A Logical Analysis of the Drosophila Gap-gene System

BODNAR, 1997, Programming the Drosophila embryo, J. theor. Biol., 188, 391, 10.1006/jtbi.1996.0328 BURSTEIN, 1995, A network model of developmental gene hierarchy, J. theor. Biol., 174, 1, 10.1006/jtbi.1995.0075 CAPOVILLA, 1992, The giant gene of Drosophila encodes a b-ZIP DNA-binding protein that regulates the expression of other segmentation gap genes, Development, 114, 99, 10.1242/dev.114.1.99 DRIEVER, 1989, Rescue of bicoid mutant Drosophila embryos by Bicoid fusion proteins containing heterologous activating sequences, Nature, 342, 149, 10.1038/342149a0 DRIEVER, 1988, The Bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner, Cell, 54, 95, 10.1016/0092-8674(88)90183-3 DRIEVER, 1989, The bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo, Nature, 337, 138, 10.1038/337138a0 DRIEVER, 1989, Determination of zygotic domains of gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen, Nature, 340, 363, 10.1038/340363a0 DUBNAU, 1996, RNA recognition and translational regulation by a homeodomain protein, Nature, 379, 694, 10.1038/379694a0 ELDON, 1991, Interactions of the Drosophila gap gene giant with maternal and zygotic pattern forming genes, Development, 111, 367, 10.1242/dev.111.2.367 GAUL, 1987, Pole region-dependent repression of the Drosophila gap gene Küppell by maternal gene products, Cell, 51, 549, 10.1016/0092-8674(87)90124-3 GAUL, 1989, Analysis of maternal effect mutant combination elucidates regulation and function of the overlap ofKrüppel and hunchback gene expression in the blastoderm Drosophila embryo, Development, 107, 651, 10.1242/dev.107.3.651 GOODWIN, 1990, Spatial harmonics and pattern specification in early Drosophila development. Part I. Bifurcation sequences and gene expression, J. theor. Biol., 144, 303, 10.1016/S0022-5193(05)80078-5 GOUZÉ, 1998, Positive and negative circuits in dynamical systems, J. Biol. Systems, 6, 11, 10.1142/S0218339098000054 HOCH, 1992, Competition for overlapping sites in the regulatory region of the Drosophila gene Krüppel, Science, 256, 94, 10.1126/science.1348871 HOCH, 1990, Cis-acting control elements for Krüppel expression in the Drosophila embryo, EMBO J., 9, 2587, 10.1002/j.1460-2075.1990.tb07440.x HÜLSKAMP, 1990, A morphogenetic gradient of hunchback protein organizes the expression of the gap genes Krüppel andknirps in the early Drosophila embryo, Nature, 346, 577, 10.1038/346577a0 HUNDING, 1990, Drosophila segmentation: supercomputer simulation of prepattern hierarchy, J. theor. Biol., 145, 369, 10.1016/S0022-5193(05)80116-X JÄCKLE, 1992, Transcriptional control by Drosophila gap genes, J. Cell Sci., 16, 39, 10.1242/jcs.1992.Supplement_16.6 JÄCKLE, 1986, Cross-regulatory interactions among the gap genes of Drosophila, Nature, 324, 668, 10.1038/324668a0 JACOB, 1991, Analysis of Krüppel control elements reveals that localized expression results from the interaction of multiple subelements, Proc. Natl Acad. Sci. U.S.A., 88, 5912, 10.1073/pnas.88.13.5912 KAUFFMAN, 1981, Pattern formation in the Drosophila embryo, Philos. Trans. R. Soc. Lond. B Biol. Sci., 295, 567, 10.1098/rstb.1981.0161 KAUFFMAN, 1990, Spatial harmonics and pattern specification in early Drosophila development. Part II. The four colour wheels model, J. theor. Biol., 144, 321, 10.1016/S0022-5193(05)80079-7 KOSMAN, 1998, Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins, Dev. Genes Evol., 208, 290, 10.1007/s004270050184 KRAUT, 1991, Spatial regulation of the gap gene giant during Drosophila development, Development, 111, 601, 10.1242/dev.111.2.601 KRAUT, 1991, Mutually repressive interactions between the gap genes giant and Krüppel define middle body regions of the Drosophila embryo, Development, 111, 611, 10.1242/dev.111.2.611 LACALLI, 1990, Modelling the Drosophila -rule pattern