The Hox Gene egl-5 Acts as a Terminal Selector for VD13 Development via Wnt Signaling

This work is licensed under a Creative Commons Attribution 4.0 International License.Nervous systems are comprised of diverse cell types that differ functionally and morphologically. During development, extrinsic signals, e.g., growth factors, can activate intrinsic programs, usually orchestrated by networks of transcription factors. Within that network, transcription factors that drive the specification of features specific to a limited number of cells are often referred to as terminal selectors. While we still have an incomplete view of how individual neurons within organisms become specified, reporters limited to a subset of neurons in a nervous system can facilitate the discovery of cell specification programs. We have identified a fluorescent reporter that labels VD13, the most posterior of the 19 inhibitory GABA (γ-amino butyric acid)-ergic motorneurons, and two additional neurons, LUAL and LUAR. Loss of function in multiple Wnt signaling genes resulted in an incompletely penetrant loss of the marker, selectively in VD13, but not the LUAs, even though other aspects of GABAergic specification in VD13 were normal. The posterior Hox gene, egl-5, was necessary for expression of our marker in VD13, and ectopic expression of egl-5 in more anterior GABAergic neurons induced expression of the marker. These results suggest egl-5 is a terminal selector of VD13, subsequent to GABAergic specification

AnnotationBustR: an R package to extract subsequences from GenBank annotations

Background DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequence records on GenBank contain more than one gene or are portions of genomes. Inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from many GenBank accessions based on annotations where gene names may vary extensively. Results The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts subsequences of interest and then writes them to a FASTA file for users to employ in their research endeavors. Conclusion FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses

Leaf reflectance spectra capture the evolutionary history of seed plants

Leaf reflection spectra have been increasingly used to assess plant diversity. However, we do not yet understand how spectra vary across the tree of life or how the evolution of leaf traits affects the differentiation of spectra among species and lineages. Here we describe a framework that integrates spectra with phylogenies and apply it to aglobal dataset of over 16 000 leaf-level spectra (400–2400 nm) for 544 seed plant species. We test for phylogenetic signal in spectra, evaluate their ability to classify lineages, and characterize their evolutionary dynamics. We show that phylogenetic signal is present in leaf spectra but that the spectral regions most strongly associated with the phylogeny vary among lineages. Despite among-lineage heterogeneity, broad plant groups, orders, and families can be identified from reflectance spectra. Evolutionary models also reveal that different spectral regions evolve at different rates and under different constraint levels, mirroring the evolution of their underlying traits. Leaf spectra capture the phylogenetic history of seed plants and the evolutionary dynamics of leaf chemistry and structure. Consequently, spectra have the potential to provide breakthrough assessments of leaf evolution and plant phylogenetic diversity at global scales

Influence of ejection fraction on cause‐specific mortality in heart failure with preserved ejection fraction

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143697/1/ejhf1040.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143697/2/ejhf1040_am.pd

Solar Neutrino Constraints on the BBN Production of Li

Using the recent WMAP determination of the baryon-to-photon ratio, 10^{10} \eta = 6.14 to within a few percent, big bang nucleosynthesis (BBN) calculations can make relatively accurate predictions of the abundances of the light element isotopes which can be tested against observational abundance determinations. At this value of \eta, the Li7 abundance is predicted to be significantly higher than that observed in low metallicity halo dwarf stars. Among the possible resolutions to this discrepancy are 1) Li7 depletion in the atmosphere of stars; 2) systematic errors originating from the choice of stellar parameters - most notably the surface temperature; and 3) systematic errors in the nuclear cross sections used in the nucleosynthesis calculations. Here, we explore the last possibility, and focus on possible systematic errors in the He3(\alpha,\gamma)Be7 reaction, which is the only important Li7 production channel in BBN. The absolute value of the cross section for this key reaction is known relatively poorly both experimentally and theoretically. The agreement between the standard solar model and solar neutrino data thus provides additional constraints on variations in the cross section (S_{34}). Using the standard solar model of Bahcall, and recent solar neutrino data, we can exclude systematic S_{34} variations of the magnitude needed to resolve the BBN Li7 problem at > 95% CL. Additional laboratory data on He3(\alpha,\gamma)Be7 will sharpen our understanding of both BBN and solar neutrinos, particularly if care is taken in determining the absolute cross section and its uncertainties. Nevertheless, it already seems that this ``nuclear fix'' to the Li7 BBN problem is unlikely; other possible solutions are briefly discussed.Comment: 21 pages, 3 ps figure

