bokchoy100Engineering of plant systems

The University of Cambridge has a long history as a centre for study of the natural history and function of plant systems. New initiatives continue to promote these activities in Cambridge. Interdisciplinary approaches to understanding the genetic and biophysical basis of morphogenesis are providing opportunities for rational design and engineering of new plant forms. The pages in this section provide links to recent research and web-based resources.

News: Plants

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AgarTrap: a Simplified Agrobacterium-Mediated Transformation Method for Sporelings of the Liverwort Marchantia polymorpha L.

AgarTrap: a Simplified Agrobacterium-Mediated Transformation Method for Sporelings of the Liverwort Marchantia polymorpha L. Plant Cell Physiol. 2013 Nov 19; Authors: Tsuboyama S, Kodama Y Abstract The liverwort Marchantia polymorpha L. is being developed as an emerging model plant, and several transformation techniques were recently reported. Examples are biolistic- and Agrobacterium-mediated transformation methods. Here, we report a simplified method for Agrobacterium-mediated transformation of sporelings, and it is termed Agar-utilized Transformation with Pouring Solutions (AgarTrap). The procedure of the AgarTrap was carried out by simply exchanging appropriate solutions in a Petri dish, and completed within a week, successfully yielding enough number of independent transformants...

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Peculiar Evolutionary History of miR390-Guided TAS3-Like Genes in Land Plants.

Peculiar Evolutionary History of miR390-Guided TAS3-Like Genes in Land Plants. ScientificWorldJournal. 2013;2013:924153 Authors: Krasnikova MS, Goryunov DV, Troitsky AV, Solovyev AG, Ozerova LV, Morozov SY Abstract PCR-based approach was used as a phylogenetic profiling tool to probe genomic DNA samples from representatives of evolutionary distant moss taxa, namely, classes Bryopsida, Tetraphidopsida, Polytrichopsida, Andreaeopsida, and Sphagnopsida. We found relatives of all Physcomitrella patens miR390 and TAS3-like loci in these plant taxa excluding Sphagnopsida. Importantly, cloning and sequencing of Marchantia polymorpha genomic DNA showed miR390 and TAS3-like sequences which were also found among genomic reads of M. polymorpha at NCBI database. Our data suggest that...

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Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha.

Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha. BMC Genomics. 2013 Dec 23;14(1):915 Authors: Sharma N, Bhalla PL, Singh MB Abstract BACKGROUND: Transcription factors (TFs) are vital elements that regulate transcription and the spatio-temporal expression of genes, thereby ensuring the accurate development and functioning of an organism. The identification of TF-encoding genes in a liverwort, Marchantia polymorpha, offers insights into TF organization in the members of the most basal lineages of land plants (embryophytes). Therefore, a comparison of Marchantia TF genes with other land plants (monocots, dicots, bryophytes) and algae (chlorophytes, rhodophytes) provides the most comprehensive view...

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CRISPR/Cas9 Mediated Targeted Mutagenesis in the Liverwort Marchantia polymorpha L.

CRISPR/Cas9 Mediated Targeted Mutagenesis in the Liverwort Marchantia polymorpha L. Plant Cell Physiol. 2014 Jan 18; Authors: Sugano SS, Shirakawa M, Takagi J, Matsuda Y, Shimada T, Hara-Nishimura I, Kohchi T Abstract Targeted genome modification technologies are key tools for functional genomics. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease Cas9 system (CRISPR/Cas9) is an emerging technology for targeted genome modification. The CRISPR/Cas9 system consists of a short guide RNA (gRNA) that specifies the target genome sequence and the Cas9 protein, which has endonuclease activity. The CRISPR/Cas9 system has been applied to model animals and flowering plants, including rice, sorghum, wheat, tobacco...

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A new subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants.

A new subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants. Plant Physiol. 2014 Feb 11; Authors: Gruhn N, Halawa M, Snel B, Seidl MF, Heyl A Abstract The two-component signaling system (TCS) - the major signaling pathway of bacteria - is found among higher eukaryotes only in plants where it regulates diverse processes such as the signaling of the phytohormone cytokinin. Cytokinin is perceived by a hybrid-histidine kinase receptor and the signal is transduced by a multi-step phospho-relay system of histidine phosphotransfer proteins (HPT) and different classes of response regulators (RR)...

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A red light-controlled synthetic gene expression switch for plant systems.

