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

Individual-based modelling of the development and transport of a Karenia mikimotoi bloom on the North-West European continental shelf

In 2006, a large and prolonged bloom of the dinoflagellate Karenia mikimotoi occurred in Scottish coastal waters, causing extensive mortalities of benthic organisms including annelids and molluscs and some species of fish ( Davidson et al., 2009). A coupled hydrodynamic-algal transport model was developed to track the progression of the bloom around the Scottish coast during June–September 2006 and hence investigate the processes controlling the bloom dynamics. Within this individual-based model, cells were capable of growth, mortality and phototaxis and were transported by physical processes of advection and turbulent diffusion, using current velocities extracted from operational simulations of the MRCS ocean circulation model of the North-west European continental shelf. Vertical and horizontal turbulent diffusion of cells are treated using a random walk approach. Comparison of model output with remotely sensed chlorophyll concentrations and cell counts from coastal monitoring stations indicated that it was necessary to include multiple spatially distinct seed populations of K. mikimotoi at separate locations on the shelf edge to capture the qualitative pattern of bloom transport and development. We interpret this as indicating that the source population was being transported northwards by the Hebridean slope current from where colonies of K. mikimotoi were injected onto the continental shelf by eddies or other transient exchange processes. The model was used to investigate the effects on simulated K. mikimotoi transport and dispersal of: (1) the distribution of the initial seed population; (2) algal growth and mortality; (3) water temperature; (4) the vertical movement of particles by diurnal migration and eddy diffusion; (5) the relative role of the shelf edge and coastal currents; (6) the role of wind forcing. The numerical experiments emphasized the requirement for a physiologically based biological model and indicated that improved modelling of future blooms will potentially benefit from better parameterisation of temperature dependence of both growth and mortality and finer spatial and temporal hydrodynamic resolution

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

Adaptive strong-field control of chemical dynamics guided by three-dimensional momentum imaging.

Shaping ultrafast laser pulses using adaptive feedback can manipulate dynamics in molecular systems, but extracting information from the optimized pulse remains difficult. Experimental time constraints often limit feedback to a single observable, complicating efforts to decipher the underlying mechanisms and parameterize the search process. Here we show, using two strong-field examples, that by rapidly inverting velocity map images of ions to recover the three-dimensional photofragment momentum distribution and incorporating that feedback into the control loop, the specificity of the control objective is markedly increased. First, the complex angular distribution of fragment ions from the nω+C2D4→C2D3++D interaction is manipulated. Second, isomerization of acetylene (nω+C2H2→C2H22+→CH2++C+) is controlled via a barrier-suppression mechanism, a result that is validated by model calculations. Collectively, these experiments comprise a significant advance towards the fundamental goal of actively guiding population to a specified quantum state of a molecule

The importance of Rydberg orbitals in dissociative ionization of small hydrocarbon molecules in intense laser fields

Much of our intuition about strong-field processes is built upon studies of diatomic molecules, which typically have electronic states that are relatively well separated in energy. In polyatomic molecules, however, the electronic states are closer together, leading to more complex interactions. A combined experimental and theoretical investigation of strong-field ionization followed by hydrogen elimination in the hydrocarbon series C2D2, C2D4 and C2D6 reveals that the photofragment angular distributions can only be understood when the field-dressed orbitals rather than the field-free orbitals are considered. Our measured angular distributions and intensity dependence show that these field-dressed orbitals can have strong Rydberg character for certain orientations of the molecule relative to the laser polarization and that they may contribute significantly to the hydrogen elimination dissociative ionization yield. These findings suggest that Rydberg contributions to field-dressed orbitals should be routinely considered when studying polyatomic molecules in intense laser fields

Subfemtosecond steering of hydrocarbon deprotonation through superposition of vibrational modes

Subfemtosecond control of the breaking and making of chemical bonds in polyatomic molecules is poised to open new pathways for the laser-driven synthesis of chemical products. The break-up of the C-H bond in hydrocarbons is an ubiquitous process during laser-induced dissociation. While the yield of the deprotonation of hydrocarbons has been successfully manipulated in recent studies, full control of the reaction would also require a directional control (that is, which C-H bond is broken). Here, we demonstrate steering of deprotonation from symmetric acetylene molecules on subfemtosecond timescales before the break-up of the molecular dication. On the basis of quantum mechanical calculations, the experimental results are interpreted in terms of a novel subfemtosecond control mechanism involving non-resonant excitation and superposition of vibrational degrees of freedom. This mechanism permits control over the directionality of chemical reactions via vibrational excitation on timescales defined by the subcycle evolution of the laser waveform

The importance of Rydberg orbitals in dissociative ionization of small hydrocarbon molecules in intense few-cycle laser pulses

Citation: Jochim, B., Siemering, R., Zohrabi, M., Voznyuk, A., Mahowald, J. B., Schmitz, D. G., . . . De Vivie-Riedle, R. (2015). The importance of Rydberg orbitals in dissociative ionization of small hydrocarbon molecules in intense few-cycle laser pulses. 635(11). doi:10.1088/1742-6596/635/11/112043We demonstrate the importance of ionization from Rydberg orbitals via experimental and theoretical work focusing on the strong-field dissociative single ionization of small hydrocarbons. Our findings suggest that Rydberg states should be routinely considered when studying polyatomic molecules in intense laser fields. © Published under licence by IOP Publishing Ltd.Additional Authors: Wells, E.;De Vivie-Riedle, R

Poplar GTL1 Is a Ca2+/Calmodulin-Binding Transcription Factor that Functions in Plant Water Use Efficiency and Drought Tolerance

Diminishing global fresh water availability has focused research to elucidate mechanisms of water use in poplar, an economically important species. A GT-2 family trihelix transcription factor that is a determinant of water use efficiency (WUE), PtaGTL1 (GT-2 like 1), was identified in Populus tremula × P. alba (clone 717-IB4). Like other GT-2 family members, PtaGTL1 contains both N- and C-terminal trihelix DNA binding domains. PtaGTL1 expression, driven by the Arabidopsis thaliana AtGTL1 promoter, suppressed the higher WUE and drought tolerance phenotypes of an Arabidopsis GTL1 loss-of-function mutation (gtl1-4). Genetic suppression of gtl1-4 was associated with increased stomatal density due to repression of Arabidopsis STOMATAL DENSITY AND DISTRIBUTION1 (AtSDD1), a negative regulator of stomatal development. Electrophoretic mobility shift assays (EMSA) indicated that a PtaGTL1 C-terminal DNA trihelix binding fragment (PtaGTL1-C) interacted with an AtSDD1 promoter fragment containing the GT3 box (GGTAAA), and this GT3 box was necessary for binding. PtaGTL1-C also interacted with a PtaSDD1 promoter fragment via the GT2 box (GGTAAT). PtaSDD1 encodes a protein with 60% primary sequence identity with AtSDD1. In vitro molecular interaction assays were used to determine that Ca2+-loaded calmodulin (CaM) binds to PtaGTL1-C, which was predicted to have a CaM-interaction domain in the first helix of the C-terminal trihelix DNA binding domain. These results indicate that, in Arabidopsis and poplar, GTL1 and SDD1 are fundamental components of stomatal lineage. In addition, PtaGTL1 is a Ca2+-CaM binding protein, which infers a mechanism by which environmental stimuli can induce Ca2+ signatures that would modulate stomatal development and regulate plant water use

Extensions of MADM (Mosaic Analysis with Double Markers) in Mice

Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM