Monthly Archives: January 2011

Patterns of resource allocation in a dioecious species

Patterns of resource allocation in a dioecious species
Patterns of resource allocation in a dioecious species

Resource allocation between vegetative and reproductive growth will vary over time, and dioecious species may also adopt different strategies for allocation between male and female plants. Sanchez Vilas and Pannell show that males and females of the annual Mercurialis annua differ in temporal patterns of resource allocation to roots, shoots and reproduction. These differences are likely to be the consequence of the different demands for resources required for producing pollen versus seeds at different times.

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Phylogenetics of Ornithogaloideae

Phylogenetics of Ornithogaloideae
Phylogenetics of Ornithogaloideae

The taxonomy of subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades, with several contradictory taxonomic treatments having been proposed. Martínez-Azorín et al.  present a phylogenetic analysis of Ornithogaloideae based on a combination of plastid and nuclear regions and a detailed morphological study. A new taxonomic arrangement is presented in which 19 clades are recognized as genera, well defined by clear morphology and biogeography. Over 100 new combinations are made and two new names are proposed to accommodate the taxa in the new arrangement.

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Plants That Earn Their Keep

I love the smell of TNT in the morning Could airport security gardens be the wave of the future? (“Please have photo ID and boarding pass ready and walk past the rhododenrons.”) How about a defensive line of bomb-sniffing tulips in Central Park in New York, or at the local shopping mall’s indoor waterfall, or lining the streets of Baghdad? Researchers at Colorado State University said Wednesday that they had created the platform for just such a plant-kingdom early warning system: plants that subtly change color when exposed to minute amounts of TNT in the air. They are redesigned to drain off chlorophyll — the stuff that makes them green — from leaves, blanching to white when bomb materials are detected. - New York Times: Plants That Earn Their Keep

Antunes MS, Morey KJ, Smith JJ, Albrecht KD, Bowen TA, et al. 2011 Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway. PLoS ONE 6(1): e16292. doi:10.1371/journal.pone.0016292
Abstract: Background: There is an unmet need to monitor human and natural environments for substances that are intentionally or unintentionally introduced. A long-sought goal is to adapt plants to sense and respond to specific substances for use as environmental monitors. Computationally re-designed periplasmic binding proteins (PBPs) provide a means to design highly sensitive and specific ligand sensing capabilities in receptors. Input from these proteins can be linked to gene expression through histidine kinase (HK) mediated signaling. Components of HK signaling systems are evolutionarily conserved between bacteria and plants. We previously reported that in response to cytokinin-mediated HK activation in plants, the bacterial response regulator PhoB translocates to the nucleus and activates transcription. Also, we previously described a plant visual response system, the de-greening circuit, a threshold sensitive reporter system that produces a visual response which is remotely detectable and quantifiable.
Methodology/Principal Findings: We describe assembly and function of a complete synthetic signal transduction pathway in plants that links input from computationally re-designed PBPs to a visual response. To sense extracellular ligands, we targeted the computational re-designed PBPs to the apoplast. PBPs bind the ligand and develop affinity for the extracellular domain of a chemotactic protein, Trg. We experimentally developed Trg fusions proteins, which bind the ligand-PBP complex, and activate intracellular PhoR, the HK cognate of PhoB. We then adapted Trg-PhoR fusions for function in plants showing that in the presence of an external ligand PhoB translocates to the nucleus and activates transcription. We linked this input to the de-greening circuit creating a detector plant.
Conclusions/Significance: Our system is modular and PBPs can theoretically be designed to bind most small molecules. Hence our system, with improvements, may allow plants to serve as a simple and inexpensive means to monitor human surroundings for substances such as pollutants, explosives, or chemical agents.

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Oxidative stress responses in two lichen phycobionts

Oxidative stress responses in two lichen phycobionts
Oxidative stress responses in two lichen phycobionts

The epiphytic lichen Ramalina farinacea contains two genetically distinct Trebouxia phycobionts. Del Hoyo et al.  analyse the effects of oxidative stress on the photosynthetic behaviour in each isolated alga and observe a better physiological response to stress in one of them, which may reflect its greater capacity to increase non-photochemical quenching and antioxidant protection, and to induce repair mechanisms. The relative abundance of each phycobiont may vary among different populations of R farinacea depending upon environmental conditions.

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Sunflower nitrogen-stress response and gene expression

Sunflower nitrogen-stress response and gene expression
Sunflower nitrogen-stress response and gene expression

The hybrid sunflower Helianthus anomalus is endemic to desert sand dunes, which have lower nutrient availability than the habitats of its parental species. Brouillette and Donovan use a cDNA microarray to compare the gene expression of H. anomalus to that of its parents under contrasting nutrient treatments, and identify five candidate genes for its ecological speciation. One of the genes may play a role in nutrient use by affecting leaf lifespan.