A red light-controlled synthetic gene expression switch for plant systems. Mol Biosyst. 2014 Jan 27; Authors: Müller K, Siegel D, Rodriguez Jahnke F, Gerrer K, Wend S, Decker EL, Reski R, Weber W, Zurbriggen MD Abstract On command control of gene expression in time and space is required for the comprehensive analysis of key plant cellular processes. Even though some chemical inducible systems showing satisfactory induction features have been developed, they are inherently limited in terms of spatiotemporal resolution and may be associated with toxic effects. We describe here the first synthetic light-inducible system for the targeted control of gene expression in plants...

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Emerging tools for synthetic biology in plants.

Emerging tools for synthetic biology in plants. Plant J. 2014 Feb 5; Authors: Small I, Puchta H Abstract Synthetic biology is generally held to be the rational design of biological components to achieve a desired purpose. It attempts to replace the inherent messiness of biology with the ordered precision and predictability of engineering. It's a tall task, and requires an intimate understanding of the biological process that is to be engineered. Not surprisingly, much of the initial work has been done in bacteria where such detailed understanding is a little easier to obtain. Complex multicellular organisms such as plants pose additional problems, but...

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Opportunities in plant synthetic biology.

Opportunities in plant synthetic biology. J Exp Bot. 2014 Feb 6; Authors: Cook C, Martin L, Bastow R Abstract Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the...

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The Biomimicry Manual: What Can Leaf-Cutter Ants Teach Us About Farming?

The Biomimicry Manual: What Can Leaf-Cutter Ants Teach Us About Farming?

About twelve thousand years ago, humans hit on a bright idea. Why not grow food in our backyards instead of having to go look for it every time our tummies grumble? It was a masterful stroke of conscious evolution, but hardly a new one. Leaf-cutter ants tapped into sustainable agriculture some 50 million years before us. These busy little beasts spend their days harvesting leaves and trucking them, one-by-one, down, in the ground, to get out, of the rain. Boom boom. But instead of eating the leaves, leaf-cutters masticate them into a thick fluffy paste, spit it into their special...

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The World’s Diet has Changed to Rely on Just a Few Standard Crops

The World’s Diet has Changed to Rely on Just a Few Standard Crops

Researchers from the International Center of Tropical Agriculture have noticed that the global diet over the past 50 years has come to rely on a few main food types. The crops that have become popular over the last half a century include wheat, rice, maize, and potato. This means is that certain traditional African and Asian crops like sorghum, millet, rye, sweet potato, cassava, and yam have fallen by the wayside. Read the rest of The World’s Diet has Changed to Rely on Just a Few Standard Crops

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Grow Up! How to Design Vertical Gardens for Tiny Spaces

Grow Up! How to Design Vertical Gardens for Tiny Spaces

If you’re one of the many people in the northern hemisphere who are counting down the days ’til springtime, chances are you may have also been daydreaming about gardening as well. March isn’t just one of the coldest months of the year—it’s also the month in which seed catalogs are sent out to green-thumbed folks everywhere, so plans can be made and plots can be mapped out in preparation for the luscious growing season ahead. If you happen to be lacking in yard space, there’s no need to feel left out! There are some brilliant ways to take full advantage...

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The Plant Organelles Database 3 (PODB3): Integrating Electron Micrographs and New Options for Plant Organelle Research.

Authors: Mano, S. - Nakamura, T. - Kondo, M. - Miwa, T. - Nishikawa, S. I. - Mimura, T. - Nagatani, A. - Nishimura, M.Journal: Plant Cell PhysiolThe Plant Organelles Database 2 (PODB2), which was first launched in 2006 as PODB, provides static image and movie data of plant organelles, protocols for plant organelle research and external links to relevant websites. PODB2 has facilitated plant organellar research and the understanding of plant organelle dynamics. To provide comprehensive information on plant organelles in more detail, PODB2 was updated to PODB3 (http://podb.nibb.ac.jp/Organellome/). PODB3 contains two additional components: the electron micrograph database and...

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Towards revealing the functions of all genes in plants.

Authors: Rhee, S. Y. - Mutwil, M.Journal: Trends Plant SciThe great recent progress made in identifying the molecular parts lists of organisms revealed the paucity of our understanding of what most of the parts do. In this review, we introduce computational and statistical approaches and omics data used for inferring gene function in plants, with an emphasis on network-based inference. We also discuss caveats associated with network-based function predictions such as performance assessment, annotation propagation, the guilt-by-association concept, and the meaning of hubs. Finally, we note the current limitations and possible future directions such as the need for gold standard...

