Study of the lineshape of the chi(c1) (3872) state

A study of the lineshape of the chi(c1) (3872) state is made using a data sample corresponding to an integrated luminosity of 3 fb(-1) collected in pp collisions at center-of-mass energies of 7 and 8 TeV with the LHCb detector. Candidate chi(c1)(3872) and psi(2S) mesons from b-hadron decays are selected in the J/psi pi(+)pi(-) decay mode. Describing the lineshape with a Breit-Wigner function, the mass splitting between the chi(c1 )(3872) and psi(2S) states, Delta m, and the width of the chi(c1 )(3872) state, Gamma(Bw), are determined to be (Delta m=185.598 +/- 0.067 +/- 0.068 Mev,)(Gamma BW=1.39 +/- 0.24 +/- 0.10 Mev,) where the first uncertainty is statistical and the second systematic. Using a Flatte-inspired model, the mode and full width at half maximum of the lineshape are determined to be (mode=3871.69+0.00+0.05 MeV.)(FWHM=0.22-0.04+0.13+0.07+0.11-0.06-0.13 MeV, ) An investigation of the analytic structure of the Flatte amplitude reveals a pole structure, which is compatible with a quasibound D-0(D) over bar*(0) state but a quasivirtual state is still allowed at the level of 2 standard deviations

Measurement of the CKM angle γγ in B±→DK±B^\pm\to D K^\pm and B±→Dπ±B^\pm \to D π^\pm decays with D→KS0h+h−D \to K_\mathrm S^0 h^+ h^-

A measurement of $CP$-violating observables is performed using the decays $B^\pm\to D K^\pm$ and $B^\pm\to D \pi^\pm$, where the $D$ meson is reconstructed in one of the self-conjugate three-body final states $K_{\mathrm S}\pi^+\pi^-$ and $K_{\mathrm S}K^+K^-$ (commonly denoted $K_{\mathrm S} h^+h^-$). The decays are analysed in bins of the $D$-decay phase space, leading to a measurement that is independent of the modelling of the $D$-decay amplitude. The observables are interpreted in terms of the CKM angle $\gamma$. Using a data sample corresponding to an integrated luminosity of $9\,\text{fb}^{-1}$ collected in proton-proton collisions at centre-of-mass energies of $7$, $8$, and $13\,\text{TeV}$ with the LHCb experiment, $\gamma$ is measured to be $\left(68.7^{+5.2}_{-5.1}\right)^\circ$. The hadronic parameters $r_B^{DK}$, $r_B^{D\pi}$, $\delta_B^{DK}$, and $\delta_B^{D\pi}$, which are the ratios and strong-phase differences of the suppressed and favoured $B^\pm$ decays, are also reported

Measurement of CP asymmetries and branching fraction ratios of B− decays to two charm mesons

The $CP$ asymmetries of seven $B^-$ decays to two charm mesons are measured using data corresponding to an integrated luminosity of $9\text{fb}^{-1}$ of proton-proton collisions collected by the LHCb experiment. Decays involving a $D^{*0}$ or $D^{*-}_s$ meson are analysed by reconstructing only the $D^0$ or $D^-_s$ decay products. This paper presents the first measurement of $\mathcal{A}^{CP}(B^- \rightarrow D^{*-}_s D^0)$ and $\mathcal{A}^{CP}(B^- \rightarrow D^{-}_s D^{*0})$, and the most precise measurement of the other five $CP$ asymmetries. There is no evidence of $CP$ violation in any of the analysed decays. Additionally, two ratios between branching fractions of selected decays are measured.The CP asymmetries of seven B$^{−}$ decays to two charm mesons are measured using data corresponding to an integrated luminosity of 9 fb$^{−1}$ of proton-proton collisions collected by the LHCb experiment. Decays involving a D$^{*0}$ or ${D}_s^{\ast -}$ meson are analysed by reconstructing only the D$^{0}$ or ${D}_s^{-}$ decay products. This paper presents the first measurement of $\mathcal{A} ^{CP}$(B$^{−}$→${D}_s^{\ast -}$D$^{0}$) and $\mathcal{A} ^{CP}$(B$^{−}$→${D}_s^{-}$D$^{∗0}$), and the most precise measurement of the other five CP asymmetries. There is no evidence of CP violation in any of the analysed decays. Additionally, two ratios between branching fractions of selected decays are measured.[graphic not available: see fulltext]The $CP$ asymmetries of seven $B^-$ decays to two charm mesons are measured using data corresponding to an integrated luminosity of $9\text{ fb}^{-1}$ of proton-proton collisions collected by the LHCb experiment. Decays involving a $D^{*0}$ or $D^{*-}_s$ meson are analysed by reconstructing only the $D^0$ or $D^-_s$ decay products. This paper presents the first measurement of $\mathcal{A}^{CP}(B^- \rightarrow D^{*-}_s D^0)$ and $\mathcal{A}^{CP}(B^- \rightarrow D^{-}_s D^{*0})$, and the most precise measurement of the other five $CP$ asymmetries. There is no evidence of $CP$ violation in any of the analysed decays. Additionally, two ratios between branching fractions of selected decays are measured

Helium identification with LHCb

The identification of helium nuclei at LHCb is achieved using a method based on measurements of ionisation losses in the silicon sensors and timing measurements in the Outer Tracker drift tubes. The background from photon conversions is reduced using the RICH detectors and an isolation requirement. The method is developed using pp collision data at √(s) = 13 TeV recorded by the LHCb experiment in the years 2016 to 2018, corresponding to an integrated luminosity of 5.5 fb-1. A total of around 105 helium and antihelium candidates are identified with negligible background contamination. The helium identification efficiency is estimated to be approximately 50% with a corresponding background rejection rate of up to O(10^12). These results demonstrate the feasibility of a rich programme of measurements of QCD and astrophysics interest involving light nuclei

