Developmental evolution of flowering plant pollen tube cell walls: callose synthase (CalS) gene expression patterns

<p>Abstract</p> <p>Background</p> <p>A number of innovations underlie the origin of rapid reproductive cycles in angiosperms. A critical early step involved the modification of an ancestrally short and slow-growing pollen tube for faster and longer distance transport of sperm to egg. Associated with this shift are the predominantly callose (1,3-β-glucan) walls and septae (callose plugs) of angiosperm pollen tubes. Callose synthesis is mediated by callose synthase (CalS). Of 12 <it>CalS </it>gene family members in <it>Arabidopsis</it>, only one (<it>CalS5</it>) has been directly linked to pollen tube callose. <it>CalS5 </it>orthologues are present in several monocot and eudicot genomes, but little is known about the evolutionary origin of <it>CalS5 </it>or what its ancestral function may have been.</p> <p>Results</p> <p>We investigated expression of <it>CalS </it>in pollen and pollen tubes of selected non-flowering seed plants (gymnosperms) and angiosperms within lineages that diverged below the monocot/eudicot node. First, we determined the nearly full length coding sequence of a <it>CalS5 </it>orthologue from <it>Cabomba caroliniana </it>(<it>CcCalS5</it>) (Nymphaeales). Semi-quantitative RT-PCR demonstrated low <it>CcCalS5 </it>expression within several vegetative tissues, but strong expression in mature pollen. <it>CalS </it>transcripts were detected in pollen tubes of several species within Nymphaeales and Austrobaileyales, and comparative analyses with a phylogenetically diverse group of sequenced genomes indicated homology to <it>CalS5</it>. We also report <it>in silico </it>evidence of a putative <it>CalS5 </it>orthologue from <it>Amborella</it>. Among gymnosperms, <it>CalS5 </it>transcripts were recovered from germinating pollen of <it>Gnetum </it>and <it>Ginkgo</it>, but a novel <it>CalS </it>paralog was instead amplified from germinating pollen of <it>Pinus taeda</it>.</p> <p>Conclusion</p> <p>The finding that CalS5 is the predominant callose synthase in pollen tubes of both early-diverging and model system angiosperms is an indicator of the homology of their novel callosic pollen tube walls and callose plugs. The data suggest that <it>CalS5 </it>had transient expression and pollen-specific functions in early seed plants and was then recruited to novel expression patterns and functions within pollen tube walls in an ancestor of extant angiosperms.</p

Toward an International Paramedic Research Agenda

Around the world the emergency medical services (EMS) profession has made tremendous strides over recent decades. We have become more professional, have a rapidly growing proportion of paramedics who are university qualified, our practice has become more evidence-based, and a growing number of paramedics are completing graduate-level programs and going on to conduct their own research. As a profession we have much to celebrate when we consider these accomplishments.In some ways we are also following in the footsteps of other professions that have developed along similar pathways. A century ago physicians were trained in hospital basements and practiced procedures that had little evidence to ensure their quality or effectiveness. A half century ago nurses were largely trained in hospital basements and again had little research to justify their practices. Members of those professions recognized that the only way out of the basement was through the university. Members of those and other health professions took it upon themselves to make a university degree a requirement to enter practice. They recognized that a university degree was a key requirement of professionalism. Today we could not imagine a physician without a university degree and almost all new nurses and allied health professionals are now graduates of university programs

Publishing re-usable phylogenetic trees, in theory and practice

Sharing and re-use of data are essential to the progressive and self-correcting nature of science. In recognition of this principle, journals and funding agencies have adopted policies to encourage sharing of information (&#x27;data&#x27;), including empirical data as well as computed inferences such as phylogenetic trees. &#xd;&#xa;Here we summarize an ongoing analysis of 1) current practices for sharing phylogenetic trees and associated data; 2) current barriers to effective sharing and reuse of such data; and 3) prospects for reducing these barriers to promote more widespread sharing and re-use. Currently, the technical infrastructure is available to support (with some limitations) rudimentary archiving in conjunction with manuscript publication. Yet, most published trees are not archived, and there is no community standard governing the recommended format or content to ensure a re-usable phylogenetic record. Without a shift in emphasis toward re-usability, along with technology and standards to support such a shift, the value of trees (whether disseminated via public archives, or by other means) will be limited. Interviews with actual or potential secondary consumers of phylogenetic results suggest that there is a considerable market for re-use, but that most attempts end in disappointment. Phylogenetic results available via author requests, journal web sites, archival repositories and project web sites rarely include the critical information that secondary consumers seek, such as unique identifiers for biological sources (including species sources and accession numbers), indicators of quality, and documentation of the analytical methods used to obtain the results.&#xd;&#xa;Based on the analysis presented here, we suggest that enabling effective re-use entails a commitment by the research community to several changes from current practice: 1) using globally unique identifiers (GUIDs) to reference informational and material entities; 2) developing and using technology for documenting and exchanging the metadata that facilitate re-use; and 3) supporting development and use of a minimal reporting standard that indicates what data and metadata are considered essential for a re-useable phylogenetic record. We suggest that re-use may be catalyzed most rapidly by identifying and targeting (with appropriate technology) the most promising circumstances for re-use. These might include the extraction of sub-trees from large trees (for use in reconciliation, classification, and comparative analysis); the re-use of seed alignments, sub-alignments and homologized characters; the linking of phylogenies to geographic information (for use in ecology, phylogeography and biogeography); and the construction of supertrees and supermatrices

Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity.

Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

BACKGROUND Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use. FINDINGS Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a much larger tree. CONCLUSIONS The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record

Figuring Out Gas &amp; Galaxies in Enzo (FOGGIE). II. Emission from the z=3 Circumgalactic Medium

Observing the circumgalactic medium (CGM) in emission provides 3D maps of the spatial and kinematic extent of the gas that fuels galaxies and receives their feedback. We present mock emission-line maps of highly resolved CGM gas from the FOGGIE project (Figuring Out Gas & Galaxies in Enzo) and link these maps back to physical and spatial properties of the gas. By increasing the spatial resolution alone, the total luminosity of the line emission increases by an order of magnitude. This increase arises in the abundance of dense small-scale structure resolved when the CGM gas is simulated to < 100 pc scales. Current integral field unit instruments like KCWI and MUSE should be able to detect the brightest knots and filaments of such emission, and from this to infer the bulk kinematics of the CGM gas with respect to the galaxy. We conclude that accounting for small-scale structure well below the level of instrument spatial resolution is necessary to properly interpret such observations in terms of the underlying gas structure driving observable emission.Comment: 18 pages, 10 figures. Submitted to ApJ. Comments welcom

Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient

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 (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.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science

Effects of sacubitril/valsartan on biomarkers of extracellular matrix regulation in patients with HFrEF

Background: Myocardial fibrosis is an important pathophysiological mechanism underlying the development of heart failure (HF). Given the biochemical targets of sacubitril/valsartan, we hypothesized that circulating biomarkers reflecting the mechanisms that determine extracellular matrix (ECM) homeostasis, including collagen synthesis, processing, and degradation, are altered by sacubitril/valsartan in comparison to enalapril. Objectives: The purpose of this study was to examine the effects of sacubitril/valsartan on biomarkers of ECM homeostasis and the association between the rate of primary composite outcome (cardiovascular death or HF hospitalization) and these biomarkers. Methods: Biomarkers at baseline (n = 2,067) and both baseline and 8 months after randomization (n = 1,776) included aldosterone, soluble ST2 (sST2), tissue inhibitor of matrix metalloproteinase (TIMP)-1, matrix metalloproteinase (MMP)-2, MMP-9, Galectin-3 (Gal-3), N-terminal propeptide of collagen I (PINP), and N-terminal propeptide of collagen III (PIIINP). The effects of sacubitril/valsartan on biomarkers were compared with enalapril. Baseline biomarker values and changes from baseline to 8 months were related to primary outcome. Results: At baseline, the profibrotic biomarkers aldosterone, sST2, TIMP-1, Gal-3, PINP, and PIIINP were higher, and biomarkers associated with collagen degradation, MMP-2 and -9, were lower than published referent control values. Eight months after randomization, aldosterone, sST2, TIMP-1, MMP-9, PINP, and PIIINP had decreased more in the sacubitril/valsartan than enalapril group. At baseline, higher values of sST-2, TIMP-1, and PIIINP were associated with higher primary outcome rates. Changes from baseline to 8 months in sST-2 and TIMP-1 were associated with change in outcomes. Conclusions: Biomarkers associated with profibrotic signaling are altered in HF with reduced ejection fraction, sacubitril/valsartan significantly decreased many of these biomarkers, and these biomarkers have important prognostic value. These findings suggest that sacubitril/valsartan may reduce profibrotic signaling, which may contribute to the improved outcomes. (This Study Will Evaluate the Efficacy and Safety of LCZ696 Compared to Enalapril on Morbidity and Mortality of Patients With Chronic Heart Failure [PARADIGM-HF]; NCT01035255