256617.

de Vries, J., T. Herzfeld, et al. (2004). "Transfer of plastid DNA from tobacco to the soil bacterium Acinetobacter sp. by natural transformation." Mol Microbiol 53(1): 323-334. http://www.ncbi.nlm.nih.gov/pubmed/15225325.

Deakin, W. J. and W. J. Broughton (2009). "Symbiotic use of pathogenic strategies: rhizobial protein secretion systems." Nat Rev Microbiol 7(4): 312-320. http://www.ncbi.nlm.nih.gov/pubmed/19270720.

Deem, A., A. Keszthelyi, et al. (2011). "Break-induced replication is highly inaccurate." PLoS Biol 9(2): e1000594. http://www.ncbi.nlm.nih.gov/pubmed/21347245.

Delelis, O., K. Carayon, et al. (2008). "Integrase and integration: biochemical activities of HIV-1 integrase." Retrovirology 5: 114. http://www.ncbi.nlm.nih.gov/pubmed/19091057.

Delepelaire, P. (2004). "Type I secretion in gram-negative bacteria." Biochim Biophys Acta 1694(1-3): 149-161. http://www.ncbi.nlm.nih.gov/pubmed/15546664.

Demattei, M. V., S. Hedhili, et al. (2011). "Nuclear importation of Mariner transposases among eukaryotes: motif requirements and homo-protein interactions." PLoS One 6(8): e23693. http://www.ncbi.nlm.nih.gov/pubmed/21876763.

Desvaux, M., L. M. Cooper, et al. (2006). "The unusual extended signal peptide region of the type V secretion system is phylogenetically restricted." FEMS Microbiol Lett 264(1): 22-30. http://www.ncbi.nlm.nih.gov/pubmed/17020545.

Dewannieux, M. and T. Heidmann (2005). "LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling." Cytogenet Genome Res 110(1-4): 35-48. http://www.ncbi.nlm.nih.gov/pubmed/16093656.

Dewannieux, M., C. Vernochet, et al. (2011). "The Mouse IAPE Endogenous Retrovirus Can Infect Cells through Any of the Five GPI-Anchored EphrinA Proteins." PLoS Pathog 7(10): e1002309. http://www.ncbi.nlm.nih.gov/pubmed/22028653.

Di Rienzi, S. C., D. Collingwood, et al. (2009). "Fragile genomic sites are associated with origins of replication." Genome Biol Evol 1: 350-363. http://www.ncbi.nlm.nih.gov/pubmed/20333204.

Diken, M., S. Kreiter, et al. (2011). "Selective uptake of naked vaccine RNA by dendritic cells is driven by macropinocytosis and abrogated upon DC maturation." Gene Ther 18(7): 702-708. http://www.ncbi.nlm.nih.gov/pubmed/21368901.

Dillingham, M. S. and S. C. Kowalczykowski (2008). "RecBCD enzyme and the repair of double-stranded DNA breaks." Microbiol Mol Biol Rev 72(4): 642-671. http://www.ncbi.nlm.nih.gov/pubmed/19052323.

Ding, W., L. Lin, et al. (2006). "L1 elements, processed pseudogenes and retrogenes in mammalian genomes." IUBMB Life 58(12): 677-685. http://www.ncbi.nlm.nih.gov/pubmed/17424906.

Dodsworth, J. A., L. Li, et al. (2010). "Interdomain conjugal transfer of DNA from bacteria to archaea." Appl Environ Microbiol 76(16): 5644-5647. .

Dong, C., R. T. Poulter, et al. (2009). "LINE-like retrotransposition in Saccharomyces cerevisiae." Genetics 181(1): 301-311. http://www.ncbi.nlm.nih.gov/pubmed/18957700.

Doucet, A. J., A. E. Hulme, et al. (2010). "Characterization of LINE-1 ribonucleoprotein particles." PLoS Genet\ 6\(10\). http://www.ncbi.nlm.nih.gov/pubmed/20949108\.

Doucet, A. l. J., A. E. Hulme, et al. (2010). "Characterization of LINE-1 Ribonucleoprotein Particles." PLoS Genet 6(10): e1001150. .

Doulatov, S., A. Hodes, et al. (2004). "Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements." Nature 431(7007): 476-481. http://www.ncbi.nlm.nih.gov/pubmed/15386016.

Draper, O., C. E. Cesar, et al. (2005). "Site-specific recombinase and integrase activities of a conjugative relaxase in recipient cells." Proc Natl Acad Sci U S A 102(45): 16385-16390. http://www.ncbi.nlm.nih.gov/pubmed/16260740.

Dubey, G. P. and S. Ben-Yehuda (2011). "Intercellular nanotubes mediate bacterial communication." Cell 144(4): 590-600. http://www.ncbi.nlm.nih.gov/pubmed/21335240.

Dubnau, D. (1999). "DNA uptake in bacteria." Annu Rev Microbiol 53: 217-244. http://www.ncbi.nlm.nih.gov/pubmed/10547691.

Dudasova, Z., A. Dudas, et al. (2004). "Non-homologous end-joining factors of Saccharomyces cerevisiae." FEMS Microbiol Rev 28(5): 581-601. http://www.ncbi.nlm.nih.gov/pubmed/15539075.

Dupont, E., A. Prochiantz, et al. (2011). "Penetratin story: an overview." Methods Mol Biol 683: 21-29. http://www.ncbi.nlm.nih.gov/pubmed/21053119.

Durand, E., D. Verger, et al. (2009). "Structural biology of bacterial secretion systems in gram-negative pathogens--potential for new drug targets." Infect Disord Drug Targets 9(5): 518-547. http://www.ncbi.nlm.nih.gov/pubmed/19594425.

Durkin, S. G. and T. W. Glover (2007). "Chromosome fragile sites." Annu Rev Genet 41: 169-192. http://www.ncbi.nlm.nih.gov/pubmed/17608616.

Duval-Valentin, G., B. Marty-Cointin, et al. (2004). "Requirement of IS911 replication before integration defines a new bacterial transposition pathway." Embo J 23(19): 3897-3906. http://www.ncbi.nlm.nih.gov/pubmed/15359283.

Edgell, D. R. (2009). "Selfish DNA: homing endonucleases find a home." Curr Biol 19(3): R115-117. http://www.ncbi.nlm.nih.gov/pubmed/19211047.

Edgell, D. R., V. R. Chalamcharla, et al. (2011). "Learning to live together: mutualism between self-splicing introns and their hosts." BMC Biol 9: 22. http://www.ncbi.nlm.nih.gov/pubmed/21481283.

Eggenberger, K., E. Birtalan, et al. (2009). "Passage of Trojan peptoids into plant cells." Chembiochem 10(15): 2504-2512. http://www.ncbi.nlm.nih.gov/pubmed/19739189.

Eggenberger, K., C. Mink, et al. (2011). "Using the peptide BP100 as a cell-penetrating tool for the chemical engineering of actin filaments within living plant cells." Chembiochem 12(1): 132-137. http://www.ncbi.nlm.nih.gov/pubmed/21154994.

Eiden, M. V. (2008). "Endogenous retroviruses--aiding and abetting genomic plasticity." Cell Mol Life Sci 65(21): 3325-3328. http://www.ncbi.nlm.nih.gov/pubmed/18818876.

Eiserling, F., A. Pushkin, et al. (1999). "Bacteriophage-like particles associated with the gene transfer agent of methanococcus voltae PS." J Gen Virol 80 ( Pt 12): 3305-3308. http://www.ncbi.nlm.nih.gov/pubmed/10567664.

El-Aneed, A. (2004). "An overview of current delivery systems in cancer gene therapy." J Control Release 94(1): 1-14. http://www.ncbi.nlm.nih.gov/pubmed/14684267.

Eldh, M., K. Ekstrom, et al. (2010). "Exosomes communicate protective messages during oxidative stress; possible role of exosomal shuttle RNA." PLoS One 5(12): e15353. http://www.ncbi.nlm.nih.gov/pubmed/21179422.

Errede, B. and G. Ammerer (1989). "STE12, a protein involved in cell-type-specific transcription and signal transduction in yeast, is part of protein-DNA complexes." Genes Dev 3(9): 1349-1361. http://www.ncbi.nlm.nih.gov/pubmed/2558054.

Errede, B., M. Company, et al. (1985). "Activation regions in a yeast transposon have homology to mating type control sequences and to mammalian enhancers." Proc Natl Acad Sci U S A 82(16): 5423-5427. http://www.ncbi.nlm.nih.gov/pubmed/2991922.

Esvelt, K. M., J. C. Carlson, et al. (2011). "A system for the continuous directed evolution of biomolecules." Nature 472(7344): 499-503. http://www.ncbi.nlm.nih.gov/pubmed/21478873.

Fahleson, J. and K. Glimelius (1999). "Protoplast fusion for symmetric somatic hybrid production in Brassicaceae." Methods Mol Biol 111: 195-209. http://www.ncbi.nlm.nih.gov/pubmed/10080989.

Fawcett, D. H., C. K. Lister, et al. (1986). "Transposable elements controlling I-R hybrid dysgenesis in D. melanogaster are similar to mammalian LINEs." Cell 47(6): 1007-1015. http://www.ncbi.nlm.nih.gov/pubmed/2430722.

Faye, B., F. Arnaud, et al. (2008). "Functional characteristics of a highly specific integrase encoded by an LTR-retrotransposon." PLoS One 3(9): e3185. http://www.ncbi.nlm.nih.gov/pubmed/18784842.

Felgner, P. L., T.R. Gadek, M. Holm, R. Roman, H.W. Chan, M. Wenz, J.P. Northrop, G.M. Ringold and M. Danielsen (1987). "Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure." Proc Nat Acad Sci USA 84: 7413–7417. http://www.ncbi.nlm.nih.gov/pubmed/2823261.

Fernandez-Gonzalez, E., H. D. de Paz, et al. (2011). "Transfer of R388 Derivatives by a Pathogenesis-Associated Type IV Secretion System into both Bacteria and Human Cells." J Bacteriol 193(22): 6257-6265. http://www.ncbi.nlm.nih.gov/pubmed/21908662.

Ficht, T. A. (2011). "Bacterial Exchange via Nanotubes: Lessons Learned from the History of Molecular Biology." Front Microbiol 2: 179. http://www.ncbi.nlm.nih.gov/pubmed/21927613.

Filee, J., N. Pouget, et al. (2008). "Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses." BMC Evol Biol 8: 320. http://www.ncbi.nlm.nih.gov/pubmed/19036122.

Filloux, A. (2004). "The underlying mechanisms of type II protein secretion." Biochim Biophys Acta 1694(1-3): 163-179. http://www.ncbi.nlm.nih.gov/pubmed/15546665.

Filloux, A. (2009). "The type VI secretion system: a tubular story." Embo J\ 28\(4\): 309-310\. http://www.ncbi.nlm.nih.gov/pubmed/19225443\.

Filloux, A. (2011). "Protein Secretion Systems in Pseudomonas aeruginosa: An Essay on Diversity, Evolution, and Function." Front Microbiol 2: 155. http://www.ncbi.nlm.nih.gov/pubmed/21811488.

Fluit, A. C. and F. J. Schmitz (2004). "Resistance integrons and super-integrons." Clin Microbiol Infect 10(4): 272-288. http://www.ncbi.nlm.nih.gov/pubmed/15059115.

Flutre, T., E. Duprat, et al. (2011). "Considering transposable element diversification in de novo annotation approaches." PLoS One 6(1): e16526. http://www.ncbi.nlm.nih.gov/pubmed/21304975.

Frankenberg-Schwager, M., M. Becker, et al. (2008). "The role of nonhomologous DNA end joining, conservative homologous recombination, and single-strand annealing in the cell cycle-dependent repair of DNA double-strand breaks induced by H(2)O(2) in mammalian cells." Radiat Res 170(6): 784-793. http://www.ncbi.nlm.nih.gov/pubmed/19138034.

Fuchs, R. P. and S. Fujii (2007). "Translesion synthesis in Escherichia coli: lessons from the NarI mutation hot spot." DNA Repair (Amst) 6(7): 1032-1041. http://www.ncbi.nlm.nih.gov/pubmed/17403618.

Fuchs, R. P., S. Fujii, et al. (2004). "Properties and functions of Escherichia coli: Pol IV and Pol V." Adv Protein Chem 69: 229-264. http://www.ncbi.nlm.nih.gov/pubmed/15588845.

Fuchs, R. P., N. Koffel-Schwartz, et al. (2001). "DNA polymerases II and V mediate respectively mutagenic (-2 frameshift) and error-free bypass of a single N-2-acetylaminofluorene adduct." Biochem Soc Trans 29(Pt 2): 191-195. http://www.ncbi.nlm.nih.gov/pubmed/11356152.

Fujii, S. and R. P. Fuchs (2007). "Interplay among replicative and specialized DNA polymerases determines failure or success of translesion synthesis pathways." J Mol Biol 372(4): 883-893. http://www.ncbi.nlm.nih.gov/pubmed/17707403.