Curvature-bias corrections using a pseudomass method

Momentum measurements for very high momentum charged particles, such as muons from electroweak vector boson decays, are particularly susceptible to charge-dependent curvature biases that arise from misalignments of tracking detectors. Low momentum charged particles used in alignment procedures have limited sensitivity to coherent displacements of such detectors, and therefore are unable to fully constrain these misalignments to the precision necessary for studies of electroweak physics. Additional approaches are therefore required to understand and correct for these effects. In this paper the curvature biases present at the LHCb detector are studied using the pseudomass method in proton-proton collision data recorded at centre of mass energy √(s)=13 TeV during 2016, 2017 and 2018. The biases are determined using Z→μ + μ - decays in intervals defined by the data-taking period, magnet polarity and muon direction. Correcting for these biases, which are typically at the 10-4 GeV-1 level, improves the Z→μ + μ - mass resolution by roughly 18% and eliminates several pathological trends in the kinematic-dependence of the mean dimuon invariant mass

Momentum scale calibration of the LHCb spectrometer

For accurate determination of particle masses accurate knowledge of the momentum scale of the detectors is crucial. The procedure used to calibrate the momentum scale of the LHCb spectrometer is described and illustrated using the performance obtained with an integrated luminosity of 1.6 fb-1 collected during 2016 in pp running. The procedure uses large samples of J/ψ → μ + μ - and B+ → J/ψ K + decays and leads to a relative accuracy of 3 × 10-4 on the momentum scale

Study of the doubly charmed tetraquark T+cc

Quantum chromodynamics, the theory of the strong force, describes interactions of coloured quarks and gluons and the formation of hadronic matter. Conventional hadronic matter consists of baryons and mesons made of three quarks and quark-antiquark pairs, respectively. Particles with an alternative quark content are known as exotic states. Here a study is reported of an exotic narrow state in the D0D0π+ mass spectrum just below the D*+D0 mass threshold produced in proton-proton collisions collected with the LHCb detector at the Large Hadron Collider. The state is consistent with the ground isoscalar T+cc tetraquark with a quark content of ccu⎯⎯⎯d⎯⎯⎯ and spin-parity quantum numbers JP = 1+. Study of the DD mass spectra disfavours interpretation of the resonance as the isovector state. The decay structure via intermediate off-shell D*+ mesons is consistent with the observed D0π+ mass distribution. To analyse the mass of the resonance and its coupling to the D*D system, a dedicated model is developed under the assumption of an isoscalar axial-vector T+cc state decaying to the D*D channel. Using this model, resonance parameters including the pole position, scattering length, effective range and compositeness are determined to reveal important information about the nature of the T+cc state. In addition, an unexpected dependence of the production rate on track multiplicity is observed

