Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism.

Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies.

Volume/perfusion ratio from lung SPECT/CT.

AIM: In pulmonary emphysema lung volume reduction procedures (LVRP) can optimize respiratory pump function. Identification of the most affected lobe can be reached using relative lobar volume (relVol) from CT, but this approach disregards the corresponding lobar perfusion. The aim of the study was therefore to establish a new parameter combining relVol from CT and relative perfusion (relPerf) from perfusion SPECT as a single parameter (volume/perfusion ratio (VPR)) to optimize the identification procedure. METHODS: As a proof of principle VPR was calculated from hybrid V-/P-SPECT/CT scans from 20 patients with severe pulmonary emphysema (SPE) before LVRP. Lung V-/P-SPECT/CT (Siemens SymbiaT) was done with Technegas and 99mTc-MAA. Quantification of lobar perfusion from scintigraphy and volume from CT was performed using "HERMES Hybrid 3D - Lung Lobe Quantification". Using normal ranges - from 12 patients with suspected pulmonary embolism and normal lung structure and perfusion - all lobes were classified as normal or abnormal to identify targets for LVRP. RESULTS: Normal values for VPR: right upper lobe 1.09 ± 0.10, middle lobe 1.31 ± 0.31, right lower lobe 0.87 ± 0.08; left upper lobe 1.09 ± 0.11, left lower lobe 0.87 ± 0.12. In the 20 SPE patients there were only 7 lobes with pathological values for rel- Vol, 14 lobes with pathological values for rel- Perf but 31 lobes with pathological VPR. CONCLUSION: Estimation of VPR from lung SPECT/CT enables a combined view of lobar volume and perfusion with one parameter. In SPE patients VPR allows identifying possible target structures with much higher sensitivity than when using relPerf or relVol alone. The specificity and the prognostic value of this new parameter have to be tested in a clinical trial.

Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

Generation of leaf shape through early patterns of growth and tissue polarity.

A major challenge in biology is to understand how buds comprising a few cells can give rise to complex plant and animal appendages like leaves or limbs. We address this problem through a combination of time-lapse imaging, clonal analysis, and computational modeling. We arrive at a model that shows how leaf shape can arise through feedback between early patterns of oriented growth and tissue deformation. Experimental tests through partial leaf ablation support this model and allow reevaluation of previous experimental studies. Our model allows a range of observed leaf shapes to be generated and predicts observed clone patterns in different species. Thus, our experimentally validated model may underlie the development and evolution of diverse organ shapes.

OMERO: flexible, model-driven data management for experimental biology.

Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.

Visualizing plant development and gene expression in three dimensions using optical projection tomography.

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, flowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as beta-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantified and visualized interactively in different ways.