Structurity: Evolutional and Developmental Genetics of Biosystem Patterns


I. Signal Transduction and Gene Regulation in Cell lineage Differentiation

1. Alea A. Mills and Allan Bradley, From mouse to man: generating megabase chromosome rearrangements, Trends in Genetics Vol.17 No.6 June 2001:331-339.
2. Andrew S.I.Loudon, Andrei G. Semikhodskii, Susan K. Crosthwaite, A brief history of circadian time, TIG Nov.2000, Vol. 16, No. 11:477-481.
3. Burks DJ, de Mora JF, Schubert M, Withers DJ, Myers MG,Towery HH, Altamuro SL, Flint CL, White MF. IRS-2 pathways integrate female reproduction and energy homeostasis. Nature. 2000 Sep 21;407(6802):377-82.
4. Chawla A, Repa JJ, Evans RM, Mangelsdorf DJ. Nuclear receptors and lipid physiology: opening the X-files. Science. 2001 Nov 30;294(5548):1866-70. Review.
5. Corder R, Douthwaite JA, Lees DM, Khan NQ, Viseu Dos Santos AC, Wood EG, Carrier MJ. Endothelin-1 synthesis reduced by red wine. Nature. 2001 Dec 20-27;414(6866):863-4.
6. Cowley MA, Smart JL, Rubinstein M, Cerdan MG, Diano S, Horvath TL, Cone RD, Low MJ. Leptin activates anorexigenic POMC neurons through a neural network in the arcuate nucleus. Nature. 2001 May 24;411(6836):480-4.
7. Daniel Vaiman, Eric Pailhoux, Mammalian sex reversal and intersexuality: deciphering the sex-determination cascade, TIG, Nov. 2000 Vol 16, No.11:488-494.
8. Darlington TK, Wager-Smith K, Ceriani MF, Staknis D, Gekakis N, Steeves TD, Weitz CJ, Takahashi JS, Kay SA. Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim. Science. 1998 Jun 5;280(5369):1599-603.
9. Dubnau J, Grady L, Kitamoto T, Tully T.Disruption of neurotransmission in Drosophila mushroom body blocks retrieval but not acquisition of memory. Nature. 2001 May 24;411(6836):476-80.
10. Edith Hummler, Timonthy J. Cole, Julie A. Blendy, Ruth Ganss, Adriano Aguzzi, Wolfgang Schmid, Friedrich Beermann and Gunther Schutz, Targeted mutation of the CREB gene: compensation within the CREB/ATF family of transcription factors, Proc.Natl.Acad.Aci.USA, Vol.91,pp.5647-5651, Junr 1994, Biochemistry:5647-5651.
11. Enzo Medico, Giovanna Gambarotta, Alessandra Gentile, Paolo M. Comoglio, and Philippe Soriano, A gene trap vector system for identifying transcriptionally responsive genes, Nature Biotechnology Vol.19, June 2001:579-582.
12. Evelyn Strauss, Longevity, Growing old together, Science, 2001 Apr 6;292(5514):41-3.
13. Foulkes NS, Borjigin J, Snyder SH, Sassone-Corsi P, Transcriptional control of circadian hormone synthesis via the CREM feedback loop, Poc Natl Acad Sci USA 1996 Nov 26;93(24):14140-5.
14. D.E.Hansel, B.A. Eipper & G.V. Ronnett, Neuropeptide Y functions as a neuroproliferative factor, Nature Vol 410:940-944, 19 Appril, 2001.
15. Heremy S.D., Michael G. D., Signaling mechanisms in pituitary morphogenesis and cell fate determination, Curr Opin Cell Biol Dec.11(6):669-771999.
16. Hsu SY, Nakabayashi K, Nishi S, Kumagai J, Kudo M, Sherwood OD, Hsueh AJ. Activation of orphan receptors by the hormone relaxin. Science. 2002 Jan 25;295(5555):671-4.