Conservation Of Gene Linkage In Dispersed Vertebrate Nk Homeobox Clusters

Nk homeobox genes are important regulators of many different developmental processes including muscle, heart, central nervous system and sensory organ development. They are thought to have arisen as part of the ANTP megacluster, which also gave rise to Hox and ParaHox genes, and at least some NK genes remain tightly linked in all animals examined so far. The protostome-deuterostome ancestor probably contained a cluster of nine Nk genes: (Msx)-(Nk4/tinman)-(Nk3/ bagpipe)-(Lbx/ladybird)-(Tlx/c15)-(Nk7)-(Nk6/hgtx)-(Nk1/slouch)-(Nk5/Hmx). Of these genes, only NKX2.6-NKX3.1, LBX1-TLX1 and LBX2-TLX2 remain tightly linked in humans. However, it is currently unclear whether this is unique to the human genome as we do not know which of these Nk genes are clustered in other vertebrates. This makes it difficult to assess whether the remaining linkages are due to selective pressures or because chance rearrangements have "missed" certain genes. In this paper, we identify all of the paralogs of these ancestrally clustered NK genes in several distinct vertebrates. We demonstrate that tight linkages of Lbx1-Tlx1, Lbx2-Tlx2 and Nkx3.1-Nkx2.6 have been widely maintained in both the ray-finned and lobe-finned fish lineages. Moreover, the recently duplicated Hmx2-Hmx3 genes are also tightly linked. Finally, we show that Lbx1-Tlx1 and Hmx2-Hmx3 are flanked by highly conserved noncoding elements, suggesting that shared regulatory regions may have resulted in evolutionary pressure to maintain these linkages. Consistent with this, these pairs of genes have overlapping expression domains. In contrast, Lbx2-Tlx2 and Nkx3.1-Nkx2.6, which do not seem to be coexpressed, are also not associated with conserved noncoding sequences, suggesting that an alternative mechanism may be responsible for the continued clustering of these genes. © 2010 Springer-Verlag.2199-10481496Adamska, M., Leger, S., Brand, M., Hadrys, T., Braun, T., Bober, E., Inner ear and lateral line expression of a zebrafish Nkx5-1 gene and its downregulation in the ears of FGF8 mutant, ace (2000) Mech Dev, 97 (1-2), pp. 161-165Adamska, M., Wolff, A., Kreusler, M., Wittbrodt, J., Braun, T., Bober, E., Five Nkx5 genes show differential expression patterns in anlagen of sensory organs in medaka: Insight into the evolution of the gene family (2001) Dev Genes Evol, 211 (7), pp. 338-349Amemiya, C.T., Prohaska, S.J., Hill-Force, A., Cook, A., Wasserscheid, J., Ferrier, D.E., Pascual-Anaya, J., Stadler, P.F., The amphioxus Hox cluster: Characterization, comparative genomics, and evolution (2008) J Exp Zoolog B Mol Dev Evol, 310 (5), pp. 465-477Amores, A., Force, A., Yan, Y.-L., Joly, L., Amemiya, C., Fritz, A., Ho, R.K., Postlethwait, J.H., Zebrafish hox clusters and vertebrate genome evolution (1998) Science, 282 (5394), pp. 1711-1714Biben, C., Hatzistavrou, T., Harvey, R.P., Expression of NK-2 class homeobox gene Nkx2-6 in foregut endoderm and heart (1998) Mech Dev, 73 (1), pp. 125-127Bober, E., Baum, C., Braun, T., Arnold, H.H., A novel NK-related mouse homeobox gene: Expression in central and peripheral nervous structures during embryonic development (1994) Dev Biol, 162 (1), pp. 288-303Brohmann, H., Jagla, K., Birchmeier, C., The role of Lbx1 in migration of muscle precursor cells (2000) Development, 127 (2), pp. 437-445Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., Batzoglou, S., LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA (2003) Genome Res, 13 (4), pp. 721-731Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., Batzoglou, S., Glocal alignment: Finding rearrangements during alignment (2003) Bioinformatics, 19 (SUPPL 1), pp. i54-i62Butts, T., Holland, P.W., Ferrier, D.E., The urbilaterian Super-Hox cluster (2008) Trends Genet, 24 (6), pp. 259-262Catchen, J., (2009) Automated Methods to Infer Ancient Homology and Synteny, , Ph.D. Dissertation, Department of Computer and Information Science, University of OregonChen, F., Liu, K.C., Epstein, J.A., Lbx2, a novel murine homeobox gene related to the Drosophila ladybird genes is expressed in the developing urogenital system, eye and brain (1999) Mech Dev, 84 (1-2), pp. 181-184Cheng, L., Arata, A., Mizuguchi, R., Qian, Y., Karunaratne, A., Gray, P.A., Arata, S., Ma, Q., Tlx3 and Tlx1 are post-mitotic selector genes determining glutamatergic over GABAergic cell fates (2004) Nat Neurosci, 7 (5), pp. 510-517Cheng, L., Samad, O.A., Xu, Y., Mizuguchi, R., Luo, P., Shirasawa, S., Goulding, M., Ma, Q., Lbx1 and Tlx3 are opposing switches in determining GABAergic versus glutamatergic transmitter phenotypes (2005) Nat Neurosci, 8 (11), pp. 1510-1515Chiu, C.H., Amemiya, C., Dewar, K., Kim, C.B., Ruddle, F.H., Wagner, G.P., Molecular evolution of the HoxA cluster in the three major gnathostome lineages (2002) Proc Natl Acad Sci U S A, 99 (8), pp. 5492-5497Cleaver, O.B., Patterson, K.D., Krieg, P.A., Overexpression