Sindbis virus proteins nsP1 and nsP2 contain homology to nonstructural proteins from several RNA plant viruses

Although the genetic organization of tobacco mosaic virus (TMV) differs considerably from that of the tripartite viruses (alfalfa mosaic virus [AlMV] and brome mosaic virus [BMV]), all of these RNA plant viruses share three domains of homology among their nonstructural proteins. One such domain, common to the AlMV and BMV 2a proteins and the readthrough portion of TMV p183, is also homologous to the readthrough protein nsP4 of Sindbis virus (Haseloff et al., Proc. Natl. Acad. Sci. U.S.A. 81:4358-4362, 1984). Two more domains are conserved among the AlMV and BMV 1a proteins and TMV p126. We show here that these domains have homology with portions of the Sindbis proteins nsP1 and nsP2, respectively. These results strengthen the view that the four viruses share mechanistic similarities in their replication strategies and may be evolutionarily related. These results also suggest that either the AlMV 1a, BMV 1a, and TMV p126 proteins are multifunctional or Sindbis proteins nsP1 and nsP2 function together as subunits in a single complex

Parameterization for subgrid-scale motion of ice-shelf calving fronts

A parameterization for the motion of ice-shelf fronts on a Cartesian grid in finite-difference land-ice models is presented. The scheme prevents artificial thinning of the ice shelf at its edge, which occurs due to the finite resolution of the model. The intuitive numerical implementation diminishes numerical dispersion at the ice front and enables the application of physical boundary conditions to improve the calculation of stress and velocity fields throughout the ice-sheet-shelf system. Numerical properties of this subgrid modification are assessed in the Potsdam Parallel Ice Sheet Model (PISM-PIK) for different geometries in one and two horizontal dimensions and are verified against an analytical solution in a flow-line setup

Parameterization for subgrid-scale motion of ice-shelf calving fronts

In order to explore the response of the Greenland ice sheet (GIS) to climate change on long (centennial to multi-millennial) time scales, a regional energy-moisture balance model has been developed. This model simulates seasonal variations of temperature and precipitation over Greenland and explicitly accounts for elevation and albedo feedbacks. From these fields, the annual mean surface temperature and surface mass balance can be determined and used to force an ice sheet model. The melt component of the surface mass balance is computed here using both a positive degree day approach and a more physically-based alternative that includes insolation and albedo explicitly. As a validation of the climate model, we first simulated temperature and precipitation over Greenland for the prescribed, present-day topography. Our simulated climatology compares well to observations and does not differ significantly from that of a simple parameterization used in many previous simulations. Furthermore, the calculated surface mass balance using both melt schemes falls within the range of recent regional climate model results. For a prescribed, ice-free state, the differences in simulated climatology between the regional energy-moisture balance model and the simple parameterization become significant, with our model showing much stronger summer warming. When coupled to a three-dimensional ice sheet model and initialized with present-day conditions, the two melt schemes both allow realistic simulations of the present-day GIS

Kinematic first-order calving law implies potential for abrupt ice-shelf retreat

Recently observed large-scale disintegration of Antarctic ice shelves has moved their fronts closer towards grounded ice. In response, ice-sheet discharge into the ocean has accelerated, contributing to global sea-level rise and emphasizing the importance of calving-front dynamics. The position of the ice front strongly influences the stress field within the entire sheet-shelf-system and thereby the mass flow across the grounding line. While theories for an advance of the ice-front are readily available, no general rule exists for its retreat, making it difficult to incorporate the retreat in predictive models. Here we extract the first-order large-scale kinematic contribution to calving which is consistent with large-scale observation. We emphasize that the proposed equation does not constitute a comprehensive calving law but represents the first-order kinematic contribution which can and should be complemented by higher order contributions as well as the influence of potentially heterogeneous material properties of the ice. When applied as a calving law, the equation naturally incorporates the stabilizing effect of pinning points and inhibits ice shelf growth outside of embayments. It depends only on local ice properties which are, however, determined by the full topography of the ice shelf. In numerical simulations the parameterization reproduces multiple stable fronts as observed for the Larsen A and B Ice Shelves including abrupt transitions between them which may be caused by localized ice weaknesses. We also find multiple stable states of the Ross Ice Shelf at the gateway of the West Antarctic Ice Sheet with back stresses onto the sheet reduced by up to 90 % compared to the present state

The Potsdam Parallel Ice Sheet Model (PISM-PIK) - Part 2: Dynamic equilibrium simulation of the Antarctic ice sheet

We present a dynamic equilibrium simulation of the ice sheet-shelf system on Antarctica with the Potsdam Parallel Ice Sheet Model (PISM-PIK). The simulation is initialized with present-day conditions for bed topography and ice thickness and then run to steady state with constant present-day surface mass balance. Surface temperature and sub-shelf basal melt distribution are parameterized. Grounding lines and calving fronts are free to evolve, and their modeled equilibrium state is compared to observational data. A physically-motivated calving law based on horizontal spreading rates allows for realistic calving fronts for various types of shelves. Steady-state dynamics including surface velocity and ice flux are analyzed for whole Antarctica and the Ronne-Filchner and Ross ice shelf areas in particular. The results show that the different flow regimes in sheet and shelves, and the transition zone between them, are captured reasonably well, supporting the approach of superposition of SIA and SSA for the representation of fast motion of grounded ice. This approach also leads to a natural emergence of sliding-dominated flow in stream-like features in this new 3-D marine ice sheet model