17. Janetopoulos C, Jin T, Devreotes P. Receptor-mediated activation of heterotrimeric G-proteins in living cells. Science. 2001 Mar 23;291(5512):2408-11.
18. Jef Defalco, Mark Tomishima, Hongyan Liu, Connie Zhao, Xiaoli Cai, Jamey D. Marth, Lynn Enquist, Jeffrey M. Friedman, Virus-assisted mapping of neural inputs to a feeding center in the hypothalamus, Science 30 March 2001, Vol 291:2608-2613.
19. Johan de Rooij, Fried J. T. Zwartkruis, Mark H. G. Verheijen, Robbert H. Cool, Sebastian M. B. Nijman, alfred Wittinghofer & Johannes L. Bos, Epac is a Rap1 guanine-nucleotide-exchange factor directly activated by cyclic AMP. Nature Vol.396:474-477, 3 Dec. 1998.
20. Kazuhiro Yagita, Filippo Tamanini, Gijsbertus T.J. wan der Horst, Hitoshi Okamura, Molecular mechanisms of the biological clock in cultured fibroblasts, Science, Vol 292:278-281, 13 Appril, 2001.
21. Kathleen M. Scully, Eric M. Jacobson, Cristen Jepsen, Victoria Lunyak, Hector Viadiu, Catherine Carriere, David W. Rose, Farideh Hooshhmand, Aneel K. Aggarwal, Michael G. Rosenfeld, Allosteric effects of Pit-1 DANN sites on long-term repression in cell type specification, Science, Vol.290:1127-1131, 10 Nov. 2000.
22. Keigo Kohara, Akihiko Kitamura, Mieko Morishima, Tadaharu Tsumoto, Activity-dependent transfer of brain-derived neurotrophic factor to postsynaptic neurons, Science, Vol 291:2419-2422, 23 March 2001.
23. Kimi Araki, Masatake Araki, Jun-ichi Miyazaki, and Pierre Vassalli, Site-specific recombination of a transgene in fertilized eggs by transient expression of Cre recombinasde, Proc.Natl.Acad.Sci.USA,Vol.92,pp. 160-164, Jan.,1995, Genetics:160-164.
24. Kraynov VS, Chamberlain C, Bokoch GM, Schwartz MA, Slabaugh S, Hahn KM.Localized Rac activation dynamics visualized in living cells. Science. 2000 Oct 13;290(5490):333-7.
25. Louis Lefebvre, Nancy Dionne, Jana Karaskova, Jeremy A. Squire & Andras Nagy, Selection for transgene homozygosity in embryonic stem cells results in extensive loss of heterozygosity, Nature Genetics Vol.27, March 2001:257-258.
26. Marita Henandez, Maria Luisa Nieto and Mariano Sanchez Crespo, Cytosolic phospholipase A2 and the distinct transcriptional programs of astrocytoma cells, TINS, Vol. 23, No. 6: 259-264, 2000.
27. Masahiro Sato, Yukiko Yasuoka, Hisako Kodama, Toshiteru Watanabe, Jun-Ichi Miyazaki, and Minoru Kimura, New approach to cell lineage analysis in mammals using the Cre-loxP system, Molecular reproduction and development 56:34-44, 2000.
28. Matthew Freeman, Feedback control of intercellular signalling in development, Nature Vol. 408:313-319., 2000.
29. Nadya Lumelsky, Olivier Blondel, Pascal Laeng, Ivan Velasco, Rea Ravin, Ron Mckay, Differentiation of embryonic stem cells to insulin-secreting structures similar to pancreatic islets, Science Vol.292, 18 May 2001:1389-1394.
30. Ogg S, Paradis S, Gottlieb S, Patterson GI, Lee L, Tissenbaum HA, Ruvkun G.The Fork head transcription factor DAF-16 transduces insulin-like metabolic and longevity signals in C. elegans. Nature. 1997 Oct 30;389(6654):994-9.
