Monthly Archives: August 2011

Barcode Wales

Image: Wikimedia Commons.

Image: Wikimedia Commons.

No, this has nothing to do with whales (they’re fish-like denizens of the deep, and has probably already been done by some countries under the guise of ‘scientific whaling’ anyway…). Nor is it a strange and unusual instruction to implant microchips into the natives of that principality within the Untied Kingdom. It’s not even a move to standardise the strange garb worn by participants at the National Eisteddfod in Wales; anyway, that would be Bard-coding…  And it is definitely not a way of keeping tabs on the founder of Wikipedia (Mr Assange of WikiLeaks probably does that on our behalf already…). Rather, it is the name of the project – led by Natasha de Vere (National Botanic Garden, Wales), along with Tim Rich (National Museum of Wales, Cardiff, Wales) and Mike Wilkinson (Aberystwyth University, Wales), and a host of volunteers – whose aim is to ‘DNA-barcode’ all of Wales’ native flowering plants. After 3 years that goal has now been achieved. Or, in more technical terms, ‘the 1,143 native flowering plants of Wales now have 5,274 DNA barcodes (3,028 for rbcL and 2,246 for MatK)’, making it the first country to have achieved such a feat. DNA barcoding uses a small section of DNA to act as a unique identifier for that species. The first step is to assemble reference barcodes for the plants that need to be identified; unknown DNA sequences can then be compared to these in order to find out what species they’ve come from. Probably the real significance of the technique is ‘forensic’, in that it can identify species from tiny fragments, different life stages, or from mixtures of samples. Species can be identified from pollen grains, fragments of seeds or roots, wood, faecal samples, stomach contents or environmental samples collected from the air, soil or water. Ironically, vital to the establishment of DNA barcodes is correctly identified source material in the first place, which means that every reference barcode must have a voucher specimen to verify its identity. So there will still be a need for proper plant ID skills (until entirely replaced by ‘technology’…). Data from this project are submitted to BOLD (the Barcode of Life Data Systems), ‘an online workbench that aids collection, management, analysis, and use of DNA barcodes’. This feat is no doubt a great coup, but, in the ‘good old days’ (and – perversely – if you’ve forgotten them, then you probably are old enough to remember them!) one went out into the field armed with an ID book and studied the whole plants that were there. Nowadays, it seems that’s not good enough (too ‘old-fashioned’?); instead, you need the services of a well-equipped molecular biology lab! Is this system better? Or just designed by agoraphobic, hay-fever-suffering individuals who would really like to be proper – ‘get-your-hands-dirty-in-the-field’ – botanists but aren’t genetically so disposed? I know it’s difficult to remember all the plants and their diagnostic characters when one gets older, but trying to do an ID from first principles helps to keep those highly prized field skills alive (though, arguably, what’s more ‘first principles’ than DNA..?).

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Chromosomes Today and the icc18 conference in UK

International Chromosome Conference #icc18

International Chromosome Conference #icc18

The International Chromosome Conference, with diverse themes from genomic medicine and plant breeding to systems biology and “chromonomics”, is meeting in Manchester. About 300 people are discussing the wide range of chromosome research, and many papers have been emphasizing new results arising from rapid changes in technology, particularly but not exclusively light microscopy, where the series of conferences have followed the move to fluorescence microscopes, then immunocytochemistry and in situ hybridization, and now the high resolution approaches.

The conference series was started by CD Darlington (subject of my short biography in press in Encyclopaedia of Genetics) back in 1964. The integration of chromosomes with DNA sequence, the importance of RNA in regulation, the roles of proteins, and the functional analyses – always asking why and how and building on detailed data – would certainly have been welcomed by Darlington. Notably, though, some questions have remained constant through the last 20 years. In particular, sessions of the first day about nuclear and chromosomal architecture, DNA replication, and then onto centromeres have been steady stories of progress, while other areas have developed from nothing.

“Chromosomes Today” was the title of a series of books arising from these International Chromosome Conferences, but, as Malcolm Ferguson-Smith pointed out, publication delays invariably meant that the published volume was “Chromosomes Yesterday”; while serving some useful purpose as a repository of failed experiments, I certainly do not mourn the passing of expensive and dated conference proceedings at this or other conferences! But every one of the talks so far, and the posters I have hardly started on studying, show the liveliness of the field of chromosome research today.