of the tinman-related genes XNkx-2.5 and XNkx-2.3 in Xenopus embryos results in myocardial hyperplasia (1996) Development, 122 (11), pp. 3549-3556De La Calle-Mustienes, E., Feijoo, C.G., Manzanares, M., Tena, J.J., Rodriguez-Seguel, E., Letizia, A., Allende, M.L., Gomez-Skarmeta, J.L., A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts (2005) Genome Res, 15 (8), pp. 1061-1072Dehal, P., Boore, J.L., Two rounds of whole genome duplication in the ancestral vertebrate (2005) PLoS Biol, 3 (10), pp. e314Deitcher, D.L., Fekete, D.M., Cepko, C.L., Asymmetric expression of a novel homeobox gene in vertebrate sensory organs (1994) J Neurosci, 14 (2), pp. 486-498Dietrich, S., Schubert, F.R., Healy, C., Sharpe, P.T., Lumsden, A., Specification of the hypaxial musculature (1998) Development, 125 (12), pp. 2235-2249Engstrom, P.G., Ho Sui, S.J., Drivenes, O., Becker, T.S., Lenhard, B., Genomic regulatory blocks underlie extensive microsynteny conservation in insects (2007) Genome Res, 17 (12), pp. 1898-1908Evans, S.M., Yan, W., Murillo, M.P., Ponce, J., Papalopulu, N., Tinman, a Drosophila homeobox gene required for heart and visceral mesoderm specification, may be represented by a family of genes in vertebrates: XNkx-2.3, a second vertebrate homologue of tinman (1995) Development, 121 (11), pp. 3889-3899Ferrier, D.E., Minguillon, C., Evolution of the Hox/ParaHox gene clusters (2003) Int J Dev Biol, 47 (7-8), pp. 605-611Fisher, S., Grice, E.A., Vinton, R.M., Bessling, S.L., McCallion, A.S., Conservation of RET regulatory function from human to zebrafish without sequence similarity (2006) Science, 312 (5771), pp. 276-279French, C.R., Erickson, T., Callander, D., Berry, K.M., Koss, R., Hagey, D.W., Stout, J., Waskiewicz, A.J., Pbx homeodomain proteins pattern both the zebrafish retina and tectum (2007) BMC Dev Biol, 7, p. 85Garcia-Fernandez, J., The genesis and evolution of homeobox gene clusters (2005) Nat Rev Genet, 6 (12), pp. 881-892Gross, M.K., Moran-Rivard, L., Velasquez, T., Nakatsu, M.N., Jagla, K., Goulding, M., Lbx1 is required for muscle precursor migration along a lateral pathway into the limb (2000) Development, 127 (2), pp. 413-424Guindon, S., Gascuel, O., A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood (2003) Syst Biol, 52 (5), pp. 696-704Guindon, S., Lethiec, F., Duroux, P., Gascuel, O., PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference (2005) Nucleic Acids Res, 33 (WEB SERVER ISSUE), pp. W557-W559Hadrys, T., Braun, T., Rinkwitz-Brandt, S., Arnold, H.H., Bober, E., Nkx5-1 controls semicircular canal formation in the mouse inner ear (1998) Development, 125 (1), pp. 33-39Hardies, S.C., Edgell, M.H., Hutchison III, C.A., Evolution of the mammalian beta-globin gene cluster (1984) J Biol Chem, 259 (6), pp. 3748-3756Hatano, M., Iitsuka, Y., Yamamoto, H., Dezawa, M., Yusa, S., Kohno, Y., Tokuhisa, T., Ncx, a Hox11 related gene, is expressed in a variety of tissues derived from neural crest cells (1997) Anat Embryol (Berl), 195 (5), pp. 419-425Herbrand, H., Guthrie, S., Hadrys, T., Hoffmann, S., Arnold, H.H., Rinkwitz-Brandt, S., Bober, E., Two regulatory genes, cNkx5-1 and cPax2, show different responses to local signals during otic placode and vesicle formation in the chick embryo (1998) Development, 125 (4), pp. 645-654Hoegg, S., Meyer, A., Phylogenomic analyses of KCNA gene clusters in vertebrates: Why do gene clusters stay intact? (2007) BMC Evol Biol, 7, p. 139Holland, P.W., Garcia-Fernandez, J., Williams, N.A., Sidow, A., Gene duplications and the origins of vertebrate development (1994) Dev Suppl, 1994, pp. 125-133Holland, P.W., Booth, H.A., Bruford, E.A., Classification and nomenclature of all human homeobox genes (2007) BMC Biol, 5, p. 47Houweling, A., Dildrop, R., Peters, T., Mummenhoff, J., Moorman, A., Ruther, U., Christoffels, V., Gene and cluster-specific expression of the Iroquois family members during mouse development (2001) Mech Dev, 107, pp. 169-174Irimia, M., Maeso, I., Garcia-Fernandez, J., Convergent evolution of clustering of Iroquois homeobox genes across metazoans (2008) Mol Biol Evol, 25 (8), pp. 1521-1525Jagla, K., Bellard, M., Frasch, M., A cluster of Drosophila homeobox genes involved in mesoderm differentiation programs (2001) Bioessays, 23 (2), pp. 125-133Jovelin, R., Yan, Y.L., He, X., Catchen, J., Amores, A., Canestro, C., Yokoi, H., Evolution of developmental regulation in the vertebrate FgfD subfamily (2009) J Exp Zoolog B Mol Dev Evol, , in pressKanamoto, T., Terada, K., Yoshikawa, H., Furukawa, T., Cloning and expression pattern of lbx3, a novel chick homeobox gene (2006) Gene Expr Patterns, 6 (3), pp. 241-246Kim, C.B., Amemiya, C., Bailey, W., Kawasaki, K., Mezey, J., Miller, W., Minoshima, S., Ruddle, F., Hox cluster genomics in the horn shark, Heterodontus francisci (2000) Proc Natl Acad Sci U S A, 97 (4), pp. 1655-1660Kimura-Yoshida, C., Kitajima, K., Oda-Ishii, I., Tian, E., Suzuki, M., Yamamoto, M., Suzuki, T., Matsuo, I., Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification (2004) Development, 131 (1), pp. 57-71Langenau, D., Palomero, T., Kanki, J., Ferrando, A., Zhou, Y., Zon, L., Look, A., Molecular cloning and developmental expression of Tlx (Hox11) genes in zebrafish (Danio rerio) (2002) Mech Dev, 117 (1-2), pp. 243-248Larroux, C., Fahey, B., Degnan, S.M., Adamski, M., Rokhsar, D.S., Degnan, B.M., The NK homeobox gene cluster predates the origin of Hox genes (2007) Curr Biol, 17 (8), pp. 706-710Lee, K.H., Xu, Q., Breitbart, R.E., A new tinman-related gene, nkx2.7, anticipates the expression of nkx2.5 and nkx2.3 in zebrafish heart and pharyngeal endoderm (1996) Dev Biol, 180 (2), pp. 722-731Lettice, L., Hecksher-Sorensen, J., Hill, R., The role of Bapx1 (Nkx3.2) in the development and evolution of the axial skeleton (2001) J Anat, 199 (PT 1-2), pp. 181-187Lettice, L.A., Heaney, S.J., Purdie, L.A., Li, L., De Beer, P., Oostra, B.A., Goode, D., De Graaff, E., A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly (2003) Hum Mol Genet, 12 (14), pp. 1725-1735Logan, C., Wingate, R.J., McKay, I.J., Lumsden, A., Tlx-1 and Tlx-3 homeobox gene expression in cranial sensory ganglia and hindbrain of the chick embryo: Markers of patterned connectivity (1998) J Neurosci, 18 (14), pp. 5389-5402Luke, G.N., Castro, L.F., McLay, K., Bird, C., Coulson, A., Holland, P.W., Dispersal of NK homeobox gene clusters in amphioxus and humans (2003) Proc Natl Acad Sci U S A, 100 (9), pp. 5292-5295Martin, B.L., Harland, R.M., A novel role for lbx1 in Xenopus hypaxial myogenesis (2006) Development, 133 (2), pp. 195-208Mazet, F., Amemiya, C.T., Shimeld, S.M., An ancient Fox gene cluster in bilaterian animals (2006) Curr Biol, 16 (9), pp. R314-R316McEwen, G.K., Woolfe, A., Goode, D., Vavouri, T., Callaway, H., Elgar, G., Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis (2006) Genome Res, 16 (4), pp. 451-465Mennerich, D., Hoffmann, S., Hadrys, T., Arnold, H.H., Bober, E., Two highly related homeodomain proteins, Nkx5-1 and Nkx5-2, display different DNA binding specificities (1999) Biol Chem, 380 (9), pp. 1041-1048Moisan, V., Bomgardner, D., Tremblay, J.J., Expression of the Ladybird-like homeobox 2 transcription factor in the developing mouse testis and epididymis (2008) BMC Dev Biol, 8, p. 22Mulley, J.F., Chiu, C.H., Holland, P.W., Breakup of a homeobox cluster after genome duplication in teleosts (2006) Proc Natl Acad Sci U S A, 103 (27), pp. 10369-10372Newman, C.S., Krieg, P.A., The Xenopus bagpipe-related homeobox gene zampogna is expressed in the pharyngeal endoderm and the visceral musculature of the midgut (1999) Dev Genes Evol, 209 (2), pp. 132-134Nicolas, S., Caubit, X., Massacrier, A., Cau, P., Le Parco, Y., Two Nkx-3-related genes are expressed in the adult and regenerating central nervous system of the urodele Pleurodeles waltl (1999) Dev Genet, 24 (3-4), pp. 319-328Nishida, W., Nakamura, M., Mori, S., Takahashi, M., Ohkawa, Y., Tadokoro, S., Yoshida, K., Sobue, K., A triad of serum response factor and the GATA and NK families governs the transcription of smooth and cardiac muscle genes (2002) J Biol Chem, 277 (9), pp. 7308-7317Pabst, O., Schneider, A., Brand, T., Arnold, H.H., The mouse Nkx2-3 homeodomain gene is expressed in gut mesenchyme during pre- and postnatal mouse development (1997) Dev Dyn, 209 (1), pp. 29-35Pascual-Anaya, J., D'Aniello, S., Garcia-Fernandez, J., Unexpectedly large number of conserved noncoding regions within the ancestral chordate Hox cluster (2008) Dev Genes Evol, 218 (11-12), pp. 591-597Patterson, K.D., Krieg, P.A., Hox11-family genes XHox11 and XHox11L2 in xenopus: XHox11L2 expression is restricted to a subset of the primary sensory neurons (1999) Dev Dyn, 214 (1), pp. 34-43Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M., Minovitsky, S., Rubin, E.M., In vivo enhancer analysis of human conserved non-coding sequences (2006) Nature, 444 (7118), pp. 499-502Pollard, S.L., Holland, P.W., Evidence for 14 homeobox gene clusters in human genome ancestry (2000) Curr Biol, 10 (17), pp. 1059-1062Postlethwait, J.H., The zebrafish genome: A review and msx gene case study (2006) Genome Dyn, 2, pp. 183-197Postlethwait, J.H., The zebrafish genome in context: Ohnologs gone missing (2007) J Exp Zoolog B Mol Dev Evol, 308 (5), pp. 563-577Qiu, M., Shimamura, K., Sussel, L., Chen, S., Rubenstein, J.L., Control of anteroposterior and dorsoventral domains of Nkx-6.1 gene expression relative to other Nkx genes during vertebrate CNS development (1998) Mech Dev, 72 (1-2), pp. 77-88Richardson, M.K., Crooijmans, R.P., Groenen, M.A., Sequencing and genomic annotation of the chicken (Gallus gallus) Hox clusters, and mapping of evolutionarily conserved regions (2007) Cytogenet Genome Res, 117 (1-4), pp. 110-119Rinkwitz-Brandt, S., Arnold, H.H., Bober, E., Regionalized expression of Nkx5-1, Nkx5-2, Pax2 and sek genes during mouse inner ear development (1996) Hear Res, 99 (1-2), pp. 