31. Prashar Y, Weissman SM.Analysis of differential gene expression by display of 3' end restriction fragments of cDNAs. Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):659-63.
32. Pawson T, Protein modules and signalling networks, Nature 1995 Feb 16;373(6515):573-80.
33. Rhodes SJ, DiMattia GE, Rosenfeld MG, Transcriptional mechanisms in anterior pituitary cell differentiation, Curr Opin Genet Dev 1994 Oct;4(5):709-17.
34. San Ming Wang, Scott C. Fears, Lin Zhang, Jian-Jun Chen, and Janet D. Rowley, Screening poly(dA/dT)- cDNAs for gene identification, PNAS, Appril 11, 2000, Vol. 97, no.8:4162-4167.
35. Teb Abel, Kelsey C. Martin, Dusan Bartsch, Eric R. Kandel, Memory suppressor genes: inhibitory constraints on the storage of long-term memory, Science, vol.279:338-341, 16 Jan. 1998.
36. Teruhiko Wakayama, Viviane Tabar, Ivan Rodriguez, Anthony C. F. Perry, Lorenz Studer, Peter Mombaerts, Differentiation of embryonic stem cell lines generated from adult somatic cells by nuclear transfer, Science 27 Appril 2001, Vol. 292:740-742.
37. Timothy J. Boucher, Kenji Okuse, David L. H. Bennett, John B. Munson, John N. Wood, Stephen B. McMahon, Potent analgesic effects of GDNF in neuropathic pain states, Science 6 Oct. 2000, Vol 290:124-127.
38. Tommaso Simoncini, Ali Hafezi-Moghadam, Derek P. Brazil, Klaus Ley, William W. Chin & James K. Liao, Interaction of oestrogen receptor with the regulatory subunit of phosphatidylinositol-3-OH kinase, Nature Vol. 407:536-541, 28 Sept. 2000.
39. Treier M, Rosenfeld MG , The hypothalamic-pituitary axis:co-development of two organs, Curr Opin Cell Biol 1996 Dec;8(6):833-43.
40. Verveer PJ, Wouters FS, Reynolds AR, Bastiaens PI. Quantitative imaging of lateral ErbB1 receptor signal propagation in the plasma membrane. Science. 2000 Nov 24;290(5496):1567-70.
41. Wang SM, Fears SC, Zhang L, Chen JJ, Rowley JD, Screening poly(dA/dT)- cDNAs for gene identification, Proc Natl Acad Sci U S A 2000 Apr 11;97(8):4162-7.
42. Watanabe M, Kinutani M, Naito M, Ochi O, Takashima Y, Distribution analysis of transferred donor cells in avian blastodermal chimas, Development 1992 Feb;114(2):331-8.
43. Yatindra Prashar and Sherman M. Weissman, Analysis of differential gene expression by display of 3` end restriction fragments of cDNAs, Proc. Natl. Acad. Sci. Vol. 93:659-663, Jan. 1996.
44. Zhou C, Tsai SY, Tsai M, From apoptosis to angiogenesis: new insights into the roles receptors, chicken ovalbumin upstream promoter-transcription during development, Biochim Biophys Acta 2000 Mar 27;1470(2)M63-M68.

II. In Vitro Culture of PGCs, Embryo and Avian Transgenesis for Oviduct Bioreactor

1. Allioli N, Verdier G, Legras C, Use of gonadal primordial germ cells (PGCs) as tools for gene transfer in chickens, Methods Mol Biol 1997;62:425-32.
2. Avram D, Fields A, Top KP, Nevrivy DJ, Ishmael JE, Leid M, Isolation of a novel family of C(2)H(2) zinc finger proteins transcriptional repression mediated by chicken ovalbumin promoter transcription factor (COUP-TF) orphan nuclear, J Biol Chem 2000 Apr 7;275(14):10315-22.