I have put together the tweets from the first day in a Storify article -http://storify.com/pathh1/18th-international-chromosome-conference-mancheste . Unfortunately, though, social media activity is very limited here at #icc18, despite the good wi-fi in the Conference Centre (and even the odd power socket in the theatre) – only @dicentric and I seem to be actively tweeting. Maybe people need to think more about dissemination in the 21st century. I certainly don’t have time to scan the 800 Journals which carry research of interest to me, nor (my blog posts notwithstanding) to attend all the conferences I would like to. Twitter and the blogs give me a real insight into what is happening and what is new; I probably get 30% of my new ideas through these routes today. I can do little more than make a longish quotation from Enrica Porcari “‘Do blogs lead to increased dissemination of research papers?’ask WorldBank researchers” : “For years, we have been advocating the use of social media to inform as broad an audience as possible of our research and also to get our research outputs into the hands of people who can make them travel even further across their own communication networks and/or apply them to their own work. Nonetheless, not everyone understands the value of social media… It usually takes time for all great inventions and innovations to become mainstream. Alexander Graham Bell’s telephone took a while to catch on, as did cell phones and email. I wonder how we could possibly cope now without email or mobile communication devices. As such, I believe it will just be a matter of time before everyone realizes that social media has an important role to play in research.”

Meanwhile, I’m trying now to adopt Tim Entwistle’s multitasking – Storify to bring together the #ICC18 posts, twitter and still some e-mail Table of Contents alerts giving me more and interesting papers I should be reading, some of which I re-tweet, others which go on to Scoop.it, and others I write to the authors to try to take follow-up actions. This morning, there is a detailed paper in GRACE, Genetic Resources and Crop Evolution, about compact spike morphology genes – can their homologues be found in the Panicum miliaceumwe are working with, but with a very loose panicle and then I’m also writing the blog, listening to the great EMBO plenary talk by Bill Earnshaw, thinking of consequences for my work, and tweeting the key points under #icc18. Chromosomes and chromosome engineering has a huge future!

Updates 1nd September 2011 – Darlington Link works above.

Days 2 and 3 now on Storify http://storify.com/pathh1/international-chromosome-conference-18-days-2-and-

And links to my own talk at the International Chromosome Conference ICC: links are given from my website http://www.molcyt.com OR directly to the 4Mb download: http://www.le.ac.uk/biology/phh4/public/HeslopHarrison_ICC18.pdf

 

 

 

 

 

 

 

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Functional inbreeding avoidance mechanism in Arabis

Functional inbreeding avoidance mechanism in Arabis

Functional inbreeding avoidance mechanism in Arabis

Variation in mating systems is common across angiosperm taxa, leading to a trade-off between inbreeding avoidance and reproductive assurance. Tedder et al. examine European populations of the alpine perennial, Arabis alpina, which is currently being developed as a model system for studying the ecological genetics of arctic–alpine environments, and show that mating system variation ranges from autonomous self-fertilization to self-incompatibility. Inbreeding avoidance is linked to a sporophytic self-incompatibility system.

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Pollinator and herbivore effects on Erysimum

Pollinator and herbivore effects on Erysimum

Pollinator and herbivore effects on Erysimum

Erysimum capitatum (Brassicaceae) is a widespread and variable plant species with generalized pollination that is attacked by a number of herbivores. Lay et al.  find that individuals of E. capitatum are visited by diverse groups of pollinators and herbivores that shift in abundance and importance in time and space. Developmental mechanisms that allow plants to make iterative decisions about reproductive resource allocation over the course of the flowering season may be under selection in this species.

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dubius research that blows you away

Image: Cpl. James L. Yarboro, US Marine Corps/US Department of Defense.

Image: Cpl. James L. Yarboro, US Marine Corps/US Department of Defense.

Elegant research should always be applauded (or publicised, which is what I’m doing here!). And they don’t come more elegant than David Greene and Mauricio Quesada’s seminal study entitled ‘The differential effect of updrafts, downdrafts and horizontal winds on the seed abscission of Tragopogon dubius’ (Functional Ecology 25: 468–472, 2010). Acknowledging that many plant species enhance wind-dispersal of their seeds (anemochory) by such features as lift-promoting wings and drag-producing fibres, the pair hypothesised that evolution would also increase dispersal capacity through the development of mechanisms that promote abscission by updrafts rather than downdrafts. Using this cosmopolitan weed, they show precisely that: a combination of morphological traits and achene orientation make updrafts much more likely than downdrafts to abscise a seed. That, and the even-more-elegant hairy pappus of the fruits, help the propagules to float away from their parent to start a new life (germination-enabling and seedling-establishment-sufficient conditions permitting!). The duo speculate – sensibly (and as all good papers should!) – that such mechanisms are common and will eventually be seen as a crucial component of long-distance seed movement for almost all wind-dispersed species. Nice work! Other species, however, use more opportunistic agents so sow their seed. For example, Kimberley Taylor and colleagues in a Montana State University Extension publication describe field studies that show the extent to which vehicles collect and disperse seeds, particularly ‘noxious weeds’. Amongst their findings were that more seeds are picked up when vehicles were driven ‘off-trail’ than on-trail, up to 5500 seeds per mile compared to approx. 400, respectively. The study at military sites showed many times more seeds were collected by vehicles driven under wet conditions than under dry conditions, but up to 99 % of seeds stayed attached to a truck after travelling 160 miles under dry conditions. Furthermore, tracked vehicles picked up more seeds than wheeled vehicles. Somewhat predictably (but disappointingly for us autohydrophobes), to help curtail spread of weeds into non-infested areas, they recommend… washing vehicles… frequently(!). Let us hope military vehicles returning from their various, far-flung war zones don’t bring back unwelcome hitch-hikers (of the botanical – or any other – kind!)