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Abstract Background Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website ( http://www.phylotastic.org ), and a server image. Conclusions Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.http://deepblue.lib.umich.edu/bitstream/2027.42/112888/1/12859_2013_Article_5897.pd

Figuring Out Gas & Galaxies in Enzo (FOGGIE). I. Resolving Simulated Circumgalactic Absorption at 2 ≤ z ≤ 2.5

We present simulations from the new "Figuring Out Gas & Galaxies in Enzo" (FOGGIE) project. In contrast to most extant simulations of galaxy formation, which concentrate computational resources on galactic disks and spheroids with fluid and particle elements of fixed mass, the FOGGIE simulations focus on extreme spatial and mass resolution in the circumgalactic medium (CGM) surrounding galaxies. Using the Enzo code and a new refinement scheme, FOGGIE reaches spatial resolutions of 381 comoving h^(−1) pc and resolves extremely low masses (≾1–100 M⊙) out to 100 comoving h^(−1) kpc from the central halo. At these resolutions, cloud and filament-like structures giving rise to simulated absorption are smaller, and better resolved, than the same structures simulated with standard density-dependent refinement. Most of the simulated absorption arises in identifiable and well-resolved structures with masses ≾10^4 M⊙, well below the mass resolution of typical zoom simulations. However, integrated quantities such as mass surface density and ionic covering fractions change at only the ≾30% level as resolution is varied. These relatively small changes in projected quantities—even when the sizes and distribution of absorbing clouds change dramatically—indicate that commonly used observables provide only weak constraints on the physical structure of the underlying gas. Comparing the simulated absorption features to the KODIAQ (Keck Observatory Database of Ionized Absorption toward Quasars) survey of z ~ 2–3.5 Lyman limit systems, we show that high-resolution FOGGIE runs better resolve the internal kinematic structure of detected absorption and better match the observed distribution of absorber properties. These results indicate that circumgalactic medium resolution is key in properly testing simulations of galaxy evolution with circumgalactic observations

FUSE Deuterium Observations: A Strong Case For Galactic Infall

Measurements of deuterium in the local interstellar medium have revealed large variations in D/H along different lines of sight. Moreover, recent {\it Far Ultraviolet Spectroscopic Explorer} (FUSE) measurements find D/H to be anticorrelated with several indicators of dust formation and survival, suggesting that interstellar deuterium suffers significant depletion onto dust grains. This in turn implies that the total deuterium abundance in the local Galactic disk could be as high as $\sim 84$ of the primordial D abundance. It was proposed that the infall/accretion of pristine gas is needed to explain such a high deuterium abundance. However, we point out that the infall needed to maintain a high present-day D/H is, within the preferred models, in tension with observations that gas represents only some $\sim 20$ of Galactic baryons, with the balance in stars. We study this tension in the context of a wide class of Galactic evolution models for baryonic processing through stars, which show that deuterium destruction is strongly and cleanly correlated with the drop in the gas fraction. We find that FUSE deuterium observations and Galactic gas fraction estimates can be reconciled in some models; these demand a significant infall rate of pristine material that almost completely balances the rate of star formation. These successful models also require that the average fraction of gas that is returned by dying stars is less than 40% of the initial stellar mass. Cosmological implications of dust depletion of D in high-redshift systems are discussed.Comment: 22 pages, 6 figures. Matches version to appear in JCAP; presentation revised and improved following referee comments; conclusions unchange