BBF RFC 106: A Standard Type IIS Syntax for Plants

Here we define a standard syntax for assembling standard parts for expression in plant cells, extensible to all other eukaryotes. Variations of the Type IIS mediated cloning method known as Golden Gate Cloning, most notably Golden Braid (GB2.0) and Golden Gate Modular Cloning (MoClo) are in common use, particularly for the assembly of plasmids for delivery to plant cells. Many characterised plant parts compatible with Type IIS mediated assembly are available outside of the Registry of Standard Parts, as well as plasmids with the features necessary for delivery of DNA to plants cells via the shuttle chassis, Agrobacterium tumefaciens. This RFC describes a consensus Type IIS syntax for plant parts to allow assembly into complete eukaryotic transcriptional units in plasmid vectors that contain the necessary features for transfection of plant chassis. We use Marchantia polymorpha, a primitive and easy-to-engineer liverwort and Nicotiana benthamiana a model plant as exemplar chassis

OptiJ: Open-source optical projection tomography of large organ samples

Abstract: The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples

OptiJ: Open-source optical projection tomography of large organ samples

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples

Optimal location for fibular osteotomy to provide maximal compression to the tibia in the management of delayed union and hypertrophic non-union of the tibia.

BACKGROUND: Tibial shaft fractures are the commonest long bone fracture, with early weight-bearing improving the rate of bony union. However, an intact fibula can act as a strut that splints the tibial segments and holds them apart. A fibular osteotomy, in which a 2.5 cm length of fibula is removed, has been used to treat delayed and hypertrophic non-union by increasing axial tibial loading. However, there is no consensus on the optimal site for the partial fibulectomy. METHODS: Nine leg specimens were obtained from formalin-embalmed cadavers. Transverse mid-shaft tibial fractures were created using an oscillating saw. A rig was designed to compress the legs with an adjustable axial load and measure the force within the fracture site in order to ascertain load transmission through the tibia over a range of weights. After 2.5cm-long fibulectomies were performed at one of three levels on each specimen, load transmission through the tibia was re-assessed. A beam structure model of the intact leg was designed to explain the findings. RESULTS: With an intact fibula, mean tibial loading at 34 kg was 15.52 ± 3.26 kg, increasing to 17.42 ± 4.13 kg after fibular osteotomy. This increase was only significant where the osteotomy was performed proximal to or at the level of the tibial fracture. Modelling midshaft tibial loading using the Euler-Bernoulli beam theory showed that 80.5% of the original force was transmitted through the tibia with an intact fibula, rising to 81.1% after a distal fibulectomy, and 100% with a proximal fibulectomy. CONCLUSION: This study describes a novel method of measuring axial tibial forces. We demonstrated that a fibular osteotomy increases axial tibial loading regardless of location, with the greatest increase after proximal fibular osteotomy. A contributing factor for this can be explained by a simple beam model. We therefore recommend a proximal fibular osteotomy when it is performed in the treatment of delayed and non-union of tibial midshaft fractures

OptiJ: Open-source optical projection tomography of large organ samples

Abstract: The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples