Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression

Homeobox genes encode a large superclass of transcription factors with widespread roles in animal development. Within chordates there are over 100 homeobox genes in the invertebrate cephalochordate amphioxus and over 200 in humans. Set against this general trend of increasing gene number in vertebrate evolution, some ancient homeobox genes that were present in the last common ancestor of chordates have been lost from vertebrates. Here, we describe the embryonic expression of four amphioxus descendants of these genes—AmphiNedxa, AmphiNedxb, AmphiMsxlx and AmphiNKx7. All four genes are expressed with a striking asymmetry about the left–right axis in the pharyngeal region of neurula embryos, mirroring the pronounced asymmetry of amphioxus embryogenesis. AmphiMsxlx and AmphiNKx7 are also transiently expressed in an anterior neural tube region destined to become the cerebral vesicle. These findings suggest significant rewiring of developmental gene regulatory networks occurred during chordate evolution, coincident with homeobox gene loss. We propose that loss of otherwise widely conserved genes is possible when these genes function in a confined role in development that is subsequently lost or significantly modified during evolution. In the case of these homeobox genes, we propose that this has occurred in relation to the evolution of the chordate pharynx and brain

Undamped nonequilibrium dynamics of a nondegenerate Bose gas in a 3D isotropic trap

We investigate anomalous damping of the monopole mode of a non-degenerate 3D Bose gas under isotropic harmonic confinement as recently reported by the JILA TOP trap experiment [D. S. Lob- ser, A. E. S. Barentine, E. A. Cornell, and H. J. Lewandowski (in preparation)]. Given a realistic confining potential, we develop a model for studying collective modes that includes the effects of anharmonic corrections to a harmonic potential. By studying the influence of these trap anharmonicities throughout a range of temperatures and collisional regimes, we find that the damping is caused by the joint mechanisms of dephasing and collisional relaxation. Furthermore, the model is complimented by Monte Carlo simulations which are in fair agreement with data from the JILA experiment.Comment: 11 pages, 6 figure

GRB Afterglows from Anisotropic Jets

Some progenitor models of gamma-ray bursts (GRBs) (e.g., collapsars) may produce anisotropic jets in which the energy per unit solid angle is a power-law function of the angle ($\propto\theta^{-k}$). We calculate light curves and spectra for GRB afterglows when such jets expand either in the interstellar medium or in the wind medium. In particular, we take into account two kinds of wind: one ($n\propto r^{-3/2}$) possibly from a typical red supergiant star and another ($n\propto r^{-2}$) possibly from a Wolf-Rayet star. We find that in each type of medium, one break appears in the late-time afterglow light curve for small $k$ but becomes weaker and smoother as $k$ increases. When $k\ge 2$, the break seems to disappear but the afterglow decays rapidly. Thus, one expects that the emission from expanding, highly anisotropic jets provides a plausible explanation for some rapidly fading afteglows whose light curves have no break. We also present good fits to the optical afterglow light curve of GRB 991208. Finally, we argue that this burst might arise from a highly anisotropic jet expanding in the wind ($n\propto r^{-3/2}$) from a red supergiant to interpret the observed radio-to-optical-band afterglow data (spectrum and light curve).Comment: 12 pages + 10 figures, accepted by Ap

Structure Speaks: User-Centered Design and Professional Development

This reflective essay situates a yearlong professional development endeavor led by a site of the National Writing Project within the language of technical communication. Developing rural writing teachers through four distinct design features—needs assessment, frequent contact, website redesign, collaborative planning through Google Docs—this work sought to put participants and providers on equal levels, sharing control of programming when possible. Professional development providers and teacher educators ultimately must model practices they desire to impacting students in the classroom

Sympathetic cooling of trapped fermions by bosons in the presence of particle losses

We study the sympathetic cooling of a trapped Fermi gas interacting with an ideal Bose gas below the critical temperature of the Bose-Einstein condensation. We derive the quantum master equation, which describes the dynamics of the fermionic component, and postulating the thermal distribution for both gases we calculate analytically the rate at which fermions are cooled by the bosonic atoms. The particle losses constitute an important source of heating of the degenerate Fermi gas. We evaluate the rate of loss-induced heating and derive analytical results for the final temperature of fermions, which is limited in the presence of particle losses.Comment: 7 pages, 2 figures, EPL style; final versio

Sequence and Expression of Amphioxus Alkali Myosin Light Chain (AmphiMLC-alk) Throughout Development: Implications for Vertebrate Myogenesis

AbstractThe lower chordate amphioxus, widely considered the closest living invertebrate relative of the vertebrates, is a key organism for understanding the relationship between gene duplications and evolution of the complex vertebrate body plan. In tetrapod vertebrates, the alkali myosin light chain genes (MLC-alk), which code for proteins associated with the globular head of the myosin heavy chain, constitute a large family with stage-, tissue-, and fiber-type-specific expression of different isoforms thought to have arisen by duplication of a single ancestral gene. In protostome invertebrates, e.g., arthropods, molluscs, and nematodes, only one MLC-alk gene has been found, but the number of such genes in deuterostome invertebrates and lower vertebrates is unknown. The present report, describing the sequence and expression throughout development of the amphioxus gene for alkali myosin light chain (AmphiMLC-alk), thus fills a major gap in understanding the relation between gene duplication and increasing diversity of muscle-cell types. A full-length clone (1 kb) of AmphiMLC-alk was isolated from a larval amphioxus cDNA library. It coded for a 149-amino-acid protein most closely related to the vertebrate embryonic form of MLC-alk. Southern blot analysis revealed only one copy of AmphiMLC-alk and suggested that it is the only MLC-alk gene in amphioxus. Northern blot analysis indicated that this gene produces only one transcript, which is expressed at all stages of development and in adults. In situ hybridizations showed expression initially in the myotomes of somites 2-5 of neurula embryos and soon thereafter in the myotomes of somite 1 and of newly forming somites progressively added posteriorly. Myotomal expression continues throughout larval development and into the adult stage as the myotomal cells differentiate into striated, mononucleate muscle cells—unlike vertebrate striated muscle cells, those of amphioxus never become multinucleate. In late larvae and adults myotomal expression of AmphiMLC-alk is localized along the medial edge of the myotome and at the ends of the cells. This is the first demonstration of intracellular localization of MLC transcripts in muscle cells of any animal. Expression of AmphiMLC-alk was also detected in smooth muscles as well as in striated muscles not derived from the myotome. These expression data are consistent with the Southern blot analysis in suggesting that there is only one MLC-alk gene in amphioxus. Thus, duplication of an ancestral vertebrate MLC-alk gene probably occurred after the vertebrate and amphioxus lineages split. We conclude that development of a segmented axial musculature preceded the evolution of multiple MLC-alk isoforms, which evidently arose about the time of multinucleation. Since myogenesis in amphioxus is similar to but far simpler than myogenesis in vertebrates at both the structural and gene levels, an understanding of myogenesis in amphioxus can give insights into both the evolutionary history and the detailed mechanisms of vertebrate myogenesis