3. Berger RR, Sanders MM, Estrogen modulases HNF-3beta mRNA levels in the development oviduct, DNA Cell Biol 2000 Feb;19(2):103-12.
4. Boerkoel CF, Federspiel MJ, Salter DW, Payne W, Crittenden LB, Kung HJ, Hughes SH, A new defective retrovial vector system based on the Bryan strain of Rous sarcoma virus, Virology 1993 Aug;195(2):669-79.
5. Bosselman RA, Hsu RY, Boggs T, Hu S, Bruszewski J, Ou S, Kozar L, Martin F, Green C, Jacobsen F, et al, Germline transmission of exogenous genes in the chicken, Science 1989 Jan 27;243(4890):533-5.
6. Bosselman RA, Hsu RY, Briskin MJ, Boggs T, Hu S, Nicolson M, Souza LM, Schultz JA, Rishell W, Stewart RG, Transmission of exogenous genes into the chicken, J Reprod Fertil Suppl 1990;41:183-95.
7. Briskin MJ, Hsu R, Boggs T, Schultz JA, Rishell W and Bosselman RA, Heritable retroviral transgenes are highly expressed in chickens, PNAS, Vol 88,1736-1740, 1991.
8. Chen HY, Garber EA, Mills E, Smith J, Kopchick JJ, DiLella AG, Smith RG, Vectors, promoters, and expression of genes in chick embryos, J Reprod Fertil Suppl 1990;41:173-82.
9. Cook RF, Cook SJ, Savon S, McGrane M, Hartitz M, Hanson RW, Hodgson CP, Liver-specific expression of a phosphoenolpyruvate carboxykinase-neo gene in genetically modified chickens, Poult Sci 1993 Mar;72(3):554-67.
10. Crittenden LB, Salter DW, Expression of retroviral genes in transgenic chickens, J Reprod Fertil Suppl 1990;41:163-71.
11. Dupin E, Ziller C, Le Douarin NM, The avian embryo as a model in developmental studies: chimeras and in vitro clonal analysis, Curr Top Dev Biol 1998;36:1-35.
12. Etches RJ, Verrinder Gibbins AM, Strategies for the production of transgenic chicken, Methods Mol Biol 1997;62:433-50.
13. Federspiel MJ, Crittenden LB, Provencher LP, Hughes SH, Experimentally introduced defective endogenous proviruses are highly expressioned in chickens, J Virol 1991 Jan;65(1):313-9.
14. Fekete DM and Cepko CL, Retroviral infection coupled with tissue transplantation limits gene transfer in the chicken embryo, PNAS, Vol 90, 2350-2354, 1993.
15. Fekete DM and Cepko CL, Replication-competent retroviral vectors encoding alkaline phosphatase reveal spatial restriction of viral gene expression/transduction in the chick embryo, Mol Cell Biol 1993 Apr;13(4):2604-13.
16. Fraser RA, Carsience RS, Clark ME, Etches RJ, Gibbins AM, Efficient incorporation of transfected blastodermal cells into chimeric chicken embryos, Int J Dev Biol 1993 Sep;37(3):381-5.
17. Gavora JS, Benkel B, Spencer JL, Gagnon C, Crittenden LB, Influence of the alv6 recombinant avian leukosis virus transgene on production traits and infection with avian tumor viruses inn chickens, Poult Sci 1995 May;74(5):852-63.
18. Hughes SH, Petropoulos CJ, Federspiel MJ, Sutrave P, Forry-Schaudies S, Bradac JA, Vectors and genes for imporovement of animal strains, J Reprod Fertil Suppl 1990;41:39-49.
19. Johnson AD, Krieg PA, pXeX, a vector for efficient expression of cloned sequences in Xenopus embryos, Gene 1994 Sep 30;147(2):223-6.
20. Karagenc L, Petitte JN, Soluble factors and the emergence of chick primordial germ cells in vitro, Poult Sci 2000 Jan;79(1):80-5.