129-138Santini, S., Boore, J.L., Meyer, A., Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters (2003) Genome Res, 13 (6), pp. 1111-1122Saudemont, A., Dray, N., Hudry, B., Le Gouar, M., Vervoort, M., Balavoine, G., Complementary striped expression patterns of NK homeobox genes during segment formation in the annelid Platynereis (2008) Dev Biol, 317 (2), pp. 430-443Schafer, K., Braun, T., Early specification of limb muscle precursor cells by the homeobox gene Lbx1h (1999) Nat Genet, 23 (2), pp. 213-216Schorderet, D.F., Nichini, O., Boisset, G., Polok, B., Tiab, L., Mayeur, H., Raji, B., Munier, F.L., Mutation in the human homeobox gene NKX5-3 causes an oculo-auricular syndrome (2008) Am J Hum Genet, 82 (5), pp. 1178-1184Schubert, F.R., Dietrich, S., Mootoosamy, R.C., Chapman, S.C., Lumsden, A., Lbx1 marks a subset of interneurons in chick hindbrain and spinal cord (2001) Mech Dev, 101 (1-2), pp. 181-185Shimeld, S.M., McKay, I.J., Sharpe, P.T., The murine homeobox gene Msx-3 shows highly restricted expression in the developing neural tube (1996) Mech Dev, 55 (2), pp. 201-210Spitz, F., Gonzalez, F., Duboule, D., A global control region defines a chromosomal regulatory landscape containing the HoxD cluster (2003) Cell, 113 (3), pp. 405-417Svensson, M.E., Haas, A., Evolutionary innovation in the vertebrate jaw: A derived morphology in anuran tadpoles and its possible developmental origin (2005) Bioessays, 27 (5), pp. 526-532Takatori, N., Butts, T., Candiani, S., Pestarino, M., Ferrier, D.E., Saiga, H., Holland, P.W., Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae (2008) Dev Genes Evol, 218 (11-12), pp. 579-590Tanaka, M., Kasahara, H., Bartunkova, S., Schinke, M., Komuro, I., Inagaki, H., Lee, Y., Izumo, S., Vertebrate homologs of tinman and bagpipe: Roles of the homeobox genes in cardiovascular development (1998) Dev Genet, 22 (3), pp. 239-249Tang, S.J., Hoodless, P.A., Lu, Z., Breitman, M.L., McInnes, R.R., Wrana, J.L., Buchwald, M., The Tlx-2 homeobox gene is a downstream target of BMP signalling and is required for mouse mesoderm development (1998) Development, 125 (10), pp. 1877-1887Taylor, J.S., Braasch, I., Frickey, T., Meyer, A., Van De Peer, Y., Genome duplication, a trait shared by 22000 species of ray-finned fish (2003) Genome Res, 13 (3), pp. 382-390Thisse, B., Heyer, V., Lux, A., Alunni, V., Degrave, A., Seiliez, I., Kirchner, J., Thisse, C., Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening (2004) Methods Cell Biol, 77, pp. 505-519Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., The CLUSTAL-X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools (1997) Nucleic Acids Res, 25 (24), pp. 4876-4882Tschopp, P., Tarchini, B., Spitz, F., Zakany, J., Duboule, D., Uncoupling time and space in the collinear regulation of Hox genes (2009) PLoS Genet, 5 (3), pp. e1000398Vavouri, T., Walter, K., Gilks, W.R., Lehner, B., Elgar, G., Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans (2007) Genome Biol, 8 (2), pp. R15Wang, W., Lo, P., Frasch, M., Lufkin, T., Hmx: An evolutionary conserved homeobox gene family expressed in the developing nervous system in mice and Drosophila (2000) Mech Dev, 99 (1), pp. 123-137Wang, W., Grimmer, J.F., Van De Water, T.R., Lufkin, T., Hmx2 and Hmx3 homeobox genes direct development of the murine inner ear and hypothalamus and can be functionally replaced by Drosophila Hmx (2004) Dev Cell, 7 (3), pp. 439-453Watanabe, S., Kondo, S., Hayasaka, M., Hanaoka, K., Functional analysis of homeodomain-containing transcription factor Lbx1 in satellite cells of mouse skeletal muscle (2007) J Cell Sci, 120 (PT 23), pp. 4178-4187Wittbrodt, J., Meyer, A., Schartl, M., More genes in fish? (1998) Bioessays, 20, pp. 511-515Woolfe, A., Elgar, G., Organization of conserved elements near key developmental regulators in vertebrate genomes (2008) Adv Genet, 61, pp. 307-338Woolfe, A., Goodson, M., Goode, D.K., Snell, P., McEwen, G.K., Vavouri, T., Smith, S.F., Elgar, G., Highly conserved non-coding sequences are associated with vertebrate development (2005) PLoS Biol, 3 (1), pp. e7Woolfe, A., Goode, D.K., Cooke, J., Callaway, H., Smith, S., Snell, P., McEwen, G.K., Elgar, G., CONDOR: A database resource of developmentally associated conserved non-coding elements (2007) BMC Dev Biol, 7, p. 100Wotton, K.R., Mazet, F., Shimeld, S.M., Expression of FoxC, FoxF, FoxL1, and FoxQ1 genes in the dogfish Scyliorhinus canicula defines ancient and derived roles for Fox genes in vertebrate development (2008) Dev Dyn, 237 (6), pp. 1590-1603Wotton, K.R., Shimeld, S.M., Comparative genomics of vertebrate Fox cluster loci (2006) BMC Genomics, 7 (1), p. 271Wotton, K.R., Weierud, F.K., Dietrich, S., Lewis, K.E., Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates (2008) BMC Evol Biol, 8, p. 171Yoshiura, K., Leysens, N.J., Reiter, R.S., Murray, J.C., Cloning, characterization, and mapping of the mouse homeobox gene Hmx1 (1998) Genomics, 50 (1), pp. 61-6

Evolutionarily Conserved Morphogenetic Movements At The Vertebrate Head-trunk Interface Coordinate The Transport And Assembly Of Hypopharyngeal Structures

The vertebrate head-trunk interface (occipital region) has been heavily remodelled during evolution, and its development is still poorly understood. In extant jawed vertebrates, this region provides muscle precursors for the throat and tongue (hypopharyngeal/hypobranchial/hypoglossal muscle precursors, HMP) that take a stereotype path rostrally along the pharynx and are thought to reach their target sites via active migration. Yet, this projection pattern emerged in jawless vertebrates before the evolution of migratory muscle precursors. This suggests that a so far elusive, more basic transport mechanism must have existed and may still be traceable today.Here we show for the first time that all occipital tissues participate in well-conserved cell movements. These cell movements are spearheaded by the occipital lateral mesoderm and ectoderm that split into two streams. The rostrally directed stream projects along the floor of the pharynx and reaches as far rostrally as the floor of the mandibular arch and outflow tract of the heart. Notably, this stream leads and engulfs the later emerging HMP, neural crest cells and hypoglossal nerve. When we (i) attempted to redirect hypobranchial/hypoglossal muscle precursors towards various attractants, (ii) placed non-migratory muscle precursors into the occipital environment or (iii) molecularly or (iv) genetically rendered muscle precursors non-migratory, they still followed the trajectory set by the occipital lateral mesoderm and ectoderm. Thus, we have discovered evolutionarily conserved morphogenetic movements, driven by the occipital lateral mesoderm and ectoderm, that ensure cell transport and organ assembly at the head-trunk interface. © 2014 The Authors.3902231246Ainsworth, S.J., Stanley, R.L., Evans, D.J., Developmental stages of the Japanese quail (2010) J Anat, 216, pp. 3-15Alvares, L.E., Schubert, F.R., Thorpe, C., Mootoosamy, R.C., Cheng, L., Parkyn, G., Lumsden, A., Dietrich, S., Intrinsic, Hox-dependent cues determine the fate of skeletal muscle precursors (2003) Dev. Cell, 5, pp. 379-390Bladt, F., Riethmacher, D., Isenmann, S., Aguzzi, A., Birchmeier, C., Essential role for the c-met receptor in the migration of myogenic precursor cells into the limb bud (1995) Nature, 376, pp. 768-771Blentic, A., Tandon, P., Payton, S., Walshe, J., Carney, T., Kelsh, R.N., Mason, I., Graham, A., The emergence of ectomesenchyme (2008) Dev. Dyn., 237, pp. 592-601Bothe, I., Dietrich, S., The molecular setup of the avian head mesoderm and its implication for craniofacial myogenesis (2006) Dev. Dyn., 235, pp. 2845-2860Brohmann, H., Jagla, K., Birchmeier, C., The role of Lbx1 in migration of muscle precursor cells (2000) Development, 127, pp. 437-445Cheng, L., Alvares, L.E., Ahmed, M.U., El-Hanfy, A.S., Dietrich, S., The epaxial-hypaxial subdivision of the avian somite (2004) Dev. Biol., 274, pp. 348-369Cole, N.J., Hall, T.E., Don, E.K., Berger, S., Boisvert, C.A., Neyt, C., Ericsson, R., Currie, P.D., Development and evolution of the muscles of the pelvic fin (2011) PLoS Biol., 9, pp. e1001168Couly, G.F., Coltey, P.M., Le Douarin, N.M., The triple origin of skull in higher vertebrates: a study in quail-chick chimeras (1993) Development, 117, pp. 409-429Dietrich, S., Abou-Rebyeh, F., Brohmann, H., Bladt, F., Sonnenberg-Riethmacher, E., Yamaai, T., Lumsden, A., Birchmeier, C., The role of SF/HGF and c-Met in the development of skeletal muscle (1999) Development, 126, pp. 1621-1629Dietrich, S., Schubert, F.R., Healy, C., Sharpe, P.T., Lumsden, A., Specification of the hypaxial musculature (1998) Development, 125, pp. 2235-2249Dietrich, S., Schubert, F.R., Lumsden, A., Control of dorsoventral pattern in the chick paraxial mesoderm (1997) Development, 124, pp. 3895-3908Diogo, R., Hinits, Y., Hughes, S.M., Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods (2008) BMC Dev. Biol., 8, p. 24Edgeworth, F.H., The development of the head muscles in Gallus domesticus, and the morphology of the head muscles in the Sauropsida (1907) Q. J. Microsc. Sci., 52, pp. 511-556Edgeworth, F.H., (1935) The Cranial Muscles of Vertebrates, , Cambridge University Press, CambridgeEricsson, R., Knight, R., Johanson, Z., Evolution and development of the vertebrate neck (2013) J. Anat., 222, pp. 67-78Ferguson, C.A., Graham, A., Redefining the head-trunk interface for the neural crest (2004) Dev. Biol., 269, pp. 70-80Franz, T., The Splotch (Sp1H) and Splotch-delayed (Spd) alleles: differential phenotypic effects on neural crest and limb musculature (1993) Anat. Embryol. (Berl.), 187, pp. 371-377Franz, T., Kothary, R., Surani, M.A.H., Halata, Z., Grim, M., The Splotch mutation interferes with muscle development in the limbs (1993) Anat. Embryol., 187, pp. 153-160Gans, C., Northcutt, R.G., Neural crest and the origin of vertebrates: a new head (1983) Science, 220, pp. 268-274Gilbert, S.F., (2000) Developmental Biology, , Sinauer Associates Inc., Sunderland, MAGoodrich, E.S., (1958) Studies on the Structure and Development of Vertebrates, , Dover Publications Inc., New YorkGoulding, M.D., Lumsden, A., Gruss, P., Signals from the notochord and floor plate regulate the region-specific expression of two Pax genes in the developing spinal cord (1993) Development, 117, pp. 1001-1016Gross, M.K., Moran-Rivard, L., Velasquez, T., Nakatsu, M.N., Jagla, K., Goulding, M., Lbx1 is required for muscle precursor migration along a lateral pathway into the limb (2000) Development, 127, pp. 413-424Gurdon, J.B., Methods for nuclear transplantation in amphibia (1977) Methods Cell Biol., 16, pp. 125-139Hamburger, V., Hamilton, H.L., A series of normal stages in the development of the chick embryo (1951) J. Morphol., 88, pp. 49-92Han, D., Zhao, H., Parada, C., Hacia, J.G., Bringas, P., Chai, Y., A TGFbeta-Smad4-Fgf6 signaling cascade controls myogenic differentiation and myoblast fusion during tongue development (2012) Development, 139, pp. 1640-1650Harland, R.M., In situ hybridization: an improved whole-mount method for Xenopus embryos (1991) Methods Cell Biol., 36, pp. 685-695Hirano, S., Tanaka, H., Ohta, K., Norita, M., Hoshino, K., Meguro, R., Kase, M., Normal ontogenic observations on the expression of Eph receptor tyrosine kinase, Cek8, in chick embryos (1998) Anat. Embryol. (Berl.), 197, pp. 187-197Hosokawa, R., Oka, K., Yamaza, T., Iwata, J., Urata, M., Xu, X., Bringas, P., Chai, Y., TGF-beta