Fujii, Y. R. (2010). "RNA Genes: Retroelements and Virally Retroposable microRNAs in Human Embryonic Stem Cells." Open Virol J 4: 63-75. http://www.ncbi.nlm.nih.gov/pubmed/20835360.

Galligan, J. T., S. E. Marchetti, et al. (2011). "Reverse transcription of the pFOXC mitochondrial retroplasmids of Fusarium oxysporum is protein primed." Mob DNA 2(1): 1. http://www.ncbi.nlm.nih.gov/pubmed/21255388.

Gamborg, O. L. and F. B. Holl (1977). "Plant protoplast fusion and hybridization." Basic Life Sci 9: 299-316. http://www.ncbi.nlm.nih.gov/pubmed/336026.

Gandolfi, F. (1998). "Spermatozoa, DNA binding and transgenic animals." Transgenic Res 7(3): 147-155. http://www.ncbi.nlm.nih.gov/pubmed/10461389.

Garcia, V., S. E. Phelps, et al. (2011). "Bidirectional resection of DNA double-strand breaks by Mre11 and Exo1." Nature. http://www.ncbi.nlm.nih.gov/pubmed/22002605.

Garcia-Perez, J. L. (2007). "LINE-1 retrotransposition in human embryonic stem cells." Hum. Mol. Genet. 16: 1569-1577. http://www.ncbi.nlm.nih.gov/pubmed/17468180.

Garcia-Perez, J. L., A. J. Doucet, et al. (2007). "Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase." Genome Res 17(5): 602-611. http://www.ncbi.nlm.nih.gov/pubmed/17416749.

Garcia-Vazquez, F. A., S. Ruiz, et al. (2010). "Production of transgenic piglets using ICSI-sperm-mediated gene transfer in combination with recombinase RecA." Reproduction 140(2): 259-272. http://www.ncbi.nlm.nih.gov/pubmed/20501790.

Garcia-Villada, L. and J. W. Drake (2010). "Mutational clusters generated by non-processive polymerases: A case study using DNA polymerase betain vitro." DNA Repair (Amst) 9(8): 871-878. http://www.ncbi.nlm.nih.gov/pubmed/20627824.

Georgiev, P., T. Tikhomirova, et al. (1997). "Insertions of hybrid P elements in the yellow gene of Drosophila cause a large variety of mutant phenotypes." Genetics 146(2): 583-594. http://www.ncbi.nlm.nih.gov/pubmed/9178008.

Gericke, G. S. (2010). "Common chromosomal fragile sites (CFS) may be involved in normal and traumatic cognitive stress memory consolidation and altered nervous system immunity." Med Hypotheses\ 74\(5\): 911-918\. http://www.ncbi.nlm.nih.gov/pubmed/20138440\.

Ghinet, M. G., E. Bordeleau, et al. (2011). "Uncovering the prevalence and diversity of integrating conjugative elements in actinobacteria." PLoS One 6(11): e27846. http://www.ncbi.nlm.nih.gov/pubmed/22114709.

Gifford, R., P. Kabat, et al. (2005). "Evolution and distribution of class II-related endogenous retroviruses." J Virol 79(10): 6478-6486. http://www.ncbi.nlm.nih.gov/pubmed/15858031.

Gifford, R. and M. Tristem (2003). "The evolution, distribution and diversity of endogenous retroviruses." Virus Genes 26(3): 291-315. http://www.ncbi.nlm.nih.gov/pubmed/12876457.

Gifford, R. J., A. Katzourakis, et al. (2008). "A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution." Proc Natl Acad Sci U S A 105(51): 20362-20367. http://www.ncbi.nlm.nih.gov/pubmed/19075221.

Gilbert, C., D. G. Maxfield, et al. (2009). "Parallel germline infiltration of a lentivirus in two Malagasy lemurs." PLoS Genet 5(3): e1000425. http://www.ncbi.nlm.nih.gov/pubmed/19300488.

Gilbert, N., S. Lutz-Prigge, et al. (2002). "Genomic deletions created upon LINE-1 retrotransposition." Cell\ 110\(3\): 315-325\. http://www.ncbi.nlm.nih.gov/pubmed/12176319\.

Gillespie, J. J., K. A. Brayton, et al. (2010). "Phylogenomics reveals a diverse Rickettsiales type IV secretion system." Infect Immun 78(5): 1809-1823. http://www.ncbi.nlm.nih.gov/pubmed/20176788.

Gillings, M. R., M. P. Holley, et al. (2005). "Integrons in Xanthomonas: a source of species genome diversity." Proc Natl Acad Sci U S A 102(12): 4419-4424. http://www.ncbi.nlm.nih.gov/pubmed/15755815.

Gimble, F. S. (2000). "Invasion of a multitude of genetic niches by mobile endonuclease genes." FEMS Microbiol Lett 185(2): 99-107. http://www.ncbi.nlm.nih.gov/pubmed/10754232.

Glover, L., J. Jun, et al. (2011). "Microhomology-mediated deletion and gene conversion in African trypanosomes." Nucleic Acids Res 39(4): 1372-1380. http://www.ncbi.nlm.nih.gov/pubmed/20965968.

Glover, T. W. (2006). "Common fragile sites." Cancer Lett 232(1): 4-12. http://www.ncbi.nlm.nih.gov/pubmed/16229941.

Godoy, V. G., F. S. Gizatullin, et al. (2000). "Some features of the mutability of bacteria during nonlethal selection." Genetics 154(1): 49-59. http://www.ncbi.nlm.nih.gov/pubmed/10628968.

Godoy, V. G., D. F. Jarosz, et al. (2007). "UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB." Mol Cell 28(6): 1058-1070. http://www.ncbi.nlm.nih.gov/pubmed/18158902.

Gogvadze, E., C. Barbisan, et al. (2007). "Tripartite chimeric pseudogene from the genome of rice blast fungus Magnaporthe grisea suggests double template jumps during long interspersed nuclear element (LINE) reverse transcription." BMC Genomics 8: 360. http://www.ncbi.nlm.nih.gov/pubmed/17922896.

Goldstone, D. C., M. W. Yap, et al. (2010). "Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface." Cell Host Microbe 8(3): 248-259. http://www.ncbi.nlm.nih.gov/pubmed/20833376.

Goodier, J. L., L. Zhang, et al. (2007). "LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex." Mol Cell Biol 27(18): 6469-6483. http://www.ncbi.nlm.nih.gov/pubmed/17562864.

Goodman, M. (2002). "Error-prone repair DNA polymerases in prokaryotes and eukaryotes." Ann Rev Biochem 71: 17-50. http://www.ncbi.nlm.nih.gov/pubmed/12045089.

Goodwin, T. J. and R. T. Poulter (2001). "The DIRS1 group of retrotransposons." Mol Biol Evol 18(11): 2067-2082. http://www.ncbi.nlm.nih.gov/pubmed/11606703.

Goodwin, T. J., R. T. Poulter, et al. (2004). "DIRS retroelements in arthropods: identification of the recently active TcDirs1 element in the red flour beetle Tribolium castaneum." Mol Genet Genomics 272(1): 47-56. http://www.ncbi.nlm.nih.gov/pubmed/15221458.

Gousset, K., E. Schiff, et al. (2009). "Prions hijack tunnelling nanotubes for intercellular spread." Nat Cell Biol 11(3): 328-336. http://www.ncbi.nlm.nih.gov/pubmed/19198598.

Gousset, K. and C. Zurzolo (2009). "Tunnelling nanotubes: a highway for prion spreading?" Prion 3(2): 94-98. http://www.ncbi.nlm.nih.gov/pubmed/19471116.

Grabundzija, I., M. Irgang, et al. (2010). "Comparative analysis of transposable element vector systems in human cells." Mol Ther 18(6): 1200-1209. http://www.ncbi.nlm.nih.gov/pubmed/20372108.

Grey, C., V. Sommermeyer, et al. (2011). "[What defines the genetic map? The specification of meiotic recombination sites]." Med Sci (Paris) 27(1): 63-69. http://www.ncbi.nlm.nih.gov/pubmed/21299964.

Groth, A. C. and M. P. Calos (2004). "Phage integrases: biology and applications." J Mol Biol 335(3): 667-678. http://www.ncbi.nlm.nih.gov/pubmed/14687564.

Gueguen, E., P. Rousseau, et al. (2005). "The transpososome: control of transposition at the level of catalysis." Trends Microbiol 13(11): 543-549. http://www.ncbi.nlm.nih.gov/pubmed/16181782.

Guo, H., M. Karberg, et al. (2000). "Group II introns designed to insert into therapeutically relevant DNA target sites in human cells." Science 289(5478): 452-457. http://www.ncbi.nlm.nih.gov/pubmed/10903206.

Guo, H., L. V. Tse, et al. (2008). "Diversity-generating retroelement homing regenerates target sequences for repeated rounds of codon rewriting and protein diversification." Mol Cell 31(6): 813-823. http://www.ncbi.nlm.nih.gov/pubmed/18922465.

Guo, H., L. V. Tse, et al. (2011). "Target site recognition by a diversity-generating retroelement." PLoS Genet 7(12): e1002414. http://www.ncbi.nlm.nih.gov/pubmed/22194701.

Hall, R. M. and H. W. Stokes (1993). "Integrons: novel DNA elements which capture genes by site-specific recombination." Genetica 90(2-3): 115-132. http://www.ncbi.nlm.nih.gov/pubmed/8119588.

Han, J. S. (2010). "Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions." Mob DNA 1(1): 15. http://www.ncbi.nlm.nih.gov/pubmed/20462415.

Hancks, D. C., A. D. Ewing, et al. (2009). "Exon-trapping mediated by the human retrotransposon SVA." Genome Res 19(11): 1983-1991. http://www.ncbi.nlm.nih.gov/pubmed/19635844.

Hancks, D. C., J. L. Goodier, et al. (2011). "Retrotransposition of marked SVA elements by human L1s in cultured cells." Hum Mol Genet 20(17): 3386-3400. http://www.ncbi.nlm.nih.gov/pubmed/21636526.

Hancks, D. C. and H. H. Kazazian, Jr. (2010). "SVA retrotransposons: Evolution and genetic instability." Semin Cancer Biol 20(4): 234-245. http://www.ncbi.nlm.nih.gov/pubmed/20416380.

Handa, N., K. Morimatsu, et al. (2009). "Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli." Genes Dev 23(10): 1234-1245. http://www.ncbi.nlm.nih.gov/pubmed/19451222.

Haren, L., B. Ton-Hoang, et al. (1999). "Integrating DNA: transposases and retroviral integrases." Annu Rev Microbiol 53: 245-281. http://www.ncbi.nlm.nih.gov/pubmed/10547692.

Hastings, P. J. (2007). "Adaptive amplification." Crit Rev Biochem Mol Biol\ 42\(4\): 271-283\. http://www.ncbi.nlm.nih.gov/pubmed/17687669\.

Hastings, P. J., G. Ira, et al. (2009). "A microhomology-mediated break-induced replication model for the origin of human  copy number variation." PLoS Genet 5(1): e1000327. http://www.ncbi.nlm.nih.gov/pubmed/19180184.

Hastings, P. J., A. Slack, et al. (2004). "Adaptive amplification and point mutation are independent mechanisms: evidence\ for various stress-inducible mutation mechanisms." PLoS Biol\ 2\(12\): e399\. http://www.ncbi.nlm.nih.gov/pubmed/15550983\.

Hayes, C. S., S. K. Aoki, et al. (2010). "Bacterial contact-dependent delivery systems." Annu Rev Genet 44: 71-90. http://www.ncbi.nlm.nih.gov/pubmed/21047256.

Hayes, W. (1968). The Genetics of Bacteria and their Viruses (2nd ed.). London, Blackwell. .

Hecht, M. M., N. Nitz, et al. (2010). "Inheritance of DNA transferred from American trypanosomes to human hosts." PLoS One 5(2): e9181. http://www.ncbi.nlm.nih.gov/pubmed/20169193.

Hedges, D. J. and M. A. Batzer (2005). "From the margins of the genome: mobile elements shape primate evolution." Bioessays 27(8): 785-794. http://www.ncbi.nlm.nih.gov/pubmed/16015599.

Heinemann, J. A. and G. F. Sprague, Jr. (1989). "Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast." Nature 340(6230): 205-209. http://www.ncbi.nlm.nih.gov/pubmed/2666856.

Heinemann, J. A. and G. F. Sprague, Jr. (1991). "Transmission of plasmid DNA to yeast by conjugation with bacteria." Methods Enzymol 194: 187-195. http://www.ncbi.nlm.nih.gov/pubmed/2005787.

Herr, A. J., M. Ogawa, et al. (2011). "Mutator suppression and escape from replication error-induced extinction in yeast." PLoS Genet 7(10): e1002282. http://www.ncbi.nlm.nih.gov/pubmed/22022273.