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An orchid that persuades wasps to date outside their species

Margaret Moran at My Growing Passion has put up a photo of Cryptostylis subulata the Large Tongue Orchid that she has growing in her garden. Her post includes an explanation of how it reproduces. It relies on wasps to pollinate the flower, so to pull in the wasp close enough it mimics a female wasp. The details are at her site.

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The Scientist Gardener on Innovation versus Investment

There’s a good post by the Scientist Gardener on Investing in Innovation. It’s a response to James (who has Giant Corn) who commented on Research Funding in a post that I would have linked to at the time if I’d been up to speed after Christmas.

He makes the point that it’s not enough to have a good idea. I think a lot of the push for relevance or real-world results ignores that the Investment, Development and Marketing of new products all require non-trivial skills. Simply asking university departments to monetise their research takes funding away from what they’re (hopefully) good at – having ideas – and funnels it into what they’re not so good at.

It reminds me of the quote from John W. Gardner:

The society which scorns excellence in plumbing as a humble activity and tolerates shoddiness in philosophy because it is an exalted activity will have neither good plumbing nor good philosophy: neither its pipes nor its theories will hold water.

Could you say something similar about the society that scorns pure research, but exalts shoddy business?

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Is the earliest wine getting earlier and earlier?

There’s been a rash of stories about how new grape varieties will be needed to fight disease if wineries are to keep flowing. As far as I can tell, because I haven’t seen anyone link to the paper, it’s based on Genetic structure and domestication history of the grape and Open Access paper in PNAS (back-up link because the doi isn’t working). Sean Myles argues that there’s plenty of room to develop new varieties of grape by careful cross-breeding.

A surprising result (to me) is that the date for domestication is by 5,000 years ago. Meanwhile in related archaeological research, the earliest evidence of wine-making equipment has been found in Areni, Armenia dating from around 4100 BC. The two don’t necessarily contradict each other. For a start the Armenian winery could have been using grapes that were abandoned for superior varieties, but I don’t know how accurate the dating is on either side as I haven’t had chance to read the papers properly. If it’s the latest common ancestor then that’s close to a match.

Myles places the earliest domestication as a region of the South Caucasus between the Caspian and Black Seas. Here’s a map with the Areni winery marked.

View Areni and Grapes in a larger map

h/t BBC News.

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Drowning in the data or the calm before the genome sequence storm? #PAG

High Throughput DNA Sequencing at PAG

High Throughput DNA Sequencing at PAG

My abiding memory of the Plant and Animal Genome (#PAG) conference this year will be not so much the talks, the many individual discussions I have had, nor the quantities of great food in southern California. It will be the huddles of people in corners earnestly discussing what to do with gigabases of short DNA sequence reads from their organism of choice. Perhaps reflecting this sequence deluge, I’m finding it unusually hard to note an ‘action’ from many talks. A surprising number stick rather rigidly to their published positions, or as Julian Catchen tweeted, “PIs cut and paste their grant reports into a PowerPoint talk, drone on like it’s a department meeting.” Despite being hugely connected and computer-literate, with a third of the audiences being on-line, the Twitter feed (#PAG) from nearly 3000 people is minimal, with few nuggets coming across.

Looking back at previous PAGs, integrating principles across all of plant biology have emerged, each conference with a big idea which has changed my research or thinking. This is the 19th annual meeting, and over the years we have seen the similarity of genes over huge phylogenetic distances; functional genomics identify the purpose of nearly every gene; new marker systems giving insight into crop diversity and their wild relatives; the ubiquity of whole genome duplication or polyploidy events providing the basis for the evolution of plants; micro and small RNAs being critical controls; the utility of genetic maps in understanding diversity; the universal genome browsers, databases and web tools to extract information. After the Science and Nature papers are out, the ideas impact a substantial majority of the papers we publish in Annals of Botany, and I hope we will publish papers from several of the presentations made here. But unlike the previous meetings, this week, I’m finding it hard to see what NEW areas we will be publishing from results being presented. Indeed, sitting at the back, I find myself mentally composing ‘return-without-review’ letters: largely in line with expectation from other species … acknowledge the huge amount of work/data but can’t see new principles … essential that the work addresses important questions … I come to conferences to hear about work in progress or incomplete, so this is something I hope to see in a presentation, but I rather suspect this criticism will remain in some papers where the hard work has not been completed.

Of course, one also (primarily?) comes to a conference for the individual discussions, and these have been as exciting as ever, with plenty of new ideas discussed, thoughts of collaboration, and updates on what people are doing. With the bigger picture of sequence data, I hope we are seeing a pause before the real biology emerges from genome-wide sequencing – or even better, can someone convince me that still being convalescent from swine flu has turned me into an old cynic and I’m missing the paradigm shift.

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