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Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication.

Authors: Duhamel, M. - Vandenkoornhuyse, P.Journal: Trends Plant SciFood demand will increase concomitantly with human population. Food production therefore needs to be high enough and, at the same time, minimize damage to the environment. This equation cannot be solved with current strategies. Based on recent findings, new trajectories for agriculture and plant breeding which take into account the belowground compartment and evolution of mutualistic strategy, are proposed in this opinion article. In this context, we argue that plant breeders have the opportunity to make use of native arbuscular mycorrhizal (AM) symbiosis in an innovative ecologically intensive agriculture.Sustainable agriculture: possible trajectories...

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Gramene 2013: comparative plant genomics resources.

Authors: Monaco, M. K. - Stein, J. - Naithani, S. - Wei, S. - Dharmawardhana, P. - Kumari, S. - Amarasinghe, V. - Youens-Clark, K. - Thomason, J. - Preece, J. - Pasternak, S. - Olson, A. - Jiao, Y. - Lu, Z. - Bolser, D. - Kerhornou, A. - Staines, D. - Walts, B. - Wu, G. - D'Eustachio, P. - Haw, R. - Croft, D. - Kersey, P. J. - Stein, L. - Jaiswal, P. - Ware, D.Journal: Nucleic Acids ResGramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently...

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The Tree That Enslaves Ants

The Tree That Enslaves Ants

The Central American acacia tree and the ant Pseudomyrmex ferrugineus live in a symbiotic relationship. The tree provides sweet nectar for the ants, and the ants protect the tree from weeds and animals. But we now know that the relationship is rather one-sided, as the tree not only causes the ants to become addicted to its nectar, but also damages the ants to make them unable to digest any other food! Martin Heil of Cinvestav Unidad Irapuato in Mexico studied the ants, and found that they are born with the ability to digest a variety of sugars, but then lose...

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Fully automated watering robot takes a big leap forward toward greenhouse automation

Fully automated watering robot takes a big leap forward toward greenhouse automation

Greenhouse owners might find [David Dorhout]’s latest invention a groundbreaking green revolution! [David]’s Aquarius robot automates the laborious process of precision watering 90,000 square feet of potted plants. Imagine a recliner sized Roomba with a 30 gallon water tank autonomously roaming around your greenhouse performing 24x7 watering chores with absolute perfection. The Aquarius robot can do it all with three easy setups; add lines up and down the aisles on the floor for the robot to follow, set its dial to the size of your pots and maybe add a few soil moisture sensors if you want the perfect amount...

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A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology.

Front Plant Sci. 2013;4:339 Authors: Emami S, Yee MC, Dinneny JR Abstract Tools that allow for rapid, accurate and inexpensive assembly of multi-component combinatorial libraries of DNA for transformation into plants will accelerate the progress of synthetic biology research. Recent innovations in molecular cloning methods has vastly expanded the repertoire with which plant biologists can engineer a transgene. Here we describe a new set of binary vectors for use in Agrobacterium-mediated plant transformation that utilizes the Golden-Gate Cloning approach. Our optimized protocol facilitates the rapid and inexpensive generation of multi-component transgenes for later introduction into plants. PMID: 24032037 [PubMed] A robust family of...

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Accelerating plant breeding.

Authors: De La Fuente, G. N. - Frei, U. K. - Lubberstedt, T.Journal: Trends Plant SciThe growing demand for food with limited arable land available necessitates that the yield of major food crops continues to increase over time. Advances in marker technology, predictive statistics, and breeding methodology have allowed for continued increases in crop performance through genetic improvement. However, one major bottleneck is the generation time of plants, which is biologically limited and has not been improved since the introduction of doubled haploid technology. In this opinion article, we propose to implement in vitro nurseries, which could substantially shorten generation...

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Violet/Blue Chrysanthemums--Metabolic Engineering of the Anthocyanin Biosynthetic Pathway Results in Novel Petal Colors.