Herr, A. J., L. N. Williams, et al. (2011). "Antimutator variants of DNA polymerases." Crit Rev Biochem Mol Biol. http://www.ncbi.nlm.nih.gov/pubmed/21977975.

Hersh, M. N., R. G. Ponder, et al. (2004). "Adaptive mutation and amplification in Escherichia coli: two pathways of genome adaptation under stress." Res Microbiol 155(5): 352-359. http://www.ncbi.nlm.nih.gov/pubmed/15207867.

Hicks, W. M., M. Kim, et al. (2010). "Increased mutagenesis and unique mutation signature associated with mitotic gene conversion." Science 329(5987): 82-85. http://www.ncbi.nlm.nih.gov/pubmed/20595613.

Hizi, A. (2008). "The reverse transcriptase of the Tf1 retrotransposon has a specific novel activity for generating the RNA self-primer that is functional in cDNA synthesis." J Virol 82(21): 10906-10910. http://www.ncbi.nlm.nih.gov/pubmed/18753200.

Hoang, M. L., F. J. Tan, et al. (2010). "Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination." PLoS Genet 6(12): e1001228. http://www.ncbi.nlm.nih.gov/pubmed/21151956.

Hockemeyer, D., H. Wang, et al. (2011). "Genetic engineering of human pluripotent cells using TALE nucleases." Nat Biotechnol 29(8): 731-734. http://www.ncbi.nlm.nih.gov/pubmed/21738127.

Holloman, W. K. (2011). "Unraveling the mechanism of BRCA2 in homologous recombination." Nat Struct Mol Biol 18(7): 748-754. http://www.ncbi.nlm.nih.gov/pubmed/21731065.

Hopwood, D. A., H. M. Wright, et al. (1977). "Genetic recombination through protoplast fusion in Streptomyces." Nature 268(5616): 171-174. http://www.ncbi.nlm.nih.gov/pubmed/593313.

Hotopp, J. C., M. E. Clark, et al. (2007). "Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes." Science 317(5845): 1753-1756. http://www.ncbi.nlm.nih.gov/pubmed/17761848.

Hou, Y., J. Rajagopal, et al. (2010). "Retrotransposon vectors for gene delivery in plants." Mob DNA 1(1): 19. http://www.ncbi.nlm.nih.gov/pubmed/20678194.

Huang, G., C. Ashton, et al. (2011). "Genetic manipulations in the rat: progress and prospects." Curr Opin Nephrol Hypertens 20(4): 391-399. http://www.ncbi.nlm.nih.gov/pubmed/21546835.

Huang, J., N. Mullapudi, et al. (2004). "Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum." Genome Biol 5(11): R88. http://www.ncbi.nlm.nih.gov/pubmed/15535864.

Huang, J., Y. Xu, et al. (2005). "The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic." Mol Biol Evol 22(11): 2142-2146. http://www.ncbi.nlm.nih.gov/pubmed/16049196.

Huang, T., T. R. Shaikh, et al. (2011). "The group II intron ribonucleoprotein precursor is a large, loosely packed structure." Nucleic Acids Res 39(7): 2845-2854. http://www.ncbi.nlm.nih.gov/pubmed/21131279.

Hunter, P. (2006). "Shedding a negative image. Research into their mechanism of infectivity reveals that prions might have important biological roles." EMBO Rep 7(12): 1196-1198. http://www.ncbi.nlm.nih.gov/pubmed/17139293.

Ishii, H. and Y. Furukawa (2004). "Alterations of common chromosome fragile sites in hematopoietic malignancies." Int J Hematol 79(3): 238-242. http://www.ncbi.nlm.nih.gov/pubmed/15168591.

Ivics, Z. and Z. Izsvak (2010). "The expanding universe of transposon technologies for gene and cell engineering." Mob DNA 1(1): 25. http://www.ncbi.nlm.nih.gov/pubmed/21138556.

Jacob-Dubuisson, F., R. Fernandez, et al. (2004). "Protein secretion through autotransporter and two-partner pathways." Biochim Biophys Acta 1694(1-3): 235-257. http://www.ncbi.nlm.nih.gov/pubmed/15546669.

Jakupciak, J. P. and R. D. Wells (2000). "Genetic instabilities of triplet repeat sequences by recombination." IUBMB Life 50(6): 355-359. http://www.ncbi.nlm.nih.gov/pubmed/11327307.

Jaratlerdsiri, W., C. J. Rodriguez-Zarate, et al. (2009). "Distribution of endogenous retroviruses in crocodilians." J Virol 83(19): 10305-10308. http://www.ncbi.nlm.nih.gov/pubmed/19605486.

Jiang, Q., K. Karata, et al. (2009). "The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP." Nature 460(7253): 359-363. http://www.ncbi.nlm.nih.gov/pubmed/19606142.

Johnsen, P. J., D. Dubnau, et al. (2009). "Episodic selection and the maintenance of competence and natural transformation in Bacillus subtilis." Genetics 181(4): 1521-1533. http://www.ncbi.nlm.nih.gov/pubmed/19189946.

Jones, J. P., 3rd, M. N. Kierlin, et al. (2005). "Retargeting mobile group II introns to repair mutant genes." Mol Ther 11(5): 687-694. http://www.ncbi.nlm.nih.gov/pubmed/15851007.

Jorgensen, L., H. M. Nielsen, et al. (2009). Chapter 5. Viral Technology for Delivery of Nucleic Acids. .

Juhas, M., D. W. Crook, et al. (2008). "Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence." Cell Microbiol 10(12): 2377-2386. http://www.ncbi.nlm.nih.gov/pubmed/18549454.

Kale, S. P., L. Moore, et al. (2005). "Heavy metals stimulate human LINE-1 retrotransposition." Int J Environ Res Public Health 2(1): 14-23. http://www.ncbi.nlm.nih.gov/pubmed/16705797.

Kapitonov, V. V. and J. Jurka (2006). "Self-synthesizing DNA transposons in eukaryotes." Proc Natl Acad Sci U S A 103(12): 4540-4545. http://www.ncbi.nlm.nih.gov/pubmed/16537396.

Karboul, A., A. Mazza, et al. (2008). "Frequent homologous recombination events in Mycobacterium tuberculosis PE/PPE multigene families: potential role in antigenic variability." J Bacteriol 190(23): 7838-7846. http://www.ncbi.nlm.nih.gov/pubmed/18820012.

Katzourakis, A., R. J. Gifford, et al. (2009). "Macroevolution of complex retroviruses." Science 325(5947): 1512. http://www.ncbi.nlm.nih.gov/pubmed/19762636.

Katzourakis, A., M. Tristem, et al. (2007). "Discovery and analysis of the first endogenous lentivirus." Proc Natl Acad Sci U S A 104(15): 6261-6265. http://www.ncbi.nlm.nih.gov/pubmed/17384150.

Kay, E., T. M. Vogel, et al. (2002). "In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria." Appl Environ Microbiol 68(7): 3345-3351. http://www.ncbi.nlm.nih.gov/pubmed/12089013.

Kejnovsky, E., Z. Kubat, et al. (2006). "Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat." Mol Genet Genomics 276(3): 254-263. http://www.ncbi.nlm.nih.gov/pubmed/16826419.

Kelman, Z. and M. F. White (2005). "Archaeal DNA replication and repair." Curr Opin Microbiol 8(6): 669-676. http://www.ncbi.nlm.nih.gov/pubmed/16242991.

Kempken, F. and U. Kuck (1998). "Evidence for circular transposition derivatives from the fungal hAT-transposon Restless." Curr Genet 34(3): 200-203. http://www.ncbi.nlm.nih.gov/pubmed/9745022.

Khalil, I. A., K. Kogure, et al. (2006). "Uptake pathways and subsequent intracellular trafficking in nonviral gene delivery." Pharmacol Rev 58(1): 32-45. http://www.ncbi.nlm.nih.gov/pubmed/16507881.

Khazina, E., V. Truffault, et al. (2011). "Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition." Nat Struct Mol Biol 18(9): 1006-1014. http://www.ncbi.nlm.nih.gov/pubmed/21822284.

Khazina, E. and O. Weichenrieder (2009). "Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame." Proc Natl Acad Sci U S A 106(3): 731-736. http://www.ncbi.nlm.nih.gov/pubmed/19139409.

Kim, T. K. and J. H. Eberwine (2010). "Mammalian cell transfection: the present and the future." Anal Bioanal Chem 397(8): 3173-3178. http://www.ncbi.nlm.nih.gov/pubmed/20549496\.

Ko, M., H. Choi, et al. (2002). "Group I self-splicing intron in the recA gene of Bacillus anthracis." J Bacteriol 184(14): 3917-3922. http://www.ncbi.nlm.nih.gov/pubmed/12081963.

Kobryn, K. and G. Chaconas (2005). "Fusion of hairpin telomeres by the B. burgdorferi telomere resolvase ResT implications for shaping a genome in flux." Mol Cell 17(6): 783-791. http://www.ncbi.nlm.nih.gov/pubmed/15780935.

Kojima, K. K. (2010). "Different integration site structures between L1 protein-mediated retrotransposition in cis and retrotransposition in trans." Mob DNA 1(1): 17. http://www.ncbi.nlm.nih.gov/pubmed/20615209.

Kojima, K. K. and J. Jurka (2011). "Crypton transposons: identification of new diverse families and ancient domestication events." Mob DNA 2(1): 12. http://www.ncbi.nlm.nih.gov/pubmed/22011512.

Kolkman, J. A. and W. P. Stemmer (2001). "Directed evolution of proteins by exon shuffling." Nat Biotechnol 19(5): 423-428. http://www.ncbi.nlm.nih.gov/pubmed/11329010.

Kolomietz, E., M. S. Meyn, et al. (2002). "The role of Alu repeat clusters as mediators of recurrent chromosomal aberrations in tumors." Genes Chromosomes Cancer 35(2): 97-112. http://www.ncbi.nlm.nih.gov/pubmed/12203773.

Konkel, M. K. and M. A. Batzer (2010). "A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome." Semin Cancer Biol 20(4): 211-221. http://www.ncbi.nlm.nih.gov/pubmed/20307669.

Koonin, E. V., K. S. Makarova, et al. (2001). "Horizontal gene transfer in prokaryotes: quantification and classification." Annu Rev Microbiol 55: 709-742. http://www.ncbi.nlm.nih.gov/pubmed/11544372.

Koskiniemi, S. and D. I. Andersson (2009). "Translesion DNA polymerases are required for spontaneous deletion formation in Salmonella typhimurium." Proc Natl Acad Sci U S A 106(25): 10248-10253. http://www.ncbi.nlm.nih.gov/pubmed/19525399.

Koskiniemi, S., D. Hughes, et al. (2010). "Effect of translesion DNA polymerases, endonucleases and RpoS on mutation rates in Salmonella typhimurium." Genetics 185(3): 783-795. http://www.ncbi.nlm.nih.gov/pubmed/20421601.

Kovacs, A. T., W. K. Smits, et al. (2009). "Ubiquitous late competence genes in Bacillus species indicate the presence of functional DNA uptake machineries." Environ Microbiol 11(8): 1911-1922. http://www.ncbi.nlm.nih.gov/pubmed/19453701.

Kowalczykowski, S. C. (2000). "Initiation of genetic recombination and recombination-dependent replication." Trends Biochem Sci 25(4): 156-165. http://www.ncbi.nlm.nih.gov/pubmed/10754547.

Kozak, C. A. (2010). "The mouse "xenotropic" gammaretroviruses and their XPR1 receptor." Retrovirology 7: 101. http://www.ncbi.nlm.nih.gov/pubmed/21118532.

Krehenbrink, M. and J. A. Downie (2008). "Identification of protein secretion systems and novel secreted proteins in Rhizobium leguminosarum bv. viciae." BMC Genomics 9: 55. http://www.ncbi.nlm.nih.gov/pubmed/18230162.

Kroeger, T. S., K. P. Watkins, et al. (2009). "A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing." Proc Natl Acad Sci U S A 106(11): 4537-4542. http://www.ncbi.nlm.nih.gov/pubmed/19251672.

Kroutter, E. N., V. P. Belancio, et al. (2009). "The RNA polymerase dictates ORF1 requirement and timing of LINE and SINE retrotransposition." PLoS Genet 5(4): e1000458. http://www.ncbi.nlm.nih.gov/pubmed/19390602.

Kulpa, D. A. and J. V. Moran (2005). "Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition." Hum. Mol. Genet. 14: 3237-3248. .

Kuzminov, A. (1999). "Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda." Microbiol Mol Biol Rev 63(4): 751-813, table of contents. http://www.ncbi.nlm.nih.gov/pubmed/10585965.

Labbate, M., R. J. Case, et al. (2009). "The integron/gene cassette system: an active player in bacterial adaptation." Methods Mol Biol 532: 103-125. http://www.ncbi.nlm.nih.gov/pubmed/19271181.

Lacroix, B. and V. Citovsky (2009). "Agrobacterium aiming for the host chromatin: Host and bacterial proteins involved in interactions between T-DNA and plant nucleosomes." Commun Integr Biol 2(1): 42-45. http://www.ncbi.nlm.nih.gov/pubmed/19513263.

Lai, W. F. and M. C. Lin (2009). "Nucleic acid delivery with chitosan and its derivatives." J Control Release 134(3): 158-168. http://www.ncbi.nlm.nih.gov/pubmed/19100795.

Lange, J., J. Pan, et al. (2011). "ATM controls meiotic double-strand-break formation." Nature. http://www.ncbi.nlm.nih.gov/pubmed/22002603.

Lavitrano, M., M. Busnelli, et al. (2006). "Sperm-mediated gene transfer." Reprod Fertil Dev 18(1-2): 19-23. http://www.ncbi.nlm.nih.gov/pubmed/16478599.

Lazowska, J., B. Meunier, et al. (1994). "Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers." Embo J 13(20): 4963-4972. http://www.ncbi.nlm.nih.gov/pubmed/7525273.

Le Beau, M. M. (1986). "Chromosomal fragile sites and cancer-specific rearrangements." Blood 67(4): 849-858. http://www.ncbi.nlm.nih.gov/pubmed/3513870.

Leclercq, S., I. Giraud, et al. (2011). "Remarkable abundance and evolution of mobile group II introns in Wolbachia bacterial endosymbionts." Mol Biol Evol 28(1): 685-697. http://www.ncbi.nlm.nih.gov/pubmed/20819906.

Letsolo, B. T., J. Rowson, et al. (2010). "Fusion of short telomeres in human cells is characterized by extensive deletion and microhomology, and can result in complex rearrangements." Nucleic Acids Res 38(6): 1841-1852. http://www.ncbi.nlm.nih.gov/pubmed/20026586.

Levin, H. L. and J. V. Moran (2011). "Dynamic interactions between transposable elements and their hosts." Nat Rev Genet 12(9): 615-627. http://www.ncbi.nlm.nih.gov/pubmed/21850042.

Lewinski, M. K. and F. D. Bushman (2005). "Retroviral DNA integration--mechanism and consequences." Adv Genet 55: 147-181. http://www.ncbi.nlm.nih.gov/pubmed/16291214.

Lindgren, M. and U. Langel (2011). "Classes and prediction of cell-penetrating peptides." Methods Mol Biol 683: 3-19. http://www.ncbi.nlm.nih.gov/pubmed/21053118.

Ling, A. and R. Cordaux (2010). "Insertion sequence inversions mediated by ectopic recombination between terminal inverted repeats." PLoS One 5(12): e15654. http://www.ncbi.nlm.nih.gov/pubmed/21187977.

Lippert, M. J., N. Kim, et al. (2011). "Role for topoisomerase 1 in transcription-associated mutagenesis in yeast." Proceedings of the National Academy of Sciences 108(2): 698-703. .

Lisby, M. and R. Rothstein (2009). "Choreography of recombination proteins during the DNA damage response." DNA Repair (Amst) 8(9): 1068-1076. http://www.ncbi.nlm.nih.gov/pubmed/19473884.

Liu, D., P. Crellin, et al. (2005). "Cyclic changes in the affinity of protein-DNA interactions drive the progression and regulate the outcome of the Tn10 transposition reaction." Nucleic Acids Res 33(6): 1982-1992. http://www.ncbi.nlm.nih.gov/pubmed/15814815.

Lotvall, J. and H. Valadi (2007). "Cell to cell signalling via exosomes through esRNA." Cell Adh Migr 1(3): 156-158. http://www.ncbi.nlm.nih.gov/pubmed/19262134.

Lowden, M. R., S. Flibotte, et al. (2011). "DNA synthesis generates terminal duplications that seal end-to-end chromosome fusions." Science 332(6028): 468-471. http://www.ncbi.nlm.nih.gov/pubmed/21512032.

Luo, Y. and S. Li (2007). "Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs." Nucleic Acids Res 35(2): 559-571. http://www.ncbi.nlm.nih.gov/pubmed/17175533.

Lusetti, S. L. and M. M. Cox (2002). "The bacterial RecA protein and the recombinational DNA repair of stalled replication forks." Annu Rev Biochem 71: 71-100. http://www.ncbi.nlm.nih.gov/pubmed/12045091.

Lutz, S. M., B. J. Vincent, et al. (2003). "Allelic heterogeneity in LINE-1 retrotransposition activity." Am J Hum Genet\ 73\(6\): 1431-1437\. http://www.ncbi.nlm.nih.gov/pubmed/14610717\.

Lyznik, L. A., W. J. Gordon-Kamm, et al. (2003). "Site-specific recombination for genetic engineering in plants." Plant Cell Rep\ 21\(10\): 925-932\. http://www.ncbi.nlm.nih.gov/pubmed/12835900\.

MacFadyen, L. P., D. Chen, et al. (2001). "Competence development by Haemophilus influenzae is regulated by the availability of nucleic acid precursors." Mol Microbiol 40(3): 700-707. http://www.ncbi.nlm.nih.gov/pubmed/11359575.

Maenhaut-Michel, G., R. Janel-Bintz, et al. (1992). "A umuDC-independent SOS pathway for frameshift mutagenesis." Mol Gen Genet 235(2-3): 373-380. http://www.ncbi.nlm.nih.gov/pubmed/1465109.

Mahaney, B. L., K. Meek, et al. (2009). "Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining." Biochem J 417(3): 639-650. http://www.ncbi.nlm.nih.gov/pubmed/19133841.

Malyarchuk, S., R. Castore, et al. (2008). "DNA repair of clustered lesions in mammalian cells: involvement of non-homologous end-joining." Nucleic Acids Res 36(15): 4872-4882. http://www.ncbi.nlm.nih.gov/pubmed/18653525.

Manthey, G. M. and A. M. Bailis (2010). "Rad51 inhibits translocation formation by non-conservative homologous recombination in Saccharomyces cerevisiae." PLoS One 5(7): e11889. http://www.ncbi.nlm.nih.gov/pubmed/20686691.

Manthey, G. M., N. Naik, et al. (2009). "Msh2 blocks an alternative mechanism for non-homologous tail removal during single-strand annealing in Saccharomyces cerevisiae." PLoS One 4(10): e7488. http://www.ncbi.nlm.nih.gov/pubmed/19834615.

Marcaida, M. J., I. G. Munoz, et al. (2010). "Homing endonucleases: from basics to therapeutic applications." Cell Mol Life Sci 67(5): 727-748. http://www.ncbi.nlm.nih.gov/pubmed/19915993.

Marlovits, T. C. and C. E. Stebbins (2010). "Type III secretion systems shape up as they ship out." Curr Opin Microbiol 13(1): 47-52. http://www.ncbi.nlm.nih.gov/pubmed/20015680.

Marquez, C. P. and E. J. Pritham (2010). "Phantom, a new subclass of Mutator DNA transposons found in insect viruses and widely distributed in animals." Genetics 185(4): 1507-1517. http://www.ncbi.nlm.nih.gov/pubmed/20457878.

Martin, J., E. Herniou, et al. (1999). "Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses." J Virol 73(3): 2442-2449. http://www.ncbi.nlm.nih.gov/pubmed/9971829.

Martin, S. L., M. Cruceanu, et al. (2005). "LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein." J Mol Biol 348(3): 549-561. http://www.ncbi.nlm.nih.gov/pubmed/15826653.

Martin, S. L., W. L. Li, et al. (2005). "The structures of mouse and human L1 elements reflect their insertion mechanism." Cytogenet Genome Res 110(1-4): 223-228. http://www.ncbi.nlm.nih.gov/pubmed/16093676.

Marton, I., A. Zuker, et al. (2010). "Nontransgenic genome modification in plant cells." Plant Physiol 154(3): 1079-1087. http://www.ncbi.nlm.nih.gov/pubmed/20876340.

Maruyama, K. and D. L. Hartl (1991). "Evidence for interspecific transfer of the transposable element mariner between\ Drosophila and Zaprionus." J Mol Evol 33(6): 514-524. http://www.ncbi.nlm.nih.gov/pubmed/1664000.

Masi, M. and C. Wandersman (2010). "Multiple signals direct the assembly and function of a type 1 secretion system." J Bacteriol 192(15): 3861-3869. http://www.ncbi.nlm.nih.gov/pubmed/20418390.

Mathivanan, S., H. Ji, et al. (2010). "Exosomes: extracellular organelles important in intercellular communication." J Proteomics 73(10): 1907-1920. http://www.ncbi.nlm.nih.gov/pubmed/20601276.

Maughan, H. and R. J. Redfield (2009). "Tracing the evolution of competence in Haemophilus influenzae." PLoS One\ 4\(6\): e5854\. http://www.ncbi.nlm.nih.gov/pubmed/19516897\.

McClintock, B. (1987). Discovery And Characterization of Transposable Elements: The Collected Papers of Barbara McClintock New York, Garland. .

McDaniel, L. D., E. Young, et al. (2010). "High Frequency of Horizontal Gene Transfer in the Oceans." Science 330(6000): 50. .

McNeil, N. (2004). "AluElements: Repetitive DNA as Facilitators of Chromosomal Rearrangement." J Assoc Genet Technol\ 30\(2\): 41-47\. http://www.ncbi.nlm.nih.gov/pubmed/15345864\.

McVey, M. and S. E. Lee (2008). "MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings." Trends Genet 24(11): 529-538. http://www.ncbi.nlm.nih.gov/pubmed/18809224.

Meaburn, K. J., T. Misteli, et al. (2007). "Spatial genome organization in the formation of chromosomal translocations." Semin Cancer Biol 17(1): 80-90. http://www.ncbi.nlm.nih.gov/pubmed/17137790.

Medhekar, B. and J. F. Miller (2007). "Diversity-generating retroelements." Curr Opin Microbiol 10(4): 388-395. http://www.ncbi.nlm.nih.gov/pubmed/17703991.

Meibom, K. L., M. Blokesch, et al. (2005). "Chitin induces natural competence in Vibrio cholerae." Science 310(5755): 1824-1827. .

Meile, L., P. Abendschein, et al. (1990). "Transduction in the archaebacterium Methanobacterium thermoautotrophicum Marburg." J Bacteriol 172(6): 3507-3508. http://www.ncbi.nlm.nih.gov/pubmed/2345156.

Menzel, G., D. Dechyeva, et al. (2006). "Mobilization and evolutionary history of miniature inverted-repeat transposable elements (MITEs) in Beta vulgaris L." Chromosome Res 14(8): 831-844. http://www.ncbi.nlm.nih.gov/pubmed/17171577.

Merendino, L., K. Perron, et al. (2006). "A novel multifunctional factor involved in trans-splicing of chloroplast introns in Chlamydomonas." Nucleic Acids Res 34(1): 262-274. http://www.ncbi.nlm.nih.gov/pubmed/16407333.

Metcalf, W. W., J. K. Zhang, et al. (1997). "A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors." Proc Natl Acad Sci U S A 94(6): 2626-2631. http://www.ncbi.nlm.nih.gov/pubmed/9122246.

Miller, J. C., S. Tan, et al. (2011). "A TALE nuclease architecture for efficient genome editing." Nat Biotechnol 29(2): 143-148. http://www.ncbi.nlm.nih.gov/pubmed/21179091.

Miller, J. L., J. Le Coq, et al. (2008). "Selective ligand recognition by a diversity-generating retroelement variable protein." PLoS Biol 6(6): e131. http://www.ncbi.nlm.nih.gov/pubmed/18532877.

Mimitou, E. P. and L. S. Symington (2009). "DNA end resection: many nucleases make light work." DNA Repair (Amst) 8(9): 983-995. http://www.ncbi.nlm.nih.gov/pubmed/19473888.

Mischo, H. E., B. Gomez-Gonzalez, et al. (2011). "Yeast Sen1 Helicase Protects the Genome from Transcription-Associated Instability." Molecular cell 41(1): 21-32. .

Miyazaki, T., D. A. Bressan, et al. (2004). "In vivo assembly and disassembly of Rad51 and Rad52 complexes during double-strand break repair." Embo J 23(4): 939-949. http://www.ncbi.nlm.nih.gov/pubmed/14765116.

Mladenov, E. and G. Iliakis (2011). "Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways." Mutat Res 711(1-2): 61-72. http://www.ncbi.nlm.nih.gov/pubmed/21329706.

Mohr, G. and A. M. Lambowitz (2003). "Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants." Nucleic Acids Res 31(2): 647-652. http://www.ncbi.nlm.nih.gov/pubmed/12527773.

Momose, M., Y. Abe, et al. (2010). "Miniature inverted-repeat transposable elements of Stowaway are active in potato." Genetics 186(1): 59-66. http://www.ncbi.nlm.nih.gov/pubmed/20610409.