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Pollen–pistil interactions in the Asteraceae (Review)

Pollen–pistil interactions in the Asteraceae (Review)

Pollen–pistil interactions in the Asteraceae (Review)

Pollen–pistil interactions are an essential prelude to fertilization in angiosperms, and self-incompatibility (SI) is the best understood of these at a molecular level. Allen et al. review studies in the Asteraceae, and consider that recent cellular and molecular work in Senecio squalidus (Oxford ragwort) have challenged the belief that sporophytic SI and pollen–pistil interactions in Asteraceae and Brassicaceae are similar. The availability of a pool of pistil-specific genes for S. squalidus offers an opportunity to elucidate the molecular mechanisms of pollen–pistil interactions and SI in the Asteraceae.

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TcCRP1 as a pollen-tube attractant in Torenia

TcCRP1 as a pollen-tube attractant in Torenia

TcCRP1 as a pollen-tube attractant in Torenia

A key factor of pollen-tube attraction to an ovule is that it is species-specific, and recently a family of secreted proteins with attractant properties has been discovered in Torenia fournieri. Kanaoka et al. study TcCRP1, an orthologous gene of TfCRP1 from T. concolor, and find it is expressed predominantly in the synergid cell. The gene product attracts pollen tubes of T. concolor in a concentration-dependent manner, but attracts far fewer tubes from pollen of T. fournieri. The results indicate that this class of CRP proteins is a common pollen-tube attractant in Torenia species and that their sequence diversity is important for species-specific pollen-tube attraction.

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Cabomba as a model basal angiosperm (Review)

Cabomba as a model basal angiosperm (Review)

Cabomba as a model basal angiosperm (Review)

Early-diverging angiosperms are important for studies of the origin and early evolution of the flower. Vialette-Guiraud et al. discuss the potential of the water lily Cabomba (Nymphaeales) as a model basal angiosperm, as it combines simplicity of floral structure, numerous pleisiomorphic angiosperm characters, and practical features that make it amenable to study using a broad range of molecular biological techniques. They also provide protocols for the growth and molecular analysis of Cabomba, a Cabomba flower EST database, and a genome size measurement of C. caroliniana.

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Darwin’s doodles digitised

Image: Francis Darwin, The Life and Letters of Charles Darwin (1887).

Image: Francis Darwin, The Life and Letters of Charles Darwin (1887).

Darwin’s doodles digitised

Were you told not to ‘scribble’ in books as a child? I was. And I obeyed. But as I get older and more inclined to forget what I’ve read, I tend to add marginal notes in books, on articles, etc. Whether Charles Darwin (botanist, naturalist, zoologist, etc.) was similarly admonished I know not, but he certainly had the ‘marginalising’ bug and now his personal library (that’s the books within the library, not the library itself…) is going digital, and is freely accessible by all. Whilst it will no doubt be interesting to see the titles in the venerable gentleman’s collection, more interest is likely to be directed at the annotations he made in many of those tomes. The Biodiversity Heritage Library has so far digitised and published online 330 of the most heavily annotated resources inDarwin’s library. ‘Every annotation, including underlines and crossed-out passages, has been painstakingly transcribed and catalogued and are searchable by keyword’. This tale reminds me of a story I once heard of how binomial nomenclature ‘came to be’. Apparently, Linnaeus wrote in terms of polynomials in his early days, but added a marginal annotation of a single word for the verbose descriptive part of the organism’s Latin descriptor. That marginal annotation subsequently became the specific epithet which, when united with the generic name, became the much-easier-to-remember binomial we know and love today. True or not, let’s hear it for those who doodle, scribble or annotate in the margins – they may just be doing posterity a great service, and not simply end up destined to be a mere footnote of history!

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Why do petals have conical epidermal cells? (Review)

Why do petals have conical epidermal cells? (Review)

Why do petals have conical epidermal cells? (Review)

The conical epidermal cells found on the petals of most Angiosperm species are so widespread that they have been used as markers of petal identity, but their function has only been analysed in recent years. Whitney et al. review the data on the roles of these cells in attracting pollinators and determine that conical cells influence flower colour, temperature, wettability and tactile properties, and so are likely to have different primary functions according to pollinator and habitat.

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