An indelible lineage marker for Xenopus using a mutated green fluorescent protein

We describe the use of a DNA construct (named GFP.RN3) encoding green fluorescent protein as a lineage marker for Xenopus embryos. This offers the following advantages over other lineage markers so far used in Xenopus. When injected as synthetic mRNA, its protein emits intense fluorescence in living embryos. It is non-toxic, and the fluorescence does not bleach when viewed under 480 nm light. It is surprisingly stable, being strongly visible up to the feeding tadpole stage (5 days), and in some tissues for several weeks after mRNA injection. We also describe a construct that encodes a blue fluorescent protein. We exemplify the use of this GFP.RN3 construct for marking the lineage of individual blastomeres at the 32- to 64-cell stage, and as a marker for single transplanted blastula cells. Both procedures have revealed that the descendants of one embryonic cell can contribute single muscle cells to nearly all segmental myotomes rather than predominantly to any one myotome. An independent aim of our work has been to follow the fate of cells in which an early regulatory gene has been temporarily overexpressed. For this purpose, we co-injected GFP.RN3 mRNA and mRNA for the early Xenopus gene Eomes, and found that a high concentration of Eomes results in ectopic muscle gene activation in only the injected cells. This marker may therefore be of general value in providing long term identification of those cells in which an early gene with ephemeral expression has been overexpressed

Following cell fate in the living mouse embryo

It has been difficult to follow many of the dramatic changes in cell fate and cell migration during mouse development. This is because there has been no enduring marker that would allow cells to be recognised in the living embryo. We believe that we have overcome this problem by developing a novel form of green fluorescent protein, named MmGFP, that proves to be easily visible and non toxic to mouse cells and does not perturb embryogenesis. We show that synthetic mRNA encoding MmGFP can be injected into blastomeres to follow the fate of their progeny during preimplantation development. We have made a stable embryonic stem cell line that expresses MmGFP and introduced these fluorescent cells into mouse embryos. For the first time, we have been able to follow the fate of embryonic stem cells in living embryos and to observe directly the contribution of these cells to distinct lineages of the postimplantation embryo. This approach should lead to a more complete description of the dynamics of cell fate in the mouse

Droplet-based microfluidic analysis and screening of single plant cells.

Droplet-based microfluidics has been used to facilitate high-throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems where phenotyping analyses typically are time-consuming and low-throughput. We report on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha at processing rates of >100,000 cells per hour. We use our microfluidic system to quantify the stochastic properties of a heat-inducible promoter across a population of transgenic protoplasts to demonstrate its potential for assessing gene expression activity in response to environmental conditions. We further demonstrate on-chip sorting of droplets containing YFP-expressing protoplasts from wild type cells using dielectrophoresis force. This work opens the door to droplet-based microfluidic analysis of plant cells for applications ranging from high-throughput characterisation of DNA parts to single-cell genomics to selection of rare plant phenotypes.BBSRC and EPSRC OpenPlant BB/L014130/

An optimised transformation protocol for Anthoceros agrestis and three more hornwort species

Land plants comprise two large monophyletic lineages, the vascular plants and the bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of the three lineages of bryophytes, only the mosses and the liverworts are systematically investigated, while the hornworts are understudied. Despite their importance for understanding fundamental questions of land plant evolution, they only recently became amenable to experimental investigation, with Anthoceros agrestis being developed as a hornwort model system. Availability of a high-quality genome assembly and a recently developed genetic transformation technique makes A. agrestis an attractive model species for hornworts. Here we describe an updated and optimised transformation protocol for A. agrestis which can be successfully used to genetically modify one more strain of A. agrestis and three more hornwort species, Anthoceros punctatus, Leiosporoceros dussi and Phaeoceros carolinianus. The new transformation method is less laborious, faster and results in the generation of greatly increased numbers of transformants compared to the previous method. We have also developed a new selection marker for transformation. Finally, we report the development of a set of different cellular localisation signal peptides for hornworts providing new tools to better understand hornwort cell biology

Oscillatory subglacial drainage in the absence of surface melt

The presence of strong diurnal cycling in basal water pressure records obtained during the melt season is well established for many glaciers. The behaviour of the drainage system outside the melt season is less well understood. Here we present borehole observations from a surge-type valley glacier in the St Elias Mountains, Yukon Territory, Canada. Our data indicate the onset of strongly correlated multi-day oscillations in water pressure in multiple boreholes straddling a main drainage axis, starting several weeks after the disappearance of a dominant diurnal mode in August 2011 and persisting until at least January 2012, when multiple data loggers suffered power failure. Jökulhlaups provide a template for understanding spontaneous water pressure oscillations not driven by external supply variability. Using a subglacial drainage model, we show that water pressure oscillations can also be driven on a much smaller scale by the interaction between conduit growth and distributed water storage in smaller water pockets, basal crevasses and moulins, and that oscillations can be triggered when water supply drops below a critical value. We suggest this in combination with a steady background supply of water from ground water or englacial drainage as a possible explanation for the observed wintertime pressure oscillations