21. Klinge CM, Role of estrogen receptor ligand and estrogen response element interaction with chicken ovalbumin upstream promoter transcription factor (COUP-TF), J Steroid Biochem Mol Biol 1999 Nov;71(1-2):1-19.
22. Kopchick JJ, Mills E, Rosenblum C, Taylor J, Macken F, Leung F, Smith J, Chen H, Methods for the introduction of recombinant DNA into chicken embryos, Biotechnology 1991;16:275-93.
23. Kuwana T, Hashimoto K, Nakanishi A, Yasuda Y, Tajima A, Naito M, Long-term culture of avian embryonic cells in vitro, Int J Dev Biol 1996 Oct;40(5):1061-4.
24. Lobe CG, Koop KE, Kreppner W, Lomeli H, Gertsenstein M, Nagy A, Z/AP, a double reporter for cre-mediated recombination, Dev Biol 1999 Apr 15;208(2):281-92.
25. Love J, Gribbin C, Mather C, Sang H, Transgenic birds by DNA microinjection, Biotechnology (N Y) 1994 Jan; 12(1):60-3.
26. Michel M. Sanders and G. Stanley McKnight, Chicken egg white genes: multihormonal regulation in a primary cell culture system, Endocrinology, Vol. 116, No. 1, 398-405, 1984.
27. Muramatsu T, Imai T, Park HM, Watanabe H, Nakamura A, Okumura J, Gene gun-mediated in vivo analysis of tissue-specific repression of gene transcription driven by the chicken ovalbumin promoter in the liver and oviduct of laying hens, Mol Cell Biochem 1998 Aug;185(1-2):27-32.
28. Nakanishi A, Iritani A, Gene transfer in the chicken by sperm-mediated methods, Mol Reprod Dev 1993 Oct;36(2):258-61.
29. Naito M, Sasaki E, Ohtaki M, Sakurai M, Introduction of exogenous DNA into somatic and germ cells of chickens by microinjection into the germinal disc of fertilized ova, Mol Reprod Dev 1994 Feb; 37(2):167-71.
30. Nathalie Allioli, Gerard Verdier, and Catherine Legras, Use of gonadal primordial germ cells (PGCs) as tools for gene transfer in chickens, Methods in Molecular Biology, 1997, Vol. 62: 425-32, Recomibinant gene expression protocols, edited by R. Tuan Humana Press Inc., Totowa, NJ.
31. Ono T, Murakami T, Mochii M, Agata K, Kino K, Otsuka K, Ohta M, Mizutani M, Yoshida M, Eguchi G, A complete culture system for avian transgenesis, supporting quail embryos from the single-cell stage to hatching, Dev Biol 1994, Jan;161(1):126-30.
32. Ono T, Muto S, Matsumoto T, Mochii M, Eguchi G, Gene transfer into circulating primordial germ cells of quail embryos, Transgenic Res 1995 Nov;4(6):369-77.
33. Petitte JN, Karagenc L, Ginsburg M, The origin of the avian germ line and transgenesis in birds, Poult Sci 1997 Aug;76(8):1084-92.
34. Pain B, Clark ME, Shen M, Nakazawa H, Sakurai M, Samarut J, Etches RJ, Long-term in vitro culture and characterisation of avian embryonic stem cells with multiple morphogenetic potentialities, Development 1996 Aug;122(8):2339-48.
35. Pain B, Chenevier P, Samarut J, Chicken embryonic stem cells and transgenic strategies, Cell Tissues Organs, 1999; 165(3-4):212-9.
36. Park HM, Muramatsu T, In vivo manipulation of foreign gene expression by steroid administration in the oviduct of laying hens, J Endocrinol 1999 Nov;163(2):173-9.
37. Petitte JN, Karagenc L, Ginsburg M, The origin of the avian germ line and transgensis in birds, Poult Sci 1997 Aug;76(8):1084-92.