Montano, S. P. and P. A. Rice (2011). "Moving DNA around: DNA transposition and retroviral integration." Curr Opin Struct Biol 21(3): 370-378. http://www.ncbi.nlm.nih.gov/pubmed/21439812.

Moran, J. and N. Gilbert (2002). Mammalian LINE-1 Retrotransposons and Related Elements, Macmillan Publishers Limited. All rights reserved. .

Moriarty, H. T. and L. R. Webster (2003). "Fragile sites and bladder cancer." Cancer Genet Cytogenet 140(2): 89-98. http://www.ncbi.nlm.nih.gov/pubmed/12645645.

Morrish, T. A., J. L. Garcia-Perez, et al. (2007). "Endonuclease-independent LINE-1 retrotransposition at mammalian telomeres." Nature 446(7132): 208-212. http://www.ncbi.nlm.nih.gov/pubmed/17344853.

Morrish, T. A., N. Gilbert, et al. (2002). "DNA repair mediated by endonuclease-independent LINE-1 retrotransposition." Nat Genet 31(2): 159-165. http://www.ncbi.nlm.nih.gov/pubmed/12006980.

Mougel, M., L. Houzet, et al. (2009). "When is it time for reverse transcription to start and go?" Retrovirology 6: 24. http://www.ncbi.nlm.nih.gov/pubmed/19261185.

Mower, J. P., S. Stefanovic, et al. (2004). "Plant genetics: gene transfer from parasitic to host plants." Nature 432(7014): 165-166. http://www.ncbi.nlm.nih.gov/pubmed/15538356.

Mueller, S., J. R. Coleman, et al. (2009). "Putting synthesis into biology: a viral view of genetic engineering through de novo gene and genome synthesis." Chem Biol 16(3): 337-347. http://www.ncbi.nlm.nih.gov/pubmed/19318214.

Muller, A. E., R. G. Atkinson, et al. (2007). "Microhomologies between T-DNA ends and target sites often occur in inverted orientation and may be responsible for the high frequency of T-DNA-associated inversions." Plant Cell Rep 26(5): 617-630. http://www.ncbi.nlm.nih.gov/pubmed/17205344.

Mullineux, S. T., M. Costa, et al. (2010). "A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions." Rna 16(9): 1818-1831. http://www.ncbi.nlm.nih.gov/pubmed/20656798.

Munoz-Adelantado, E., J. San Filippo, et al. (2003). "Mobility of the Sinorhizobium meliloti group II intron RmInt1 occurs by reverse splicing into DNA, but requires an unknown reverse transcriptase priming mechanism." J Mol Biol 327(5): 931-943. http://www.ncbi.nlm.nih.gov/pubmed/12662921.

Munoz-Lopez, M. and J. L. Garcia-Perez (2010). "DNA transposons: nature and applications in genomics." Curr Genomics 11(2): 115-128. .

Murray, J. A. (1987). "Bending the rules: the 2-mu plasmid of yeast." Mol Microbiol 1(1): 1-4. http://www.ncbi.nlm.nih.gov/pubmed/3330752.

Myers, R. S. and F. W. Stahl (1994). "Chi and the RecBC D enzyme of Escherichia coli." Annu Rev Genet 28: 49-70. http://www.ncbi.nlm.nih.gov/pubmed/7893137.

Napolitano, R., R. Janel-Bintz, et al. (2000). "All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis." Embo J 19(22): 6259-6265. http://www.ncbi.nlm.nih.gov/pubmed/11080171.

Naranjo, T. and E. Corredor (2008). "Nuclear architecture and chromosome dynamics in the search of the pairing partner in meiosis in plants." Cytogenet Genome Res 120(3-4): 320-330. http://www.ncbi.nlm.nih.gov/pubmed/18504361.

Navarro, J., R. Risco, et al. (2008). "Gene therapy and intracytoplasmatic sperm injection (ICSI) - a review." Placenta 29 Suppl B: 193-199. http://www.ncbi.nlm.nih.gov/pubmed/18790332.

Nehls, R., G. Krumbiegel-Schroeren, et al. (1986). "Development of protoplast fusion products." Results Probl Cell Differ 12: 67-108. http://www.ncbi.nlm.nih.gov/pubmed/3529272.

Nern, A., B. D. Pfeiffer, et al. (2011). "Multiple new site-specific recombinases for use in manipulating animal genomes." Proc Natl Acad Sci U S A 108(34): 14198-14203. http://www.ncbi.nlm.nih.gov/pubmed/21831835.

Neumann, P., A. Navratilova, et al. (2011). "Plant centromeric retrotransposons: a structural and cytogenetic perspective." Mob DNA 2(1): 4. http://www.ncbi.nlm.nih.gov/pubmed/21371312.

Nielsen, H. and S. D. Johansen (2009). "Group I introns: Moving in new directions." RNA Biol 6(4): 375-383. http://www.ncbi.nlm.nih.gov/pubmed/19667762.

Nikoh, N. and A. Nakabachi (2009). "Aphids acquired symbiotic genes via lateral gene transfer." BMC Biol 7: 12. http://www.ncbi.nlm.nih.gov/pubmed/19284544.

Nikoh, N., K. Tanaka, et al. (2008). "Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes." Genome Res 18(2): 272-280. http://www.ncbi.nlm.nih.gov/pubmed/18073380.

Nisa-Martinez, R., J. I. Jimenez-Zurdo, et al. (2007). "Dispersion of the RmInt1 group II intron in the Sinorhizobium meliloti genome upon acquisition by conjugative transfer." Nucleic Acids Res 35(1): 214-222. http://www.ncbi.nlm.nih.gov/pubmed/17158161.

Nishant, K. T. and M. R. Rao (2006). "Molecular features of meiotic recombination hot spots." Bioessays 28(1): 45-56. http://www.ncbi.nlm.nih.gov/pubmed/16369948.

Nishihara, H. and N. Okada (2008). "Retroposons: genetic footprints on the evolutionary paths of life." Methods Mol Biol 422: 201-225. http://www.ncbi.nlm.nih.gov/pubmed/18629669.

Noah, J. W., S. Park, et al. (2006). "Atomic force microscopy reveals DNA bending during group II intron ribonucleoprotein particle integration into double-stranded DNA." Biochemistry 45(41): 12424-12435. http://www.ncbi.nlm.nih.gov/pubmed/17029398.

Novick, P. A., J. D. Smith, et al. (2011). "The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis." Genome Biol Evol 3: 1-14. http://www.ncbi.nlm.nih.gov/pubmed/21127169.

O'Keefe, L. V. and R. I. Richards (2006). "Common chromosomal fragile sites and cancer: focus on FRA16D." Cancer Lett 232(1): 37-47. http://www.ncbi.nlm.nih.gov/pubmed/16242840.

O'Neill, C., G. V. Horvath, et al. (1993). "Chloroplast transformation in plants: polyethylene glycol (PEG) treatment of protoplasts is an alternative to biolistic delivery systems." Plant J 3(5): 729-738. http://www.ncbi.nlm.nih.gov/pubmed/8397038.

Odom, O. W., D. L. Shenkenberg, et al. (2004). "A horizontally acquired group II intron in the chloroplast psbA gene of a psychrophilic Chlamydomonas: in vitro self-splicing and genetic evidence for maturase activity." RNA 10(7): 1097-1107. http://www.ncbi.nlm.nih.gov/pubmed/15208445.

Ogiwara, H. and T. Kohno (2011). "Essential factors for incompatible DNA end joining at chromosomal DNA double strand breaks in vivo." PLoS One 6(12): e28756. http://www.ncbi.nlm.nih.gov/pubmed/22194904.

Ohshima, K., M. Hattori, et al. (2003). "Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates." Genome Biol 4(11): R74. http://www.ncbi.nlm.nih.gov/pubmed/14611660.

Ohshima, K. and N. Okada (2005). "SINEs and LINEs: symbionts of eukaryotic genomes with a common tail." Cytogenet Genome Res 110(1-4): 475-490. http://www.ncbi.nlm.nih.gov/pubmed/16093701.

Ostertag, E. M., J. L. Goodier, et al. (2003). "SVA elements are nonautonomous retrotransposons that cause disease in humans." Am J Hum Genet 73(6): 1444-1451. http://www.ncbi.nlm.nih.gov/pubmed/14628287.

Pacher, M., W. Schmidt-Puchta, et al. (2007). "Two unlinked double-strand breaks can induce reciprocal exchanges in plant genomes via homologous recombination and nonhomologous end joining." Genetics 175(1): 21-29. http://www.ncbi.nlm.nih.gov/pubmed/17057227.

Pajunen, M. I., T. S. Rasila, et al. (2010). "Universal platform for quantitative analysis of DNA transposition." Mob DNA 1(1): 24. http://www.ncbi.nlm.nih.gov/pubmed/21110848.

Pannunzio, N. R., G. M. Manthey, et al. (2010). "RAD59 and RAD1 cooperate in translocation formation by single-strand annealing in Saccharomyces cerevisiae." Curr Genet 56(1): 87-100. http://www.ncbi.nlm.nih.gov/pubmed/20012294.

Pannunzio, N. R., G. M. Manthey, et al. (2010). "RAD59 and RAD1 cooperate in translocation formation by single-strand annealing in\ Saccharomyces cerevisiae." Curr Genet\ 56\(1\): 87-100\. http://www.ncbi.nlm.nih.gov/pubmed/20012294\.

Pappas, K. M. and S. C. Winans (2003). "Plant transformation by coinoculation with a disarmed Agrobacterium tumefaciens strain and an Escherichia coli strain carrying mobilizable transgenes." Appl Environ Microbiol 69(11): 6731-6739. http://www.ncbi.nlm.nih.gov/pubmed/14602634.

Paprotka, T., K. A. Delviks-Frankenberry, et al. (2011). "Recombinant origin of the retrovirus XMRV." Science 333(6038): 97-101. http://www.ncbi.nlm.nih.gov/pubmed/21628392.

Patel, G. B., J. H. Nash, et al. (1994). "Natural and Electroporation-Mediated Transformation of Methanococcus voltae Protoplasts." Appl Environ Microbiol 60(3): 903-907. http://www.ncbi.nlm.nih.gov/pubmed/16349218.

Patel, M., Q. Jiang, et al. (2010). "A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V." Crit Rev Biochem Mol Biol 45(3): 171-184. http://www.ncbi.nlm.nih.gov/pubmed/20441441.

Patnaik, R., S. Louie, et al. (2002). "Genome shuffling of Lactobacillus for improved acid tolerance." Nat Biotechnol 20(7): 707-712. http://www.ncbi.nlm.nih.gov/pubmed/12089556.

Pedersen, M. and A. Phillips (2009). "Towards programming languages for genetic engineering of living cells." J R Soc Interface\ 6 Suppl 4\: S437-450\. http://www.ncbi.nlm.nih.gov/pubmed/19369220\.

Pegtel, D. M., K. Cosmopoulos, et al. (2010). "Functional delivery of viral miRNAs via exosomes." Proc Natl Acad Sci U S A 107(14): 6328-6333. http://www.ncbi.nlm.nih.gov/pubmed/20304794.

Pegtel, D. M., M. D. van de Garde, et al. (2011). "Viral miRNAs exploiting the endosomal-exosomal pathway for intercellular cross-talk and immune evasion." Biochim Biophys Acta 1809(11-12): 715-721. http://www.ncbi.nlm.nih.gov/pubmed/21855666.

Pelczar, P., V. Kalck, et al. (2004). "Agrobacterium proteins VirD2 and VirE2 mediate precise integration of synthetic T-DNA complexes in mammalian cells." EMBO Rep 5(6): 632-637. http://www.ncbi.nlm.nih.gov/pubmed/15153934.

Pennisi, E. (2009). "Genetic engineering. Two steps forward for synthetic biology." Science\ 325\(5943\): 928-929\. http://www.ncbi.nlm.nih.gov/pubmed/19696321\.

Perler, F. B. (2002). "InBase: the Intein Database." Nucleic Acids Res 30(1): 383-384. http://www.ncbi.nlm.nih.gov/pubmed/11752343.

Perrin, D., E. Ballestar, et al. (2007). "Specific hypermethylation of LINE-1 elements during abnormal overgrowth and differentiation of human placenta." Oncogene 26(17): 2518-2524. http://www.ncbi.nlm.nih.gov/pubmed/17043645.

Perrin, D., E. Ballestar, et al. (2007). "Specific hypermethylation of LINE-1 elements during abnormal overgrowth and\ differentiation of human placenta." Oncogene\ 26\(17\): 2518-2524\. http://www.ncbi.nlm.nih.gov/pubmed/17043645\.

Pham, P., S. Rangarajan, et al. (2001). "Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli." Proc Natl Acad Sci U S A 98(15): 8350-8354. http://www.ncbi.nlm.nih.gov/pubmed/11459974.

Picard, G. (1976). "Non-mendelian female sterility in Drosophila melanogaster: hereditary transmission of I factor." Genetics 83(1): 107-123. http://www.ncbi.nlm.nih.gov/pubmed/817964.

Pichiorri, F., H. Ishii, et al. (2008). "Molecular parameters of genome instability: roles of fragile genes at common fragile sites." J Cell Biochem 104(5): 1525-1533. http://www.ncbi.nlm.nih.gov/pubmed/18393361.

Pickeral, O. K., W. Makalowski, et al. (2000). "Frequent human genomic DNA transduction driven by LINE-1 retrotransposition." Genome Res 10(4): 411-415. http://www.ncbi.nlm.nih.gov/pubmed/10779482.

Piednoel, M. and E. Bonnivard (2009). "DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms." BMC Evol Biol 9: 86. http://www.ncbi.nlm.nih.gov/pubmed/19400949.

Pietrokovski, S. (2001). "Intein spread and extinction in evolution." Trends Genet 17(8): 465-472. http://www.ncbi.nlm.nih.gov/pubmed/11485819.

Pitcher, R. S., N. C. Brissett, et al. (2007). "Nonhomologous end-joining in bacteria: a microbial perspective." Annu Rev Microbiol 61: 259-282. http://www.ncbi.nlm.nih.gov/pubmed/17506672.

Pitcher, R. S., T. E. Wilson, et al. (2005). "New insights into NHEJ repair processes in prokaryotes." Cell Cycle 4(5): 675-678. .

Podar, M., L. Mullineaux, et al. (2002). "Bacterial group II introns in a deep-sea hydrothermal vent environment." Appl Environ Microbiol 68(12): 6392-6398. http://www.ncbi.nlm.nih.gov/pubmed/12450865.

Poma, A., T. Limongi, et al. (2006). "Current state and perspectives of truffle genetics and sustainable biotechnology." Appl Microbiol Biotechnol 72(3): 437-441. http://www.ncbi.nlm.nih.gov/pubmed/16802150.

Pomerantseva, E., I. Biryukova, et al. (2006). "Transposition of Regulatory Elements by P-Element-Mediated Rearrangements in Drosophila melanogaster." Genetics 172(4): 2283-2291. http://www.ncbi.nlm.nih.gov/pubmed/16387869.

Postberg, J., K. Heyse, et al. (2008). "Spatial and temporal plasticity of chromatin during programmed DNA-reorganization in Stylonychia macronuclear development." Epigenetics Chromatin 1(1): 3. http://www.ncbi.nlm.nih.gov/pubmed/19014664.

Poteete, A. R., A. C. Fenton, et al. (2004). "Chromosomal duplications and cointegrates generated by the bacteriophage lamdba Red system in Escherichia coli K-12." BMC Mol Biol 5(1): 22. http://www.ncbi.nlm.nih.gov/pubmed/15596011.

Potrykus, I. (1990). "Gene transfer methods for plants and cell cultures." Ciba Found Symp 154: 198-208; discussion 208-112. http://www.ncbi.nlm.nih.gov/pubmed/2086036.

Poulter, R. T. and T. J. Goodwin (2005). "DIRS-1 and the other tyrosine recombinase retrotransposons." Cytogenet Genome Res 110(1-4): 575-588. http://www.ncbi.nlm.nih.gov/pubmed/16093711.

Prangishvili, D. (2003). "Evolutionary insights from studies on viruses of hyperthermophilic archaea." Res Microbiol 154(4): 289-294. http://www.ncbi.nlm.nih.gov/pubmed/12798234.

Prangishvili, D., S. V. Albers, et al. (1998). "Conjugation in archaea: frequent occurrence of conjugative plasmids in Sulfolobus." Plasmid 40(3): 190-202. http://www.ncbi.nlm.nih.gov/pubmed/9806856.

Prangishvili, D., P. Forterre, et al. (2006). "Viruses of the Archaea: a unifying view." Nat Rev Microbiol 4(11): 837-848. http://www.ncbi.nlm.nih.gov/pubmed/17041631.

Prangishvili, D. and R. A. Garrett (2005). "Viruses of hyperthermophilic Crenarchaea." Trends Microbiol 13(11): 535-542. http://www.ncbi.nlm.nih.gov/pubmed/16154357.

Prangishvili, D., R. A. Garrett, et al. (2006). "Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life." Virus Res 117(1): 52-67. http://www.ncbi.nlm.nih.gov/pubmed/16503363.

Pritham, E. J. and C. Feschotte (2007). "Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus." Proc Natl Acad Sci U S A 104(6): 1895-1900. http://www.ncbi.nlm.nih.gov/pubmed/17261799.

Pukatzki, S., S. B. McAuley, et al. (2009). "The type VI secretion system: translocation of effectors and effector-domains." Curr Opin Microbiol 12(1): 11-17. http://www.ncbi.nlm.nih.gov/pubmed/19162533.

Pyle, A. M. (2010). "The tertiary structure of group II introns: implications for biological function and evolution." Crit Rev Biochem Mol Biol 45(3): 215-232. http://www.ncbi.nlm.nih.gov/pubmed/20446804.

Radman-Livaja, M., C. Shaw, et al. (2003). "Arm sequences contribute to the architecture and catalytic function of a lambda integrase-Holliday junction complex." Mol Cell 11(3): 783-794. http://www.ncbi.nlm.nih.gov/pubmed/12667459.

Raiz, J., A. Damert, et al. (2011). "The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery." Nucleic Acids Res. http://www.ncbi.nlm.nih.gov/pubmed/22053090.

Rajeev, L., K. Malanowska, et al. (2009). "Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions." Microbiol Mol Biol Rev 73(2): 300-309. http://www.ncbi.nlm.nih.gov/pubmed/19487729.

Ramachandran, S. and V. Palanisamy (2011). "Horizontal transfer of RNAs: exosomes as mediators of intercellular communication." Wiley Interdiscip Rev RNA. http://www.ncbi.nlm.nih.gov/pubmed/22012863.

Raman, B. and M. Stopfer (2008). "Olfactory coding: non-linear amplification separates smells." Curr Biol\ 18\(1\): R29-32\. http://www.ncbi.nlm.nih.gov/pubmed/18177710\.

Ramos, C., D. Bonenfant, et al. (2002). "Cell hybridization by electrofusion on filters." Anal Biochem 302(2): 213-219. http://www.ncbi.nlm.nih.gov/pubmed/11878799.

Ramos, K. S., Q. He, et al. (2007). "Computational and biological inference of gene regulatory networks of the LINE-1  retrotransposon." Genomics 90(2): 176-185. http://www.ncbi.nlm.nih.gov/pubmed/17521869.

Rawsthorne, H., K. N. Turner, et al. (2006). "Multicopy integration of heterologous genes, using the lactococcal group II intron targeted to bacterial insertion sequences." Appl Environ Microbiol 72(9): 6088-6093. http://www.ncbi.nlm.nih.gov/pubmed/16957233.

Redfield, R. J., W. A. Findlay, et al. (2006). "Evolution of competence and DNA uptake specificity in the Pasteurellaceae." BMC Evol Biol\ 6\: 82\. http://www.ncbi.nlm.nih.gov/pubmed/17038178\.

Rego, A. T., V. Chandran, et al. (2010). "Two-step and one-step secretion mechanisms in Gram-negative bacteria: contrasting the type IV secretion system and the chaperone-usher pathway of pilus biogenesis." Biochem J 425(3): 475-488. http://www.ncbi.nlm.nih.gov/pubmed/20070257.

Reilly, J. D. and R. F. Silva (1996). "Construction of portable intron cassettes for the delivery and expression of\ foreign genes." DNA Cell Biol\ 15\(12\): 1113-1120\. http://www.ncbi.nlm.nih.gov/pubmed/8985125\.

Repanas, K., N. Zingler, et al. (2007). "Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease." Nucleic Acids Res 35(14): 4914-4926. http://www.ncbi.nlm.nih.gov/pubmed/17626046.

Ricci, V., S. Regis, et al. (2003). "An Alu-mediated rearrangement as cause of exon skipping in Hunter disease." Hum Genet\ 112\(4\): 419-425\. http://www.ncbi.nlm.nih.gov/pubmed/12579417\.

Rice, P. A., K. W. Mouw, et al. (2010). "Orchestrating serine resolvases." Biochem Soc Trans 38(2): 384-387. http://www.ncbi.nlm.nih.gov/pubmed/20298188.

Richardson, A. O. and J. D. Palmer (2007). "Horizontal gene transfer in plants." J Exp Bot 58(1): 1-9. http://www.ncbi.nlm.nih.gov/pubmed/17030541.

Rocco, J. M. and G. Churchward (2006). "The integrase of the conjugative transposon Tn916 directs strand- and sequence-specific cleavage of the origin of conjugal transfer, oriT, by the endonuclease Orf20." J Bacteriol 188(6): 2207-2213. http://www.ncbi.nlm.nih.gov/pubmed/16513750.

Rong, Y. S. and K. G. Golic (2003). "The homologous chromosome is an effective template for the repair of mitotic DNA double-strand breaks in Drosophila." Genetics 165(4): 1831-1842. http://www.ncbi.nlm.nih.gov/pubmed/14704169.

Rossier, O., J. Dao, et al. (2008). "The type II secretion system of Legionella pneumophila elaborates two aminopeptidases, as well as a metalloprotease that contributes to differential infection among protozoan hosts." Appl Environ Microbiol 74(3): 753-761. http://www.ncbi.nlm.nih.gov/pubmed/18083880.

Roth, J. R. and D. I. Andersson (2004). "Amplification-mutagenesis--how growth under selection contributes to the origin\ of genetic diversity and explains the phenomenon of adaptive mutation." Res Microbiol 155(5): 342-351. http://www.ncbi.nlm.nih.gov/pubmed/15207866.

Rouchka, E., D. E. Montoya-Durango, et al. (2010). "Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data." BMC Bioinformatics 11 Suppl 9: S12. http://www.ncbi.nlm.nih.gov/pubmed/21044359.

Rowe-Magnus, D. A. (2009). "Integrase-directed recovery of functional genes from genomic libraries." Nucleic Acids Res 37(17): e118. http://www.ncbi.nlm.nih.gov/pubmed/19596808.

Rudzinski, W. E. and T. M. Aminabhavi (2010). "Chitosan as a carrier for targeted delivery of small interfering RNA." Int J Pharm 399(1-2): 1-11. http://www.ncbi.nlm.nih.gov/pubmed/20732398.

Ruiz-Herrera, A. and T. J. Robinson (2007). "Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies." BMC Evol Biol 7: 199. http://www.ncbi.nlm.nih.gov/pubmed/17958882.

Rupnik, A., N. F. Lowndes, et al. (2010). "MRN and the race to the break." Chromosoma 119(2): 115-135. http://www.ncbi.nlm.nih.gov/pubmed/19862546.

Salacha, R., F. Kovacic, et al. (2010). "The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system." Environ Microbiol 12(6): 1498-1512. http://www.ncbi.nlm.nih.gov/pubmed/20192961.

San Filippo, J., P. Sung, et al. (2008). "Mechanism of eukaryotic homologous recombination." Annu Rev Biochem 77: 229-257. http://www.ncbi.nlm.nih.gov/pubmed/18275380.

Savitha, S., S. Sadhasivam, et al. (2010). "Regeneration and molecular characterization of an intergeneric hybrid between Graphium putredinis and Trichoderma harzianum by protoplasmic fusion." Biotechnol Adv 28(3): 285-292. http://www.ncbi.nlm.nih.gov/pubmed/20064604.

Schaeffer, P., B. Cami, et al. (1976). "Fusion of bacterial protoplasts." Proc Natl Acad Sci U S A 73(6): 2151-2155. http://www.ncbi.nlm.nih.gov/pubmed/819934.

Schafer, B., L. Gan, et al. (2003). "Reverse transcriptase and reverse splicing activities encoded by the mobile group\ II intron cobI1 of fission yeast mitochondrial DNA." J Mol Biol\ 329\(2\): 191-206\. http://www.ncbi.nlm.nih.gov/pubmed/12758069\.

Schlacher, K., P. Pham, et al. (2006). "Roles of DNA polymerase V and RecA protein in SOS damage-induced mutation." Chem Rev\ 106\(2\): 406-419\. http://www.ncbi.nlm.nih.gov/pubmed/16464012\.

Schroder, G., R. Schuelein, et al. (2011). "Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae." Proc Natl Acad Sci U S A 108(35): 14643-14648. http://www.ncbi.nlm.nih.gov/pubmed/21844337.

Schulte-Uentrop, L., R. A. El-Awady, et al. (2008). "Distinct roles of XRCC4 and Ku80 in non-homologous end-joining of endonuclease- and ionizing radiation-induced DNA double-strand breaks." Nucleic Acids Res 36(8): 2561-2569. http://www.ncbi.nlm.nih.gov/pubmed/18332040.

Seitz, E. M., C. A. Haseltine, et al. (2001). "DNA recombination and repair in the archaea." Adv Appl Microbiol 50: 101-169. http://www.ncbi.nlm.nih.gov/pubmed/11677683.

