Summary for non-specialists Archives - Page 4 of 6

Thinking about phytoplankton

by Charis Cook

Categories: Summary for non-specialists

Tags: algae, summary for non-specialists

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Published on: October 16, 2012

H. akashiwo on the right, with predator Favella sp.

I’m aware phytoplankton are not usual subjects for plant science research, but these small algae are quite plant-like, in general – although they don’t have organs to complicate things. Like plants, they photosynthesize and are able to respond to their environment. Importantly, unlike plants, phytoplankton are mobile, hence the name which in Greek means ‘drifting plants’. Being extremely tiny ‘plants’, phytoplankton present an excellent opportunity for plant scientists to consider synthetic biology, which seems more feasible on a cell-scale rather than an entire plant. The super-theme of the FP7 2013 funding call was ‘The Oceans of Tomorrow,’ and while that call closes in a few short months, synthetic biology, water security and bio-sensors are important research themes which are here to stay.

Highlighted article: Elizabeth L. Harvey and Susanne Menden-Deuer (2012) Predator-Induced Fleeing Behaviors in Phytoplankton: A New Mechanism for Harmful Algal Bloom Formation? PLoS ONE 7(9): e46438. doi:10.1371/journal.pone.0046438

This research focuses on toxic phytoplankton Heterosigma akashiwo, a known cause of harmful algal blooms (HABs; for a fairly recent review of HABs and their effects on human health, see Backer and McGillicuddy Jr., 2006). (more…)

Pollen epigenetics

by Charis Cook

Categories: epigenetics, Summary for non-specialists

Tags: Arabidopsis, epigenetics, summary for non-specialists

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Published on: October 11, 2012

Biology learned in school and as a first year undergraduate is easily forgotten if it is not relevant to your current research. Today’s highlighted article required me to refresh my memory of plant germ line development, so I included my basic research here.

Highlighted article: Joseph P. Calarco, Filipe Borges, Mark T.A. Donoghue, Frédéric Van Ex, Pauline E. Jullien, Telma Lopes, Rui Gardner, Frédéric Berger, José A. Feijó, Jörg D. Becker and Robert A. Martienssen (2012) Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA. Cell 151:194-205.

Germline biosynthesis: A pollen mother cell undergoes meiosis to make haploid microspores, which unevenly split into a larger vegetative cell and a small generative cell. The generative cell splits symmetrically into two – these are the plant ‘sperm’ cells. Each pollen grain contains two sperm cells, which are surrounded by a vegetative cell. The vegetative nucleus contains completely decondensed heterochromatin, but DNA in generative nuclei is tightly condensed.

The female gametophyte develops from a megaspore mother cell. Both the megaspore mother cell and pollen mother cell are specified from somatic cells in developing flowers.

GFP staining in the two sperm nuclei and vegetative nucleus in the vegetative cell.

Bisulphite sequencing is a DNA sequencing method which determines methylation pattern by treating DNA with sodium bisulphite before sequencing it using a conventional DNA sequencing method. Bisulphite induces the conversion of unmethylated cytosines to uracil, but this is not a perfect technique so unmethylated DNA may be recorded as methylated. Additionally, bisulphite treatment can cause DNA degradation. Sequencing the DNA of interest multiple times, in the case of Calarco et al., anywhere from 7 to 17 times, improves reliability of the method. There is a brief overview of DNA methylation in this post. (more…)

The cost of glucosinolate biosynthesis

by Charis Cook

Categories: Summary for non-specialists, systems biology, teaching resources

Tags: glucosinolates, New Phytologist, plant defence, systems biology

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Published on: October 2, 2012

Highighted article: Michaël Bekaert, Patrick P. Edger, Corey M. Hudson, J.Chris Pires, Gavin C. Conant (2012) Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis. New Phytologist 196:596–605.

