...Plant synthetic biology is a burgeoning field that is attracting attention from both the synthetic biology and plant science communities (Osbourn et al., 2012; Cook et al., 2014), as illustrated by the recent funding of OpenPlant by the UK government through the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC), to develop foundational technologies for plant synthetic biology. The development of this new field is in part due to rapid technological advances allowing quick, easy and efficient manipulation of genomic and transgenic plant DNA, and therefore the summer school mainly focussed on these cutting-edge tools and applications, with the aim of encouraging their use by up-and-coming researchers.
The 20 summer school participants had a variety of research backgrounds and levels of experience, from theorists and computer scientists to molecular, plant and synthetic biologists, and from new PhD students to postdoctoral researchers. Some of the participants had no previous plant science knowledge, so the major challenge was to devise a programme that would be engaging and instructive. As a result, participants were trained through a diverse course of lectures, practical sessions and group projects, covering a wide range of theoretical, technical and ethical content in this expanding discipline. Lectures: cutting-edge training from world-leading experts
The lecture programme was designed to teach the participants about synthetic biology concepts and new technologies both in theory and application, as well as introducing them to several model plant systems. In addition, technical talks provided practical details including plant transformation, bioinformatics and metabolite analysis. Discussion was encouraged following the talks, with participants taking the opportunity to meet and question world-leading experts.
Claes Gustafsson, from the San Francisco-based DNA synthesis company DNA2.0, set the scene by introducing the theory behind the application of engineering values to synthetic biology, including the experimental cycle of designing, building, testing and learning that underpins effective synthetic biology research. Consistent with recent developments in plant synthetic biology, DNA assembly and genome engineering techniques were at the forefront of the more technical talks, and, importantly, illustrated with recent applications. Golden Gate cloning, a newly developed technique for assembling multigene DNA constructs in a modular fashion, was highlighted by several speakers, including Aymeric Leveau (Osbourn Laboratory, John Innes Centre, UK), who discussed its use in his work in metabolic engineering of wheat, whilst Samantha Fox (Coen laboratory, John Innes Centre, UK) explained how she had used Golden Gate cloning to develop a modular Cre-Lox system for inducible expression of a gene of interest in Arabidopsis thaliana. The talks were compiled to introduce the participants to cutting-edge methodologies driving the development of the plant synthetic biology field – notably, Diego Orzaez (Technical University of Valencia, Spain) outlined the GoldenBraid cloning system he has developed, based on Golden Gate, for iterative modular DNA assembly for plant biotechnology applications (Sarrion-Perdigones et al., 2011), and Jim Haseloff (University of Cambridge/OpenPlant, UK) promoted the simple liverwort plant Marchantia polymorpha as a new, tractable model system for plant synthetic biology.
Genome editing in plants was also emphasized in the lectures as an increasingly invaluable and widespread synthetic biology tool, due to its relatively straightforward and efficient application. Sebastian Schornack (University of Cambridge, UK) described how the code for recognition of target DNA by TAL effectors was discovered (Boch et al., 2009) and how TAL effector proteins have been repurposed for genome engineering functions, while the extension of the ubiquitous CRISPR/Cas9 system to plants was outlined in a technical talk from Kate Caves (DNA2.0, USA), and exemplified in work described by Jen Sheen (Havard University, MA, USA) (Li et al., 2013)....
" we developed and implemented a comprehensive molecular toolbox for multifaceted CRISPR/Cas9 applications in plants. This toolbox provides researchers with a protocol and reagents to quickly and efficiently assemble functional CRISPR/Cas9 T-DNA constructs for monocots and dicots using Golden Gate and Gateway cloning methods. It comes with a full suite of capabilities, including multiplexed gene editing and transcriptional activation or repression of plant endogenous genes. We report the functionality and effectiveness of this toolbox in model plants such as tobacco, Arabidopsis and rice, demonstrating its utility for basic and applied plant research."
Here's an interesting OPEN paper in PNAS. The gene was identified by activation tagging, meaning that the mutant overexpresses a normal protein, resulting in big rice grains. The overexpressed gene encodes an uncharacterized membrane-localized protein that affects auxin transport. Lots more work to do, but an interesting and potentially useful phenotype!
Another terrific set of activities from Peggy Lemaux and Barbara Alonso. Free to download. In lesson 2 - make a tasty plant cell using goodies for the different compartments. I love the idea for how to represent the energetic mitochondria!
"Today's forests have been greatly altered by human activity and face increasing threats from drought, insect infestations and fire. A Special Section in Science this week examines forest health from the tropics to the boreal forests of the north."
"Caroline Dean is a plant biologist based at the John Innes Centre in Norwich, UK. She helped to establish Arabidopsis as a model plant organism, and has worked for many years on the epigenetic mechanisms that regulate vernalisation, the process by which plants accelerate their flowering after periods of prolonged cold. We met Caroline at the recent Spring Meeting of the British Society for Developmental Biology. We asked her about her career, her thoughts on the plant field and being awarded this year's FEBS EMBO Women in Science Award."
This article requires a subscription to Cell, but the data show that students who watched a video prior to class and then spent some class time working problems (interspersed with lectures) performed better on tests than students who spent time in a traditional lecture. But we all know that right? Actively engaging students, through problems, discussions etc., is the better use of class time than passively listening to a lecture.
The other interesting finding is that for their pre-class assignment, students who watched a video explaining the material on average did better and were more motivated than those who were provided with a reading assignment. That's the bit I find interesting. The article doesn't elaborate on the content of the videos. If the video used images, diagrams and animations effectively, I can see why they may have had a positive impact. On the other hand, videos used for pre-class assignments are often not well made and don't take advantage of video capabilities (for example, simply are a recorded lecture). Given a choice of a book or a even a poor quality video, my children would chose a video but I would prefer a book, partly because I read faster than most people speak. Maybe it's a generational thing.
Topics include measures of average (mean, median, and mode), variability (range and standard deviation), uncertainty (standard error and 95% confidence interval), Chi-square analysis, student t-test, Hardy-Weinberg equation, frequency calculations, and more.
Mary Williams's insight:
Free download of this very useful primer on using statistics in biology, with examples.
Plants have evolved intracellular immune receptors to detect pathogen proteins known as effectors. How these immune receptors detect effectors remains poorly understood. Here we describe the structural basis for direct recognition of AVR-Pik, an effector from the rice blast pathogen, by the rice intracellular NLR immune receptor Pik. AVR-PikD binds a dimer of the Pikp-1 HMA integrated domain with nanomolar affinity. The crystal structure of the Pikp-HMA/AVR-PikD complex enabled design of mutations to alter protein interaction in yeast and in vitro, and perturb effector-mediated response both in a rice cultivar containing Pikp and upon expression of AVR-PikD and Pikp in the model plant Nicotiana benthamiana. These data reveal the molecular details of a recognition event, mediated by a novel integrated domain in an NLR, which initiates a plant immune response and resistance to rice blast disease. Such studies underpin novel opportunities for engineering disease resistance to plant pathogens in staple food crops.
In our pilot episode, we chat with Professor Ian Godwin from The University of Queensland about genetically modified food crops. Ian believes that GMO foods and organic agriculture are perfectly compatible. He explains that scientists are creating GMO plants to achieve a more sustainable agriculture. The idea is to create plants resistant to pests and diseases, that don’t require the use of chemicals, but provide the same productivity and food quality.
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