38. Perry MM, Sang HM, Transgenesis in chickens, Transgenic Res 1993 May;2(3):125-33.
39. Reddy ST, Stoker AW and Bissell MJ, Expression of rouse sarcoma virus-derived retroviral vectors in the avian blastoderm: potential as stable genetic markers, PNAS, Vol 88, 10505-10509, 1991.
40. Robert J. Etches and Ann M. Verrinder Gibbins, Strategies for the production of transgenic chickens, Methods in Molecular Biology, Vol. 62: Recombinant Gene Expression Protocols, Edited by R. Tuan Humana Press Inc., Totowa, NJ.
41. Sanders MM, McKnight GS, Positive and negative regulatory elements control the steroid ovalbumine promoter, Biochemistry 1998 Aug 23;27(17):6550-7.
42. Sanders MM, McKnight GS, Chicken egg white genes: multihormonal regulation in a primary system, Endocrinology 1985 Jan;116(1):398-405.
43. Salter DW, Crittenden LB, Insertion of a disease resistance gene into the chicken germline, Biotechnology 1991;16:125-31.
44 Salter DW, Smith EJ, Hughes SH, Wright SE, Crittenden LB, Transgenic chickens: insertion of retroviral genes into the chicken germ line, Virology 1987 Mar;157(1):236-40.
45. Sang H, Transgenic chickens-methods and potential applications, Trends Biotechnol 1994 Oct;12(10):415-20.
46. Sang H, Perry MM, Episomal replication of cloned DNA injected into the fertilised ovum of the hen, Gallus domesticus, Mol Reprod Dev 1989;1(2):98-106.
47. Seema Agarwala, Timonthy A. Sanders, Clifton W. Ragsdale, Sonic hedgehog control of size and shape in midbrain pattern formation, Science Vol.291:2147-2150, 16 March 2001.
48. Shuman RM, Production of transgenic birds, Experientia 1991 Sep 15;47(9):897-905.
49. Stern CD, Chick stem cells, Curr Top Microbiol Immunol 1996;212:195-206.
50. Sugiyama T, Wang JC, Scott DK, Granner DK, Transcription activation by the orphan nuclear receptor, ovalbumin upstream promoter-transcription factor I (COUP-TFI)---, J Biol Chem 2000 Feb 4;275(5):3446-54.
51. Tanaka K, Wada T, Koga O, Nishio Y, Hertelendy F, Chick production by in vitro fertilization of the fowl ovum, J Reprod Fertil 1994, Mar; 100(2):447-9.
52. Thomas JL, Afanassieff M, Cosset FL, Molina RM, Ronfort C, Drynda A, Legras C, Chebloune Y, Nigon VM, Verdier G, In situ expression of helper-free avian leukosis virus (ALV)-based retrovirus in early chick embryos, Int J Dev Biol 1992 Jun;36(2):215-27.
53. Thoraval P, Afanassieff M, Cosset FL, Lasserre F, Verdier G, Coudert F, Dambrine G, Germline transmission of exogenous genes in chickens using helper-free ecotropic avian leukosis virus-based vectors, Transgenic Res 1995 Nov;4(6):369-77.
54. Upadhyay R, Gupta S, Kanungo MS, Trans-acting factors that interact with the proximal promoter of ovalbumin gene are tissue-specific and age-related, Mol Cell Biochem 1999 Nov;201(1-2):65-72.
55. Vazquez JC, Nogues C, Rucker EB, Piedrahita JA, Factors affecting the efficiency of introducing precise genetic changes in ES cells by homologous recombination: tag-and-exchange versus the Cre-loxp system, Transgenic Res 1998 May;7(3):181-93.
56. Vick L, Li Y, Simkiss K, Transgenic birds from transformed primordial germ cells, Proc R Soc Lond B Biol Sci 1993 Mar 22;251(1332):179-82.

Structurity Bulletin