Research published in a current New Phytologist paper uses a systems biology approach to demonstrate the metabolic and evolutionary costs of producing glucosinolates for defence. Bekart et al. used AraGEM (Oliveira Dal’Molin et al., 2010) as a starting point. They collected data on Arabidopsis glucosinolate genes by scouring published papers and downloading their expression patterns from AtGenExpress. This information was integrated into the basic dataset from AraGEM. The complete list of genes involved in glucosinolate reactions, including references, is in Supplementary Table S1 of the paper.

The team performed flux balance analysis on the integrated database to estimate metabolic and energy flux through reactions in the system both with glucosinolate biosynthesis activity and with none. They found that glucosinolate biosynthesis affected flux incidentally through 241 reactions in addition to the 196 reactions which are only active when glucosinolates are being produced.

The main finding of the research is the heavy cost of glucosinolate biosynthesis. Sulphur import dramatically increased when glucosinolates were being synthesised, and demand for water, carbon dioxide, ammonia, and photons increased too. Despite the increase in substrate import, biomass synthesis fell by around 15% during glucosinolate production. This cost is reflected in other studies demonstrating that the evolutionary competitive edge glucosinolates give to plants is a disadvantage when there are no predators around (Mauricio, 1997), and reduces the number of seeds and flowers produced per plant compared to non-producers (Stowe and Marquis, 2011). (more…)

Working with Natural Antisense Transcripts

by Charis Cook

Categories: methods, resource, Summary for non-specialists, systems biology

Tags: methods, resource

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Published on: September 27, 2012

In January of this year Nucleic Acids Research published a paper describing a database of plant natural antisense transcripts (NATs), PlantNATsDB (Chen, Yuan et al., 2012). It contains around 2 million NATs from 69 plant species, and has a simple viewer showing the two loci involved in each NAT, any overlap, the NAT type, and an option for more detail. It is also possible for search for NATs for specific loci. It is important to note however that the database was last updated a year ago, in September 2011.

This month’s Plant Methods also features a NATs tool, a protocol for NAT identification in plant tissue (Collani and Baraccia, 2012). It is a simple PCR based method, and relies on prior knowledge of the existence of a NAT, as specific primers are needed. Used in association with PlantNATsDB, this is a useful technique. (more…)

Traditional varieties are key to modern rice farming

by Charis Cook

Categories: biofortified foods, Summary for non-specialists, teaching resources

Tags: agriculture, biofortified foods, plant nutrients, rice, summary for non-specialists, teaching resources

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Published on: September 13, 2012

Analysing root growth and yield of rice plants.

Highlighted article: Rico Gamuyao, Joong Hyoun Chin, Juan Pariasca-Tanaka, Paolo Pesaresi, Sheryl Catausan, Cheryl Dalid, Inez Slamet-Loedin, Evelyn Mae Tecson-Mendoza, Matthias Wissuwa & Sigrid Heuer (2012). The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488, 535–539 doi:10.1038/nature11346

Over centuries, many local rice varieties have been bred into a few modern varieties which are extensively farmed throughout much of Asia. In regions where soil is poor such as western India and Thailand, rice crops are dependent on rainfall, frequently suffering from floods and draughts, and importantly also require phosphorus fertilizer. Phosphorus is an essential plant nutrient, and as phosphorus fertilizer is made from a finite store of phosphorus rock the current situation in the parts of Asia with poor soil is not sustainable.

A solution to this problem was found in a traditional rice variety, Kasalath. Another traditional rice variety has already supplied modern rice breeders with submergence tolerant gene SUB1, which enables rice plants to survive up to two weeks of flooding. A decade ago, a major quantitative trait locus was identified in Kasalath that conferred tolerance to phosphorus deficient soil. This locus was labelled Pup1, and last year the Heuer group at the International Rice Research Institute defined a core set of Pup1 markers and used them to backcross Pup1 into modern rice varieties, which were grown in their natural environments and all produced significantly more rice in P-deficient conditions than their wildtype counterpart. These Pup1 introgression lines also showed improved root growth under stress. (more…)

High-throughput, cheap, reliable DNA extraction method

by Charis Cook

Categories: methods, Summary for non-specialists

Tags: DNA extraction, methods

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Published on: September 11, 2012

Highlighted article: Zhanguo Xin and Junping Chen (2012) A high throughput DNA extraction method with high yield and quality. Plant Methods 2012, 8:26 doi:10.1186/1746-4811-8-26

Judging by the fact that it was accessed 1400 times in less than a month, the DNA extraction method described by Xin and Chen in last month’s Plant Methods must be worth a look.

