Pattern regulation in the eyebud of Xenopus studied with a vital-dye fiber-tracing technique

Evidence for pattern regulation in the developing Xenopus visual system has previously been obtained after surgical manipulations of the eyebud early in development. In one experimental paradigm, a "compound" eye is produced by combining a nasal (anterior) half-eyebud with normal dorsoventral polarity and a temporal (posterior) half-eyebud with inverted dorsoventral polarity. The adult retinotectal projection from such compound eyes, as assayed by electrophysiological mapping techniques, shows normal dorsoventral polarity in both halves, indicating an apparent reversal in the polarity of the surgically-inverted half. We have utilized a fluorescent vital-dye fiber-tracing technique to investigate the early events in this regulatory process. The results show that the change in dorsoventral polarity is not due to cell movements in the eyebud after surgery. Interestingly, the experiments also demonstrate that the pattern of connections initially formed by the developing eye does not reflect the pattern regulation observed in the adult retinotectal map; instead, the temporal half of the eye projects to the tectum with inverted dorsoventral order. Thus, the regulation observed in the adult does not become evident in the pattern of the projection until after early larval development.     

Insights into activity-dependent map formation from the retinotectal system: a middle-of-the-brain perspective

The development of orderly topographic maps in the central nervous system (CNS) results from a collaboration of chemoaffinity cues that establish the coarse organization of the projection and activity-dependent mechanisms that fine-tune the map. Using the retinotectal projection as a model system, we describe evidence that biochemical tags and patterned neural activity work in parallel to produce topographically ordered axonal projections. Finally, we review recent experiments in other CNS projections that support the proposition that cooperation between molecular guidance cues and activity-dependent processes constitutes a general paradigm for CNS map formation.     

Dynamic aspects of filopodial formation by reorganization of microfilaments

The coelomocytes of the sea urchin, Strongylocentrotus droebachiensis, may be prevented from clotting with 50 mM ethylene glycol-bis(beta-aminoethyl)-N,N,N',N'-tetraacetate, 50 mM Tris-HCl, pH 7.8 and subsequently separated into various cell types on sucrose gradients. One cell type, the petaloid coelomocyte, spontaneously undergoes a striking morphological transformation to a form exhibiting numerous, t-in cytoplasmic projections (filopodia). Moreover, the transformation is reversible. Ultrastructurally, the formation of the filopodia results from a progressive reorganization of actin-containing filaments into bundles that are radially oriented. The formation of the filament bundles is initiated at the cell's periphery and proceeds inward. Simultaneously, the cytoplasm in between the bundles is withdrawn, exposing finger-like filopodia. Ultimately, the filopodia can be extended by up to four times their original length. Biochemically, actin is the most abundant protein in while cell homogenates and is extractable in milligram quantities via acetone powders. An actomyosin complex may also be isolated from these cells and is presumed to be active in producing the various forms of motility observed.     

Development and regeneration of the retinotectal map in goldfish: a computational study

We present a simple computational model to study the interplay of activity-dependent and intrinsic processes thought to be involved in the formation of topographic neural projections. Our model consists of two input layers which project to one target layer. The connections between layers are described by a set of synaptic weights. These weights develop according to three interacting developmental rules: (i) an intrinsic fibre-target interaction which generates chemospecific adhesion between afferent fibres and target cells; (ii) an intrinsic fibre-fibre interaction which generates mutual selective adhesion between the afferent fibres; and (iii) an activity-dependent fibre-fibre interaction which implements Hebbian learning. Additionally, constraints are imposed to keep synaptic weights finite. The model is applied to a set of eleven experiments on the regeneration of the retinotectal projection in goldfish. We find that the model is able to reproduce the outcome of an unprecedented range of experiments with the same set of model parameters, including details of the size of receptive and projective fields. We expect this mathematical framework to be a useful tool for the analysis of developmental processes in general. <br>     

Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB

In the Escherichia coli system catalysing oxidative protein folding, disulphide bonds are generated by the cooperation of DsbB and ubiquinone and transferred to substrate proteins through DsbA. The structures solved so far for different forms of DsbB lack the Cys104–Cys130 initial‐state disulphide that is directly donated to DsbA. Here, we report the 3.4 Å crystal structure of a DsbB–Fab complex, in which DsbB has this principal disulphide. Its comparison with the updated structure of the DsbB–DsbA complex as well as with the recently reported NMR structure of a DsbB variant having the rearranged Cys41–Cys130 disulphide illuminated conformational transitions of DsbB induced by the binding and release of DsbA. Mutational studies revealed that the membrane‐parallel short α‐helix of DsbB has a key function in physiological electron flow, presumably by controlling the positioning of the Cys130‐containing loop. These findings demonstrate that DsbB has developed the elaborate conformational dynamism to oxidize DsbA for continuous protein disulphide bond formation in the cell.     

A simple model can unify a broad range of phenomena in retinotectal map development

A paradigm model system for studying the development of patterned connections in the nervous system is the topographic map formed by retinal axons in the optic tectum/superior colliculus. Starting in the 1970s, a series of computational models have been proposed to explain map development in both normal conditions, and perturbed conditions where the retina and/or tectum/superior colliculus are altered. This stands in contrast to more recent models that have often been simpler than older ones, and tend to address more limited data sets, but include more recent genetic manipulations. The original exploration of many of the early models was one-dimensional and limited by the computational resources of the time. This leaves open the ability of these early models to explain both map development in two dimensions, and the genetic manipulation data that have only appeared more recently. In this article, we show that a two-dimensional and updated version of the XBAM model (eXtended Branch Arrow Model), first proposed in 1982, reproduces a range of surgical map manipulations not yet demonstrated by more modern models. A systematic exploration of the parameter space of this model in two dimensions also reveals richer behavior than that apparent from the original one-dimensional versions. Furthermore, we show that including a specific type of axon?Caxon interaction can account for the map collapse recently observed when particular receptor levels are genetically manipulated in a subset of retinal ganglion cells. Together these results demonstrate that balancing multiple influences on map development seems to be necessary to explain many biological phenomena in retinotectal map formation, and suggest important constraints on the underlying biological variables.     

Alteration of the retinotectal projection map by the graft of mesencephalic floor plate or sonic hedgehog

The floor plate plays crucial roles in the specification and differentiation of neurons along the dorsal-ventral (DV) axis of the neural tube. The transplantation of the mesecephalic floor plate (mfp) into the dorsal mesencephalon in chick embryos alters the fate of the mesencephalon adjacent to the transplant from the tectum to the tegmentum, a ventral tissue of the mesencephalon. In this study, to test whether the mfp is involved in the specification of the DV polarity of the tectum and affects the projection patterns of retinal fibers to the tectum along the DV axis, we transplanted quail mfp into the dorsal mesencephalon of chick embryos, and analyzed projection patterns of dorsal and ventral retinal fibers to the tectum. In the embryos with the mfp graft, dorsal retinal fibers grew into the dorsal part of the tectum which is the original target for ventral but not dorsal retinal fibers and formed tight focuses there. In contrast, ventral retinal fibers did not terminate at any part of the tectum. Transplantation of Sonic hedgehog (Shh)-secreting quail fibroblasts into the dorsal mesencephalon also induced the ectopic tegmentum and altered the retinotectal projection along the DV axis, as the mfp graft did. These results suggest that some factors from the mesencephalic floor plate or the tegmentum, or Shh itself, play a crucial role in the establishment of the DV polarity of the tectum and the retinotectal projection map along the DV axis.     