by reaction-diffusion: gap input and pattern control in a 4-morphogen system, J. theor. Biol., 144, 171, 10.1016/S0022-5193(05)80317-0 LEHMAN, 1987, hunchback, a gene required for segmentation of an anterior and posterior region of the Drosophila embryo, Dev. Biol., 119, 402, 10.1016/0012-1606(87)90045-5 LEWIS, 1977, Thresholds in development, J. theor. Biol., 65, 579, 10.1016/0022-5193(77)90216-8 MACDONALD, 1986, A molecular gradient in early Drosophila embryos and its role in specifying the body pattern, Nature, 324, 537, 10.1038/324537a0 MEINHARDT, 1977, A model of pattern formation in insect embryogenesis, J. Cell Sci., 23, 177, 10.1242/jcs.23.1.117 MEINHARDT, 1978, Space-dependent cell determination under the control of morphogen gradient, J. theor. Biol., 74, 307, 10.1016/0022-5193(78)90078-4 MEINHARDT, 1986, Hierarchical inductions of cell states: a model for segmentation in Drosophila, J. Cell Sci., 4, 357, 10.1242/jcs.1986.Supplement_4.20 MEINHARDT, 1989, Models for positional signalling with application to the dorsoventral patterning of insects and segregation into different cell types, Development, 107, 160, 10.1242/dev.107.Supplement.169 MLODZIK, 1985, Isolation of caudal, a Drosopghila homeo box-containing gene with maternal expression, whose transcripts form a concentration gradient at the pre-blastoderm stage, EMBO J., 4, 2961, 10.1002/j.1460-2075.1985.tb04030.x MLODZIK, 1987, Expression of the caudal gene in the germ line of Drosophila. Formation of an RNA and protein gradient during early embryogenesis, Cell, 48, 465, 10.1016/0092-8674(87)90197-8 MOHLER, 1989, A novel spatial transcription pattern associated with the segmentation gene, giant, ofDrosophila, EMBO J., 8, 1539, 10.1002/j.1460-2075.1989.tb03538.x MURATA, 1995, Binding of pumilio to maternal hunchback mRNA is required for posterior patterning in Drosophila embryos, Cell, 80, 747, 10.1016/0092-8674(95)90353-4 NAGY, 1994, Insect embryogenesis: a glance posterior, Curr. Biol., 4, 811, 10.1016/S0960-9822(00)00179-2 NAGY, 1994, Conservation of wingless patterning functions in the short-germ embryos of Tribolium castaneum, Nature, 367, 460, 10.1038/367460a0 NÜSSLEIN-VOLHARD, 1980, Mutations affecting segment number and polarity in Drosophila, Nature, 287, 795, 10.1038/287795a0 PANKRATZ, 1989, Krüppel requirement for knirps enhancement reflects overlapping gap gene activities in theDrosophila embryo, Nature, 341, 337, 10.1038/341337a0 PANKRATZ, 1993, Blastoderm segmentation, 451 PATEL, 1994, Developmental evolution: insights from studies of insect embryogenesis, Science, 266, 581, 10.1126/science.7939712 PATEL, 1994, Pair-rule expression of even-skipped arwe found in both short- and long-germ beetles, Nature, 367, 429, 10.1038/367429a0 PLAHTE, 1995, Feedback loops, stability and multistationarity in dynamical systems, J. Biol. Systems, 3, 409, 10.1142/S0218339095000381 RAFF, 1983 REINITZ, 1998, Stripe forming architecture of the gap gene system, Dev. Genet., 23, 11, 10.1002/(SICI)1520-6408(1998)23:1<11::AID-DVG2>3.0.CO;2-9 REINITZ, 1995, Model for cooperative control of positional information in Drosophila by bicoid and maternalhunchback, J. Exp. Zool., 271, 47, 10.1002/jez.1402710106 REINITZ, 1995, Mechanism of eve stripe formation, Mech. Dev., 49, 133, 10.1016/0925-4773(94)00310-J RIVERA-POMAR, 1996, From gradients to stripes in Drosophila embryogenesis: filling in the gaps, Trends Genet., 12, 478, 10.1016/0168-9525(96)10044-5 RIVERA-POMAR, 1995, Activation of posterior gap gene expression in the Drosophila blastoderm, Nature, 376, 253, 10.1038/376253a0 RIVERA-POMAR, 1996, RNA binding and translational suppression by bicoid, Nature, 379, 746, 10.1038/379746a0 SÁNCHEZ, 1997, Establishment of the dorso-ventral pattern during embryonic development of Drosophila melanogaster: a logical