Selmecki, A., A. Forche, et al. (2010). "Genomic plasticity of the human fungal pathogen Candida albicans." Eukaryot Cell 9(7): 991-1008. http://www.ncbi.nlm.nih.gov/pubmed/20495058.

Senf, F., J. Tommassen, et al. (2008). "Polar secretion of proteins via the Xcp type II secretion system in Pseudomonas aeruginosa." Microbiology 154(Pt 10): 3025-3032. http://www.ncbi.nlm.nih.gov/pubmed/18832308.

Sezutsu, H., E. Nitasaka, et al. (1995). "Evolution of the LINE-like I element in the Drosophila melanogaster species subgroup." Mol Gen Genet 249(2): 168-178. http://www.ncbi.nlm.nih.gov/pubmed/7500938.

Sheen, F. M., S. T. Sherry, et al. (2000). "Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition." Genome Res 10(10): 1496-1508. http://www.ncbi.nlm.nih.gov/pubmed/11042149.

Shegokar, R., L. Al Shaal, et al. (2011). "SiRNA delivery: challenges and role of carrier systems." Pharmazie 66(5): 313-318. http://www.ncbi.nlm.nih.gov/pubmed/21699063.

Shim, M. S. and Y. J. Kwon (2010). "Efficient and targeted delivery of siRNA in vivo." FEBS J 277(23): 4814-4827. http://www.ncbi.nlm.nih.gov/pubmed/21078116.

Siddique, A., N. Buisine, et al. (2011). "The transposon-like Correia elements encode numerous strong promoters and provide a potential new mechanism for phase variation in the meningococcus." PLoS Genet 7(1): e1001277. http://www.ncbi.nlm.nih.gov/pubmed/21283790.

Silverman, R. H., C. Nguyen, et al. (2010). "The human retrovirus XMRV in prostate cancer and chronic fatigue syndrome." Nat Rev Urol 7(7): 392-402. http://www.ncbi.nlm.nih.gov/pubmed/20517289.

Simoes-Barbosa, A., E. R. Arganaraz, et al. (2006). "Hitchhiking Trypanosoma cruzi minicircle DNA affects gene expression in human host cells via LINE-1 retrotransposon." Mem Inst Oswaldo Cruz 101(8): 833-843. http://www.ncbi.nlm.nih.gov/pubmed/17293976.

Simon, D. M., N. A. Clarke, et al. (2008). "Group II introns in eubacteria and archaea: ORF-less introns and new varieties." RNA 14(9): 1704-1713. http://www.ncbi.nlm.nih.gov/pubmed/18676618.

Singer, T., M. J. McConnell, et al. (2010). "LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes?" Trends Neurosci 33(8): 345-354. http://www.ncbi.nlm.nih.gov/pubmed/20471112.

Singh, P., P. Tripathi, et al. (2009). "Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA binding, helical distortion, and cleavage compared with a canonical LAGLIDADG homing endonuclease." J Biol Chem 284(38): 25912-25928. http://www.ncbi.nlm.nih.gov/pubmed/19605345.

Slack, A., P. C. Thornton, et al. (2006). "On the mechanism of gene amplification induced under stress in Escherichia coli." PLoS Genet 2(4): e48. http://www.ncbi.nlm.nih.gov/pubmed/16604155.

Sladewski, T. E., K. M. Hetrick, et al. (2011). "Escherichia coli Rep DNA helicase and error-prone DNA polymerase IV interact physically and functionally." Mol Microbiol 80(2): 524-541. http://www.ncbi.nlm.nih.gov/pubmed/21320186.

Smalheiser, N. R. (2007). "Exosomal transfer of proteins and RNAs at synapses in the nervous system." Biol Direct 2: 35. http://www.ncbi.nlm.nih.gov/pubmed/18053135.

Smith, K. and C. Spadafora (2005). "Sperm-mediated gene transfer: applications and implications." Bioessays 27(5): 551-562. http://www.ncbi.nlm.nih.gov/pubmed/15832378.

Smith, M. C., W. R. Brown, et al. (2010). "Site-specific recombination by phiC31 integrase and other large serine recombinases." Biochem Soc Trans 38(2): 388-394. http://www.ncbi.nlm.nih.gov/pubmed/20298189.

Snir, S. and E. Trifonov (2010). "A novel technique for detecting putative horizontal gene transfer in the sequence space." J Comput Biol 17(11): 1535-1548. http://www.ncbi.nlm.nih.gov/pubmed/20973741.

Snyder, J. C., K. Stedman, et al. (2003). "Viruses of hyperthermophilic Archaea." Res Microbiol 154(7): 474-482. http://www.ncbi.nlm.nih.gov/pubmed/14499933.

Soppa, J. (2006). "From genomes to function: haloarchaea as model organisms." Microbiology 152(Pt 3): 585-590. http://www.ncbi.nlm.nih.gov/pubmed/16514139.

Soppa, J., A. Baumann, et al. (2008). "Genomics and functional genomics with haloarchaea." Arch Microbiol 190(3): 197-215. http://www.ncbi.nlm.nih.gov/pubmed/18493745.

Spadafora, C. (2007). "Sperm-mediated gene transfer: mechanisms and implications." Soc Reprod Fertil Suppl 65: 459-467. http://www.ncbi.nlm.nih.gov/pubmed/17644984.

Spadafora, C. (2008). "A reverse transcriptase-dependent mechanism plays central roles in fundamental\ biological processes." Syst Biol Reprod Med\ 54\(1\): 11-21\. http://www.ncbi.nlm.nih.gov/pubmed/18543862\.

Sprague, G. F., Jr. (1991). "Genetic exchange between kingdoms." Curr Opin Genet Dev 1(4): 530-533. http://www.ncbi.nlm.nih.gov/pubmed/1822285.

Srikanta, D., S. K. Sen, et al. (2009). "Internal priming: an opportunistic pathway for L1 and Alu retrotransposition in hominins." Gene 448(2): 233-241. http://www.ncbi.nlm.nih.gov/pubmed/19501635.

Srikanta, D., S. K. Sen, et al. (2009). "An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair." Genomics 93(3): 205-212. http://www.ncbi.nlm.nih.gov/pubmed/18951971.

St Laurent, G., 3rd, N. Hammell, et al. (2010). "A LINE-1 component to human aging: do LINE elements exact a longevity cost for evolutionary advantage?" Mech Ageing Dev 131(5): 299-305. http://www.ncbi.nlm.nih.gov/pubmed/20346965.

Stabell, F. B., N. J. Tourasse, et al. (2007). "Group II intron in Bacillus cereus has an unusual 3' extension and splices 56 nucleotides downstream of the predicted site." Nucleic Acids Res 35(5): 1612-1623. http://www.ncbi.nlm.nih.gov/pubmed/17301069.

Stanton, T. B. (2007). "Prophage-like gene transfer agents-novel mechanisms of gene exchange for Methanococcus, Desulfovibrio, Brachyspira, and Rhodobacter species." Anaerobe 13(2): 43-49. http://www.ncbi.nlm.nih.gov/pubmed/17513139.

Stechmann, A., M. Baumgartner, et al. (2006). "The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic." BMC Evol Biol 6: 101. http://www.ncbi.nlm.nih.gov/pubmed/17123440.

Stoddard, B. L. (2005). "Homing endonuclease structure and function." Q Rev Biophys 38(1): 49-95. http://www.ncbi.nlm.nih.gov/pubmed/16336743.

Stracker, T. H. and J. H. Petrini (2011). "The MRE11 complex: starting from the ends." Nat Rev Mol Cell Biol 12(2): 90-103. http://www.ncbi.nlm.nih.gov/pubmed/21252998.

Sundin, G. W. and M. R. Weigand (2007). "The microbiology of mutability." FEMS Microbiol Lett 277(1): 11-20. http://www.ncbi.nlm.nih.gov/pubmed/17714481.

Suzuki, J., K. Yamaguchi, et al. (2009). "Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition." PLoS Genet 5(4): e1000461. http://www.ncbi.nlm.nih.gov/pubmed/19390601.

Szekvolgyi, L. and A. Nicolas (2010). "From meiosis to postmeiotic events: homologous recombination is obligatory but flexible." FEBS J 277(3): 571-589. http://www.ncbi.nlm.nih.gov/pubmed/20015080.

Takahashi, M. and B. Norden (1994). "Structure of RecA-DNA complex and mechanism of DNA strand exchange reaction in homologous recombination." Adv Biophys 30: 1-35. http://www.ncbi.nlm.nih.gov/pubmed/7709802.

Takahashi, T., G. Burguiere-Slezak, et al. (2011). "Topoisomerase 1 provokes the formation of short deletions in repeated sequences upon high transcription in Saccharomyces cerevisiae." Proceedings of the National Academy of Sciences 108(2): 692-697. .

Tam, W., S. H. Hughes, et al. (2002). "Avian bic, a gene isolated from a common retroviral site in avian leukosis virus-induced lymphomas that encodes a noncoding RNA, cooperates with c-myc in lymphomagenesis and erythroleukemogenesis." J Virol 76(9): 4275-4286. http://www.ncbi.nlm.nih.gov/pubmed/11932393.

Tanaka, H. and M. C. Yao (2009). "Palindromic gene amplification--an evolutionarily conserved role for DNA inverted repeats in the genome." Nat Rev Cancer 9(3): 216-224. http://www.ncbi.nlm.nih.gov/pubmed/19212324.

Tang, W., M. Dominska, et al. (2011). "Friedreich's ataxia (GAA)n*(TTC)n repeats strongly stimulate mitotic crossovers in Saccharomyces cerevisae." PLoS Genet 7(1): e1001270. http://www.ncbi.nlm.nih.gov/pubmed/21249181.

Thomas, J., M. Sorourian, et al. (2011). "The limited distribution of Helitrons to vesper bats supports horizontal transfer." Gene 474(1-2): 52-58. http://www.ncbi.nlm.nih.gov/pubmed/21193022.

Thompson, B. K. and S. M. Christensen (2011). "Independently derived targeting of 28S rDNA by A- and D-clade R2 retrotransposons: Plasticity of integration mechanism." Mob Genet Elements 1(1): 29-37. http://www.ncbi.nlm.nih.gov/pubmed/22016843.

Tippin, B., P. Pham, et al. (2004). "Error-prone replication for better or worse." Trends Microbiol\ 12\(6\): 288-295\. http://www.ncbi.nlm.nih.gov/pubmed/15165607\.

Tourasse, N. J. and A. B. Kolsto (2008). "Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution." Nucleic Acids Res 36(14): 4529-4548. http://www.ncbi.nlm.nih.gov/pubmed/18587153.

Tourasse, N. J., F. B. Stabell, et al. (2010). "Structural and functional evolution of group II intron ribozymes: insights from unusual elements carrying a 3' extension." N Biotechnol 27(3): 204-211. http://www.ncbi.nlm.nih.gov/pubmed/20219707.

Trontelj, K., M. Usaj, et al. (2010). "Cell electrofusion visualized with fluorescence microscopy." J Vis Exp(41). http://www.ncbi.nlm.nih.gov/pubmed/20644506.

Tsai, H. H., C. H. Huang, et al. (2008). "Terminal proteins of Streptomyces chromosome can target DNA into eukaryotic nuclei." Nucleic Acids Res 36(10): e62. http://www.ncbi.nlm.nih.gov/pubmed/18480119.

Tseng, T. T., B. M. Tyler, et al. (2009). "Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology." BMC Microbiol 9 Suppl 1: S2. http://www.ncbi.nlm.nih.gov/pubmed/19278550.

Turan, S., M. Galla, et al. (2011). "Recombinase-mediated cassette exchange (RMCE): traditional concepts and current challenges." J Mol Biol 407(2): 193-221. http://www.ncbi.nlm.nih.gov/pubmed/21241707.

Tzfira, T. and V. Citovsky (2006). "Agrobacterium-mediated genetic transformation of plants: biology and biotechnology." Curr Opin Biotechnol 17(2): 147-154. http://www.ncbi.nlm.nih.gov/pubmed/16459071.

Vaisvila, R., R. D. Morgan, et al. (2001). "Discovery and distribution of super-integrons among pseudomonads." Mol Microbiol 42(3): 587-601. http://www.ncbi.nlm.nih.gov/pubmed/11722728.

Valles, Y., K. M. Halanych, et al. (2008). "Group II introns break new boundaries: presence in a bilaterian's genome." PLoS One 3(1): e1488. http://www.ncbi.nlm.nih.gov/pubmed/18213396.

van Boxtel, R. and E. Cuppen (2010). "Rat traps: filling the toolbox for manipulating the rat genome." Genome Biol 11(9): 217. http://www.ncbi.nlm.nih.gov/pubmed/20887642.

van der Kuyl, A. C., M. Cornelissen, et al. (2010). "Of Mice and Men: On the Origin of XMRV." Front Microbiol 1: 147. http://www.ncbi.nlm.nih.gov/pubmed/21687768.