mediated FGF10 signaling in cranial neural crest cells controls development of myogenic progenitor cells through tissue-tissue interactions during tongue morphogenesis (2010) Dev. Biol., 341, pp. 186-195Huang, R., Zhi, Q., Izpisua-Belmonte, J.C., Christ, B., Patel, K., Origin and development of the avian tongue muscles (1999) Anat. Embryol. (Berl.), 200, pp. 137-152Huang, R., Zhi, Q., Patel, K., Wilting, J., Christ, B., Contribution of single somites to the skeleton and muscles of the occipital and cervical regions in avian embryos (2000) Anat. Embryol. (Berl.), 202, pp. 375-383Kallius, E., Beitráge zur entwickelung der zunge. Teil I. Amphibien und reptilien (1901) Anat. Hefte, Abt., 1 (16), pp. 531-760Kimmel, C.B., Ballard, W.W., Kimmel, S.R., Ullmann, B., Schilling, T.F., Stages of embryonic development of the zebrafish (1995) Dev. Dyn., 203, pp. 253-310Kuo, B.R., Erickson, C.A., Vagal neural crest cell migratory behavior: a transition between the cranial and trunk crest (2011) Dev. Dyn., 240, pp. 2084-2100Kuratani, S., Horigome, N., Hirano, S., Developmental morphology of the head mesoderm and reevaluation of segmental theories of the vertebrate head: evidence from embryos of an agnathan vertebrate, Lampetra japonica (1999) Dev. Biol., 210, pp. 381-400Kuratani, S.C., Kirby, M.L., Migration and distribution of circumpharyngeal crest cells in the chick embryo. Formation of the circumpharyngeal ridge and E/C8+ crest cells in the vertebrate head region (1992) Anat. Rec., 234, pp. 263-280Kusakabe, R., Kuraku, S., Kuratani, S., Expression and interaction of muscle-related genes in the lamprey imply the evolutionary scenario for vertebrate skeletal muscle, in association with the acquisition of the neck and fins (2011) Dev. Biol., 350, pp. 217-227Kusakabe, R., Kuratani, S., Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey (2005) Dev. Dyn., 234, pp. 824-834Latinkic, B.V., Cooper, B., Towers, N., Sparrow, D., Kotecha, S., Mohun, T.J., Distinct enhancers regulate skeletal and cardiac muscle-specific expression programs of the cardiac alpha-actin gene in Xenopus embryos (2002) Dev. Biol., 245, pp. 57-70Lours, C., Dietrich, S., The dissociation of the Fgf-feedback loop controls the limbless state of the neck (2005) Development, 132, pp. 5553-5564Mackenzie, S., Walsh, F.S., Graham, A., Migration of hypoglossal myoblast precursors (1998) Dev. Dyn., 213, pp. 349-358Maina, F., Casagranda, F., Audero, E., Simeone, A., Comoglio, P.M., Klein, R., Ponzetto, C., Uncoupling of Grb2 from the Met receptor in vivo reveals complex roles in muscle development (1996) Cell, 87, pp. 531-542Manner, J., Seidl, W., Steding, G., Correlation between the embryonic head flexures and cardiac development. An experimental study in chick embryos (1993) Anat. Embryol. (Berl.), 188, pp. 269-285Martin, B.L., Harland, R.M., A novel role for lbx1 in Xenopus hypaxial myogenesis (2006) Development, 133, pp. 195-208Merrell, A.J., Kardon, G., Development of the diaphragm - a skeletal muscle essential for mammalian respiration (2013) FEBS J., 280, pp. 4026-4035Mootoosamy, R.C., Dietrich, S., Distinct regulatory cascades for head and trunk myogenesis (2002) Development, 129, pp. 573-583Neal, H.V., Development of the hypoglossus musculature in Petromyzon and Squalus (1897) Anat. Anz., 13, pp. 441-463Neyt, C., Jagla, K., Thisse, C., Thisse, B., Haines, L., Currie, P.D., Evolutionary origins of vertebrate appendicular muscle (2000) Nature, 408, pp. 82-86Nieuwkoop, P.D., Faber, J., (1994) Normal Table of Xenopus laevis, , Garland Publishing Inc., New York, (Daudin) (Ed.)Noden, D.M., The embryonic origins of avian cephalic and cervical muscles and associated connective tissues (1983) Am. J. Anat., 168, pp. 257-276Noden, D.M., Francis-West, P., The differentiation and morphogenesis of craniofacial muscles (2006) Dev. Dyn., 235, pp. 1194-1218Ochi, H., Westerfield, M., Lbx2 regulates formation of myofibrils (2009) BMC Dev. Biol., 9, p. 13Prunotto, C., Crepaldi, T., Forni, P.E., Ieraci, A., Kelly, R.G., Tajbakhsh, S., Buckingham, M., Ponzetto, C., Analysis of Mlc-lacZ Met mutants highlights the essential function of Met for migratory precursors of hypaxial muscles and reveals a role for Met in the development of hyoid arch-derived facial muscles (2004) Dev. Dyn., 231, pp. 582-591Qu, S., Tucker, S.C., Zhao, Q., deCrombrugghe, B., Wisdom, R., Physical and genetic interactions between Alx4 and Cart1 (1999) Development, 126, pp. 359-369Ramel, D., Wang, X., Laflamme, C., Montell, D.J., Emery, G., Rab11 regulates cell-cell communication during collective cell movements (2013) Nat Cell Biol, 15, pp. 317-324Sabo, M.C., Nath, K., Elinson, R.P., Lbx1 expression and frog limb development (2010) Dev. Genes Evol.Schäfer, K., Braun, T., Early specification of limb muscle precursor cells by the homeobox gene Lbx1h (1999) Nat. Genet., 23, pp. 213-216Schubert, F.R., Mootoosamy, R.C., Walters, E.H., Graham, A., Tumiotto, L., Munsterberg, A.E., Lumsden, A., Dietrich, S., Wnt6 marks sites of epithelial transformations in the chick embryo (2002) Mech. Dev., 114, pp. 143-148Šošic, D., Brand-Saberi, B., Schmidt, C., Christ, B., Olson, E.N., Regulation of paraxis expression and somite formation by ectoderm- and neural tube-derived signals (1997) Dev. Biol., 185, pp. 229-243Takahashi, M., Tamura, K., Buscher, D., Masuya, H., Yonei-Tamura, S., Matsumoto, K., Naitoh-Matsuo, M., Shiroishi, T., The role of Alx-4 in the establishment of anteroposterior polarity during vertebrate limb development (1998) Development, 125, pp. 4417-4425Thisse, B., Heyer, V., Lux, A., Alunni, V., Degrave, A., Seiliez, I., Kirchner, J., Thisse, C., Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening (2004) Methods Cell Biol., 77, pp. 505-519Tremblay, P., Dietrich, S., Meriskay, M., Schubert, F.R., Li, Z., Paulin, D., A crucial role for Pax3 in the development of the hypaxial musculature and the long-range migration of muscle precursors (1998) Dev. Biol., 203, pp. 49-61Vasyutina, E., Stebler, J., Brand-Saberi, B., Schulz, S., Raz, E., Birchmeier, C., CXCR4 and Gab1 cooperate to control the development of migrating muscle progenitor cells (2005) Genes Dev., 19, pp. 2187-2198Wachtler, F., Jacob, M., Origin and development of the cranial skeletal muscles (1986) Bibl. Anat., 29, pp. 24-46Zhu, M., Yu, X., Ahlberg, P.E., Choo, B., Lu, J., Qiao, T., Qu, Q., Blom, H., A Silurian placoderm with osteichthyan-like marginal jaw bones (2013) Nature, 502, pp. 188-19