analysis, J. theor. Biol., 189, 377, 10.1006/jtbi.1997.0523 SANDER, 1976, Specification of the basic body pattern in insect embryogenesis, Adv. Insect Physiol., 12, 125, 10.1016/S0065-2806(08)60255-6 SAUER, 1991, Concentration-dependent transcriptional activation or repression by KRÜPPEL from a single binding site, Nature, 353, 563, 10.1038/353563a0 SCHRÖDER, 1993, A comparison of transplanted bicoid activity and partial bicoid homeobox sequences in severalDrosophila and blowfly species (Calliphoridae), Roux's Arch. Dev. Biol., 203, 34, 10.1007/BF00539888 SHARP, 1998, Prediction of mutant expression patterns using gene circuits, Biosystems, 47, 79, 10.1016/S0303-2647(98)00014-8 SIMPSON-BROSE, 1994, Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila, Cell, 78, 855, 10.1016/S0092-8674(94)90622-X SNOUSSI, 1989, Qualitative dynamics of piece-linear differential equations: a discrete mapping approach, Dyn. Stability Systems, 4, 189 SNOUSSI, 1998, Necessary conditions for multistationarity and stable periodicity, J. Biol. Systems, 6, 3, 10.1142/S0218339098000042 SNOUSSI, 1993, Logical identification of all steady states: the concept of feedback loop characteristic states, Bul. Math. Biol., 55, 973, 10.1007/BF02460695 SOMMER, 1991, Segmentation gene expression in the housefly Musca domestica, Development, 113, 419, 10.1242/dev.113.2.419 SOMMER, 1993, Involvement of an orthologue of the Drosophila pair-rule gene hairy in segment formation of the short germ-band embryo of Tribolium (Coleoptera), Nature, 361, 448, 10.1038/361448a0 SPRENGER, 1993, The terminal system of axis determination in the Drosophila embryo, 365 ST. JOHNSTON, 1992, The origin of pattern and polarity in the Drosophila embryo, Cell, 68, 201, 10.1016/0092-8674(92)90466-P STAUBER, 1999, The anterior determinant bicoid of Drosophila is a derived Hox class 3 gene, Proc. Natl Acad. Sci. U.S.A., 96, 3786, 10.1073/pnas.96.7.3786 STRUHL, 1989, Differing strategies for organising anterior and posterior body pattern in Drosophila embryos, Nature, 338, 741, 10.1038/338741a0 STRUHL, 1992, Control of Drosophila body pattern by the hunchback morphogen gradient, Cell, 69, 237, 10.1016/0092-8674(92)90405-2 STRUHL, 1989, The gradient morphogen bicoid is a concentration-dependent transcriptional activator, Cell, 57, 1259, 10.1016/0092-8674(89)90062-7 THIEFFRY, 1993, Formalization of regulatory networks: a logical method and its automatization, Math. Modelling Sci. Comput., 2, 144 THOMAS, 1973, Boolean formalization of genetic control circuits, J. theor. Biol., 42, 563, 10.1016/0022-5193(73)90247-6 THOMAS, 1991, Regulatory networks seen as asynchronous automata: a logical description, J. theor. Biol., 153, 1, 10.1016/S0022-5193(05)80350-9 THOMAS, 1990 THOMAS, 1995, Dynamical behaviour of biological regulatory networks. I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state, Bul. Math. Biol., 57, 247, 10.1007/BF02460618 TREISMAN, 1989, The products of the Drosophila gap genes hunchback and Krüppel bind to thehunchback promotors, Nature, 341, 335, 10.1038/341335a0 TURING, 1952, The chemical basis of morphogenesis, Philos. Trans. R. Soc. Lond. B, 237, 37, 10.1098/rstb.1952.0012 WARRIOR, 1990, Dose-dependent regulation of pair-rule stripes by gap proteins and the initiation of segment polarity, Development, 110, 759, 10.1242/dev.110.3.759 WIMMER, 2000, bicoid-independent formation of thoracic segments in Drosophila, Science, 287, 2476, 10.1126/science.287.5462.2476 WOLPERT, 1969, Positional information and the spatial pattern of cellular differentiation, J. theor. Biol., 25, 1, 10.1016/S0022-5193(69)80016-0 WOLPERT, 1971, Positional information and pattern formation, Curr. Top. Dev. Biol., 6, 183, 10.1016/S0070-2153(08)60641-9 WOLPERT, 1989, Positional information revisited, Development, 107, 3, 10.1242/dev.107.Supplement.3