Vanhooff, V., C. Normand, et al. (2010). "Control of directionality in the DNA strand-exchange reaction catalysed by the tyrosine recombinase TnpI." Nucleic Acids Res 38(6): 2044-2056. http://www.ncbi.nlm.nih.gov/pubmed/20044348.

Venken, K. J., K. L. Schulze, et al. (2011). "MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes." Nat Methods 8(9): 737-743. http://www.ncbi.nlm.nih.gov/pubmed/21985007.

Von Hoff, D. D. (1991). "New mechanisms of gene amplification in drug resistance (the episome model)." Cancer Treat Res\ 57\: 1-11\. http://www.ncbi.nlm.nih.gov/pubmed/1686710\.

Wagner, J., H. Etienne, et al. (2002). "Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II, IV and V) deal with lesion/sequence context diversity." DNA Repair (Amst) 1(2): 159-167. http://www.ncbi.nlm.nih.gov/pubmed/12509262.

Wagner, J., P. Gruz, et al. (1999). "The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis." Mol Cell 4(2): 281-286. http://www.ncbi.nlm.nih.gov/pubmed/10488344.

Wahls, W. P. and M. K. Davidson (2010). "Discrete DNA sites regulate global distribution of meiotic recombination." Trends Genet 26(5): 202-208. http://www.ncbi.nlm.nih.gov/pubmed/20381894.

Walker, T. L., S. Purton, et al. (2005). "Microalgae as bioreactors." Plant Cell Rep 24(11): 629-641. http://www.ncbi.nlm.nih.gov/pubmed/16136314.

Wallace, N., B. J. Wagstaff, et al. (2008). "LINE-1 ORF1 protein enhances Alu SINE retrotransposition." Gene 419(1-2): 1-6. http://www.ncbi.nlm.nih.gov/pubmed/18534786.

Wang, G. and R. J. Maier (2008). "Critical role of RecN in recombinational DNA repair and survival of Helicobacter pylori." Infect Immun 76(1): 153-160. http://www.ncbi.nlm.nih.gov/pubmed/17954726.

Wang, H., J. Xing, et al. (2005). "SVA elements: a hominid-specific retroposon family." J Mol Biol 354(4): 994-1007. http://www.ncbi.nlm.nih.gov/pubmed/16288912.

Wang, Y., S. D. Goodman, et al. (2002). "Natural transformation and DNA uptake signal sequences in Actinobacillus actinomycetemcomitans." J Bacteriol 184(13): 3442-3449. http://www.ncbi.nlm.nih.gov/pubmed/12057937.

Waters, L. S., B. K. Minesinger, et al. (2009). "Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance." Microbiol Mol Biol Rev 73(1): 134-154. http://www.ncbi.nlm.nih.gov/pubmed/19258535.

Weber-Lotfi, F., N. Ibrahim, et al. (2009). "Developing a genetic approach to investigate the mechanism of mitochondrial competence for DNA import." Biochim Biophys Acta 1787(5): 320-327. http://www.ncbi.nlm.nih.gov/pubmed/19056337.

Wei, X. X., Z. Y. Shi, et al. (2010). "A mini-Mu transposon-based method for multiple DNA fragment integration into bacterial genomes." Appl Microbiol Biotechnol 87(4): 1533-1541. http://www.ncbi.nlm.nih.gov/pubmed/20508928.

Westwood, J. H., J. K. Roney, et al. (2009). "RNA translocation between parasitic plants and their hosts." Pest Manag Sci 65(5): 533-539. http://www.ncbi.nlm.nih.gov/pubmed/19253417.

Whitaker, J. W., G. A. McConkey, et al. (2009). "The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes." Genome Biol 10(4): R36. http://www.ncbi.nlm.nih.gov/pubmed/19368726.

Wicker, T., F. Sabot, et al. (2007). "A unified classification system for eukaryotic transposable elements." Nat Rev Genet 8(12): 973-982. http://www.ncbi.nlm.nih.gov/pubmed/17984973.

Williams, G. J., S. P. Lees-Miller, et al. (2010). "Mre11-Rad50-Nbs1 conformations and the control of sensing, signaling, and effector responses at DNA double-strand breaks." DNA Repair (Amst) 9(12): 1299-1306. http://www.ncbi.nlm.nih.gov/pubmed/21035407.

Wilson, T. E. and M. R. Lieber (1999). "Efficient processing of DNA ends during yeast nonhomologous end joining. Evidence for a DNA polymerase beta (Pol4)-dependent pathway." J Biol Chem 274(33): 23599-23609. http://www.ncbi.nlm.nih.gov/pubmed/10438542.

Winans, S. C. (1992). "Two-way chemical signaling in Agrobacterium-plant interactions." Microbiol Rev 56(1): 12-31. http://www.ncbi.nlm.nih.gov/pubmed/1579105.

Wolff, J. A. and V. Budker (2005). "The mechanism of naked DNA uptake and expression." Adv Genet 54: 3-20. http://www.ncbi.nlm.nih.gov/pubmed/16096005.

Wolff, J. A., R. W. Malone, et al. (1990). "Direct gene transfer into mouse muscle in vivo." Science 247(4949 Pt 1): 1465-1468. http://www.ncbi.nlm.nih.gov/pubmed/1690918.

Worrell, V. E., D. P. Nagle, Jr., et al. (1988). "Genetic transformation system in the archaebacterium Methanobacterium thermoautotrophicum Marburg." J Bacteriol 170(2): 653-656. http://www.ncbi.nlm.nih.gov/pubmed/3422229.

Wu, D., L. M. Topper, et al. (2008). "Recruitment and dissociation of nonhomologous end joining proteins at a DNA double-strand break in Saccharomyces cerevisiae." Genetics 178(3): 1237-1249. http://www.ncbi.nlm.nih.gov/pubmed/18245831.

Wu, Y., T. Sugiyama, et al. (2006). "DNA annealing mediated by Rad52 and Rad59 proteins." J Biol Chem\ 281\(22\): 15441-15449\. http://www.ncbi.nlm.nih.gov/pubmed/16565518\.

Yamada, M., T. Nunoshiba, et al. (2006). "Involvement of Y-family DNA polymerases in mutagenesis caused by oxidized nucleotides in Escherichia coli." J Bacteriol 188(13): 4992-4995. http://www.ncbi.nlm.nih.gov/pubmed/16788208.

Yamada-Inagawa, T., A. J. Klar, et al. (2007). "Schizosaccharomyces pombe switches mating type by the synthesis-dependent strand-annealing mechanism." Genetics 177(1): 255-265. http://www.ncbi.nlm.nih.gov/pubmed/17660548.

Yamamoto, E., M. Toyota, et al. (2008). "LINE-1 hypomethylation is associated with increased CpG island methylation in Helicobacter pylori-related enlarged-fold gastritis." Cancer Epidemiol Biomarkers Prev 17(10): 2555-2564. http://www.ncbi.nlm.nih.gov/pubmed/18842996.

Yamanaka, S. and H. M. Blau (2010). "Nuclear reprogramming to a pluripotent state by three approaches." Nature 465(7299): 704-712. http://www.ncbi.nlm.nih.gov/pubmed/20535199.

Yan, Y., Q. Liu, et al. (2010). "Evolution of functional and sequence variants of the mammalian XPR1 receptor for mouse xenotropic gammaretroviruses and the human-derived retrovirus XMRV." J Virol 84(22): 11970-11980. http://www.ncbi.nlm.nih.gov/pubmed/20844050.

Yanagimachi, R. (2005). "Intracytoplasmic injection of spermatozoa and spermatogenic cells: its biology and applications in humans and animals." Reprod Biomed Online 10(2): 247-288. http://www.ncbi.nlm.nih.gov/pubmed/15823233.

Yano, K. and D. J. Chen (2008). "Live cell imaging of XLF and XRCC4 reveals a novel view of protein assembly in the non-homologous end-joining pathway." Cell Cycle 7(10): 1321-1325. http://www.ncbi.nlm.nih.gov/pubmed/18418068.

Yano, K., K. Morotomi-Yano, et al. (2009). "Molecular mechanism of protein assembly on DNA double-strand breaks in the non-homologous end-joining pathway." J Radiat Res (Tokyo) 50(2): 97-108. http://www.ncbi.nlm.nih.gov/pubmed/19346677.

Yano, K., K. Morotomi-Yano, et al. (2009). "Cernunnos/XLF: a new player in DNA double-strand break repair." Int J Biochem Cell Biol 41(6): 1237-1240. http://www.ncbi.nlm.nih.gov/pubmed/18992362.

Yao, J. and A. M. Lambowitz (2007). "Gene targeting in gram-negative bacteria by use of a mobile group II intron ("Targetron") expressed from a broad-host-range vector." Appl Environ Microbiol 73(8): 2735-2743. http://www.ncbi.nlm.nih.gov/pubmed/17322321.

Yoshitake, K., H. Aoyagi, et al. (2010). "Creation of a novel telomere-cutting endonuclease based on the EN domain of telomere-specific non-long terminal repeat retrotransposon, TRAS1." Mob DNA 1(1): 13. http://www.ncbi.nlm.nih.gov/pubmed/20359340.

Yu, A. M. and M. McVey (2010). "Synthesis-dependent microhomology-mediated end joining accounts for multiple types of repair junctions." Nucleic Acids Res 38(17): 5706-5717. http://www.ncbi.nlm.nih.gov/pubmed/20460465.

Yu, F., N. Zingler, et al. (2001). "Methyl-CpG-binding protein 2 represses LINE-1 expression and retrotransposition but not Alu transcription." Nucleic Acids Res 29(21): 4493-4501. http://www.ncbi.nlm.nih.gov/pubmed/11691937.

Yuan, X., S. Naguib, et al. (2011). "Recent advances of siRNA delivery by nanoparticles." Expert Opin Drug Deliv 8(4): 521-536. http://www.ncbi.nlm.nih.gov/pubmed/21413903.

Yunis, J. J. (1987). "Multiple recurrent genomic rearrangements and fragile sites in human cancer." Somat Cell Mol Genet 13(4): 397-403. http://www.ncbi.nlm.nih.gov/pubmed/3331831.

Zhang, F., L. Cong, et al. (2011). "Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription." Nat Biotechnol 29(2): 149-153. http://www.ncbi.nlm.nih.gov/pubmed/21248753.

Zhu, L. and R. I. Mahato (2010). "Lipid and polymeric carrier-mediated nucleic acid delivery." Expert Opin Drug Deliv 7(10): 1209-1226. http://www.ncbi.nlm.nih.gov/pubmed/20836625.

Zhuang, F., M. Mastroianni, et al. (2009). "Linear group II intron RNAs can retrohome in eukaryotes and may use nonhomologous end-joining for cDNA ligation." Proc Natl Acad Sci U S A 106(43): 18189-18194. http://www.ncbi.nlm.nih.gov/pubmed/19833873.

Zillig, W., D. Prangishvilli, et al. (1996). "Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea." FEMS Microbiol Rev 18(2-3): 225-236. http://www.ncbi.nlm.nih.gov/pubmed/8639330.

Zimmerly, S., J. V. Moran, et al. (1999). "Group II intron reverse transcriptase in yeast mitochondria. Stabilization and regulation of reverse transcriptase activity by the intron RNA." J Mol Biol 289(3): 473-490. http://www.ncbi.nlm.nih.gov/pubmed/10356323.

Zingler, N., U. Willhoeft, et al. (2005). "Analysis of 5' junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5'-end attachment requiring microhomology-mediated end-joining." Genome Res 15(6): 780-789. http://www.ncbi.nlm.nih.gov/pubmed/15930490.

Zolotukhin, A. S., R. Schneider, et al. (2008). "The RNA transport element RTE is essential for IAP LTR-retrotransposon mobility." Virology 377(1): 88-99. http://www.ncbi.nlm.nih.gov/pubmed/18485438.

Zomer, A., T. Vendrig, et al. (2010). "Exosomes: Fit to deliver small RNA." Commun Integr Biol 3(5): 447-450. http://www.ncbi.nlm.nih.gov/pubmed/21057637.

Zuhorn, I. S., R. Kalicharan, et al. (2002). "Lipoplex-mediated transfection of mammalian cells occurs through the cholesterol-dependent clathrin-mediated pathway of endocytosis." J Biol Chem 277(20): 18021-18028. http://www.ncbi.nlm.nih.gov/pubmed/11875062.

Zupan, J., T. R. Muth, et al. (2000). "The transfer of DNA from agrobacterium tumefaciens into plants: a feast of fundamental insights." Plant J 23(1): 11-28. http://www.ncbi.nlm.nih.gov/pubmed/10929098.

Zupan, J. R. and P. Zambryski (1995). "Transfer of T-DNA from Agrobacterium to the plant cell." Plant Physiol 107(4): 1041-1047. http://www.ncbi.nlm.nih.gov/pubmed/7770515.