Structure of a marine bacteriophage as revealed by the negative-staining technique

Valentine, Artrice F. (Georgetown University, Washington, D.C.), Peter K. Chen, Rita R. Colwell, and George B. Chapman. Structure of a marine bacteriophage as revealed by the negative-staining technique. J. Bacteriol. 91:819-822. 1966.-The morphology of a marine bacteriophage has been determined by negative-staining techniques and electron microscopy. The virus possesses a head, 600 A in diameter, and a tail which may be from 860 to 1,000 A in lenght. No tail sheath is seen. The appearance of the terminal tail structure is discussed.     

Genome structure in soybean revealed by a genomewide genetic map constructed from a single population

A complete genetic linkage map of the soybean, in which sequence-based (SB) genetic markers are evenly distributed genomewide, was constructed from an F(12) population composed of 113 recombinant inbred lines derived from an interspecific cross involving Korean genotypes Hwangkeum and IT182932. Several approaches were employed for the development of 112 novel SB markers targeting both the gaps and the ends of the linkage groups (LGs). The resultant map harbored 20 well-resolved LGs presumed to correspond to the 20 pairs of soybean chromosomes. The map allowed us to identify the important chromosomal structures that were not observed in the integrated genetic maps, to identify the new potentially gene-rich regions, to detect segregation distortion regions within the whole genome, and to extend the ends of the LGs. The results will facilitate the further discovery of agronomically relevant genetic loci in the heretofore neglected chromosomal regions and should also provide some important links between the soybean genetic, physical, and genome sequence maps in the regions.     

The association of medial collagenous tissue with atheroma formation in the aging human aorta as revealed by a special technique

A new technique which brilliantly colors collagen fibers in a field of polarized light reveals that during mid-life the smooth muscle cells in the tunica media of the human aorta begin to disappear. The connective tissue is divided between two regions; one below the subintimal layer and the other under the adventitia. Fine collagen fibers extend upward from the former into the subintima and beyond into the intima and the overlying atheromatous plaques of the aging aorta. Thus, the source of fibrous thickening of the vessel is not confined solely to the intimal layer; at least, a portion of the total collagen content arises deep within the aortic wall.     

On some aspects of photosynthesis revealed by photoacoustic studies: a critical evaluation

Photoacoustic techniques have been widely developed in photosynthesis research since the 1970s. We can divide the progress in this field into three periods. In the first period, a pioneer, William W. Parson (and his co-workers) discovered that the photochemical charge separation is accompanied by a conformation change. In the second period, the technique was essentially used to measure the two components of photochemical activity detected in the gas phase: energy storage (photothermal effect) and gas exchange (photobaric effect). In the third period, the time resolution and sensitivity of detection in liquid phase were significantly improved. In reviewing this last period, we shall focus on three aspects: conformation changes, thermodynamic parameters, and quantum yield spectra. This revised version was published online in August 2006 with corrections to the Cover Date.     

Dynamic evolution of clonal epialleles revealed by methclone

We describe methclone, a novel method to identify epigenetic loci that harbor large changes in the clonality of their epialleles (epigenetic alleles). Methclone efficiently analyzes genome-wide DNA methylation sequencing data. We quantify the changes using a composition entropy difference calculation and also introduce a new measure of global clonality shift, loci with epiallele shift per million loci covered, which enables comparisons between different samples to gauge overall epiallelic dynamics. Finally, we demonstrate the utility of methclone in capturing functional epiallele shifts in leukemia patients from diagnosis to relapse. Methclone is open-source and freely available at https://code.google.com/p/methclone.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0472-5) contains supplementary material, which is available to authorized users.     

Dynamic behavior of FCHO1 revealed by live-cell imaging microscopy: its possible involvement in clathrin-coated vesicle formation

The intracellular behavior of human FCHO1 protein was investigated by live-cell imaging microscopy. The fluorescence intensity of green fluorescent protein (GFP)-FCHO1 fluctuated periodically in a perinuclear region approximately every 100 s, reminding us of the periodic fluctuations of clathrin reported in our recent work. The periodicity of FCHO1 was temporally correlated with that of clathrin, suggesting that FCHO1 is involved in clathrin-coated vesicle formation.