Having had a look, I can tell you it seems to be an invaluable method for cheap, reliable high-throughput DNA extraction. It works on seeds and leaves from a number of plants, and according to the abstract, one person can manage 192 extractions in a working day. Using the price estimation in the paper, this would cost about £13 in total for consumables.

The protocol is clear and easy to follow, setting out exactly what reagents, consumables and equipment you will need so there will be no panicked begging of microtitr plates from a friend halfway through the extraction. As well as standard lab equipment which should be accessible to most researchers, you will need MagAttract Suspension G. MagAttract provides the simple, efficient clean up step, while the rest of the protocol is based on a traditional CTAB extraction method.

Method: New and improved multiplex PCR

by Charis Cook

Categories: methods, Summary for non-specialists

Tags: methods, PCR, Plant Methods, summary for non-specialists

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Published on: August 30, 2012

Highlighted article: Daxing Wen and Chuqing Zhang (2012) Universal Multiplex PCR: a novel method of simultaneous amplification of multiple DNA fragments. Plant Methods 8:32 (Online preview) doi: 10.1186/1746-4811-8-32

Background

Multiplex PCR allows amplification of multiple targets in a single PCR experiment. It is possible to amplify several sections of a single template, or to amplify different templates using a number of primer sets. If there are multiple primers in a reaction, it can be difficult optimise the PCR reaction to maximise the efficiency of every primer, and it is likely that some cross-hybridisation and mis-priming will occur.

Figure 3B from Wen and Zhange (2012). A comparison of multiplex PCR (Lanes 1-4) and universal multiplex PCR (lanes 5-8), using the same primers with universal adaptors. The band intensity from traditional PCR is very variable, but it is consistently strong when the universal adaptors are used.

Image credit: BioMed Central

The Method

Wen and Zhang from Shandong Agricultural University have devised a way around the inconveniences of multiplex PCR to develop a universal multiplex PCR method. ‘Universal adaptors’ are linked to specific primers, making the annealing temperature of the adaptor-primer structures 70°C. (more…)

NGS and root endophyte assembly cues

by Charis Cook

Categories: Summary for non-specialists, teaching resources, Workshops

Tags: endophyte, microbiology, plant-microbe interactions, teaching resources

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Published on: August 24, 2012

Cologne and Sanssouci, close to Golm: what effect do the soils at these two historic locations have on the local plant roots?

Highlighted article: Davide Bulgarelli, Matthias Rott, Klaus Schlaeppi, Emiel Ver Loren van Themaat, Nahal Ahmadinejad, Federica Assenza, Philipp Rauf, Bruno Huettel, Richard Reinhardt, Elmon Schmelzer, Joerg Peplies, Frank Oliver Gloeckner, Rudolf Amann, Thilo Eickhorst, and Paul Schulze-Lefert (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota Nature 488:91

Background

Although plant-microbe and plant-soil dynamics are widely studied areas of plant science, up until now there has been no broad picture of plant endophytic systems: which phyla are common endophytes; how the populations form; and what affects them. Endophytes colonise plant tissues, where unlike pathogens they do not cause harm or an immune response, and unlike endosymbionts they do not live inside plant cells or have an obvious mutually beneficial relationship with the plant. A recent review on bacterial endophytes is this one by Reinhold-Hurek and Hurek (2011).

Here, Bulgarelli et al. use an Arabidopsis system to shed light on the specifics of below ground plant-bacteria interactions, and set out a methodology for future investigations into other plants and soil types. This study and another article in the same issue of Nature by Lundberg et al. use next generation sequencing (NGS) to show similar cues for assembly of root endophytes. (more…)

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