Authors: Brugliera, F. - Tao, G. Q. - Tems, U. - Kalc, G. - Mouradova, E. - Price, K. - Stevenson, K. - Nakamura, N. - Stacey, I. - Katsumoto, Y. - Tanaka, Y. - Mason, J. G.Journal: Plant Cell PhysiolChrysanthemums (Chrysanthemumxmorifolium Ramat.) are an important cut-flower and potted plant crop in the horticultural industry world wide. Chrysanthemums express the flavonoid 3'-hydroxylase (F3'H) gene and thus accumulate anthocyanins derived from cyanidin in their inflorescences which appear pink/red. Delphinidin-based anthocyanins are lacking due to the deficiency of a flavonoid 3', 5'-hydroxylase (F3'5'H), and so violet/blue chrysanthemum flower colors are not found...

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How To Turn Your Camera Into A Photosynthesis Detector

How To Turn Your Camera Into A Photosynthesis Detector

Veggie Vision Note: Not all camera models are easy to hack, so attempt only with those you're willing to ruin. Courtesy Chris Fastie/public Lab Members of Public Lab, an online civic science community, wanted to build an inexpensive tool to measure plant health. Their solution: convert an obsolete camera into a photosynthesis detector, called the Infragram. During photosynthesis, leaves soak up blue and red light but reflect invisible near-infrared light. The Infragram blocks red light and—because it's missing a thin glass filter common to digital cameras—can detect near-infrared light. This way, the camera sees only blue, green, and near-infrared, and Infragram.org can convert the...

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PRDA1, a novel chloroplast-nucleoid protein, is required for early chloroplast development and is involved in the regulation of plastid gene expression in Arabidopsis.

Authors: Qiao, J. - Li, J. - Chu, W. - Luo, M.Journal: Plant Cell PhysiolChloroplast development requires accurate spatiotemporal expression of plastid genes. The regulation of plastid genes mediated by plastid-encoded RNA polymerase (PEP) is rather complex, and its related mechanism remains largely unclear. Here, we report the identification of a novel protein that is essential for plant development, PEP-Related Development Arrested 1 (PRDA1). Knock-out of PRDA1in Arabidopsis (prda1 mutant) caused a seedling-lethal, albino phenotype and arrested the development of leaf chloroplasts. Localization analysis showed that PRDA1 was specifically targeted to chloroplasts and co-localized with chloroplast nucleoids, revealing that PRDA1...

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The planTree Hydroponic Cultivator Helps Households Grow Organic Food Indoors

The planTree Hydroponic Cultivator Helps Households Grow Organic Food Indoors

Designed by Nur Yıldırım for the kitchens of  the future, planTree is a hydroponic based system that allows homes to grow organic food from seed. The system uses automatic water and nutrition circulation to reduce the need for maintenance and plant care, and vertically combined modules provide space efficiency and flexibility. A simple interface also lets users set up values such as pH, moisture and light for optimum growing. By allowing people to grow the vegetables and greens at home, planTree promotes a greener lifestyle while contributing to the health of living spaces. planTree was honored in International Design Awards 2011 with...

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Synthetic biology in plastids.

Plant J. 2013 Oct 21; Authors: Scharff LB, Bock R Abstract Plastids (chloroplasts) harbor a small gene-dense genome that is amenable to genetic manipulation by transformation. During one billion years of evolution from the cyanobacterial endosymbiont to present-day chloroplasts, the plastid genome has undergone a dramatic size reduction, mainly due to gene losses and the large-scale transfer of genes to the nuclear genome. Thus, the plastid genome can be regarded as a naturally evolved miniature genome whose gradual size reduction and compaction provide a blueprint for the design of minimum genomes. Furthermore, due to the largely prokaryotic genome structure and gene expression...

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Chloroplast phosphoglycerate kinase is involved in the targeting of Bamboo mosaic virus to chloroplasts in Nicotiana benthamiana plants.

Authors: Cheng, S. F. - Huang, Y. P. - Chen, L. H. - Hsu, Y. H. - Tsai, C. H.Journal: Plant PhysiolThe Bamboo mosaic virus (BaMV) is a positive-sense single-stranded RNA virus. Previously, we identified that the chloroplast phosphoglycerate kinase (chl-PGK) from Nicotiana benthamiana is one of the viral RNA binding proteins involved in the BaMV infection cycle. Because chl-PGK is transported to the chloroplast, we hypothesized that chl-PGK might be involved in viral RNA localization in the chloroplasts. To test this hypothesis, we constructed 2 GFP-fused mislocalized PGK mutants, the transit peptide deletion mutant (NOTP-PGK-GFP) and the nucleus location...

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www.synbio.org.uk

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www.marchantia.org

Online resources, including bibliography, weblinks and posters, for work with the simple plant system, Marchantia polymorpha.