In this Research Article, Picker et al. show how cells in the retina get their spatial coordinates.

BackgroundRab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood.Methodology/Principal FindingsComparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics.Conclusions/SignificanceWe have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity.

The optimization and validation of a method for the determination of phosphine in plant materials are described. The method is based on headspace sampling over the sample heated in 5% sulfuric acid. Critical factors such as sample amount, equilibration conditions, method of quantitation, and matrix effects are discussed, and validation data are presented. Grinding of coarse samples does not lead to lower results and is a prerequisite for standard addition experiments, which present the most reliable approach for quantitation because of notable matrix effects. Two interlaboratory comparisons showed that results varied considerably and that an uncertainty of measurement of about 50% has to be assessed. Flame photometric and mass spectrometric detection gave similar results. The proposed method is well reproducible within one laboratory, and results from the authors' laboratories using different injection and detection techniques are very close to each other. The considerable variation in the interlaboratory comparison shows that this analysis is still challenging in practice and further proficiency testing is needed.

The paired-like homeodomain transcription factor Pitx2c has an evolutionarily conserved role in determining asymmetric positioning and organogenesis of the internal organs. Normally it is expressed only on the left side of the embryo in the lateral plate mesoderm and in organs that will become asymmetrically positioned with respect to the midline. Disturbances in Pitx2c's expression pattern lead to laterality defects that affect both asymmetric morphogenesis and positioning. Neither its transcriptional targets nor the molecular mechanisms through which it exerts its patterning function in the lateral plate mesoderm are known.Here we provide evidence that the N-terminal domain of Pitx2c is important for this activity. We demonstrate that overexpression of the Pitx2c N-terminus in ovo is capable of randomizing the direction of heart looping, the first morphological asymmetry conserved in vertebrate embryos. We also demonstrate that leucine-41 is critical for this effect. The Pitx2c N-terminus does not inhibit the transactivation function of Pitx2c in transient transfection studies and leucine-41 does not appear to be critical for full-length Pitx2c to activate expression of bicoid responsive promoters in transient transfection assays. Thus, our data suggest that the ectopically expressed Pitx2c N-terminal domain competes with endogenous Pitx2c for binding to a protein interaction partner required for asymmetric morphogenesis along the left-right axis.We are currently performing a yeast two-hybrid screen to identify these partners. These data will be presented. During embryonic development, pattern formation must be tightly synchronized with tissue morphogenesis to coordinate the establishment of spatial cell identities with cell movements. In the vertebrate retina, patterning along the dorsal-ventral and nasaltemporal axis is required for correct spatial representation in the retinotectal map. But it is unknown how specification of axial cell positions in the retina can occur during the complex process of early eye morphogenesis. Studying zebrafish embryos, we found that the morphogenetic tissue re-arrangements during eye evagination result in progenitor cells in the nasal half of the retina primordium being brought into proximity to the sources of three fibroblast growth factor molecules, Fgf8/3/24, outside the eye. Triple mutant analysis shows that this combined Fgf signal fully controls nasal retina identity by regulating the nasal transcription factor Foxg1. Surprisingly, nasal-temporal axis specification occurs very early along the dorsal-ventral axis of the evaginating eye. By in vivo imaging GFP-tagged retinal progenitor cells in transgenic embryos, we find that subsequent eye morphogenesis requires gradual tissue compaction in the nasal half and directed cell movements into the temporal half of the retina. Balancing these processes drives the progressive alignment of the nasal temporal retina axis with the anterior-posterior body axis and is controlled by a feed-forward effect of Fgf signaling on Foxg1-medi...

This paper describes the development strategies for an integrated tool to support scientists in the creative exploration of data relating to biochemical pathways. The multiple user groups, diverse functionalities, and many types and sources of data demanded a flexible yet coherent approach. This paper summarises the software requirements and the implied modules and functions, and focuses on the design decisions relevant to the representation, management and flow of data. Finally, several case studies in the use of the software are described and evaluated, and recommendations are made for future work.