A Phd in Plant Geekery....

[alanelliott]

Today, Alan is : Presenting 2yrs worth of BBSRC funded PhD work  to University of Edinburgh Institute of Molecular Plant Sciences symposium today

(Attachment Link)

Thanks for that Maggie. The whole day was bonkers. Should have stayed a gardener merrily weeding at Branklyn.

[Afloden]

Alan,
 
 Whats become of the odd Thalictrum-esque plant you reported on from Nepal? New species, different genus, or new genus? While I may be working on the treatment of Polygonatum for Nepal I doubt I'll get to go before I finish that work.

[alanelliott]

tentatively Thalictrum rostellatum but I'm not quite convinced.

[Maggi Young]

Out of interest  :Thalictrum rostellatum   herbarium specimen from 1971 ....  http://www.iiim.res.in/herbarium/ranunculaceae/images/thalictrum_rostellatum.jpg

 photo: http://plantsoftibet.lifedesks.org/pages/46197

[alanelliott]

Part of what I do [badly] is molecular lab work. This is another dark art of plant science.



I’ll take you through the basics steps over a couple of posts.

First you need a sacrificial plant, or more accurately a leaf. I work from material that is stored and dried in silica gel, same stuff your new shoes come with.



Now I know what you are thinking a small bag of white powder. Just cause I lived in Dundee don’t go tarnishing me with that brush thank you very much! Incidentally if you ever want an interesting conversation with good people at an airport take a couple of kilos with you on fieldwork.

You do not need much leaf about the size of your wee finger nail. This get put in a tube with a steel grinding ball. The sample then gets literally put through the mill and the end result is a fine powder in the tube.

I use a cheap and cheerful method of extracting the DNA from the ground up powder using a “homemade” mixture of chemicals called CTAB, brace yourselves, Hexadecyltrimethylammonium bromide.

The CTAB is mixed with beta-mercaptoethanol (which is toxic, reeks and is the most dangerous thing in the whole process) and heated to 65°C. 1ml of the heated CTAB/ mercaptoethanol buffer is added to your tube of powdered leaf. This is then incubated for 30min on a heated block.

The CTAB buffer is nothing more than a detergent that helps break down lipids in the cells to release the DNA and “wash way the rest”

0.5ml of Chloroform-IAA is added to the tube then it is placed on an orbital shaker to gently mix it all together. After about 20min the tube is centrifuged at 13,000rpm and this creates a two layered mixture, an upper layer which you want and a murky-green sludgy layer below which is discarded.

The upper layer is removed and 0.6ml of ice cold isopropanol (alcohol) is added. This helps the DNA to precipitate out of the solution. At this stage it is left in the freezer overnight if the leaf material is fresh but can be left for weeks if you are working with old herbarium material.

I find lab work a bit tedious and massively frustrating; just like weeding but at least you get some fresh air with that.

As a reward for getting this far this is the plant that was in the bag of suspect white powder.


Clematis gracilifolia from the ACE expedition collection number 1834 for anyone interested.

[alanelliott]

Yesterday I presented a modified version of the talk I gave at the University of Edinburgh last month at the “Inter-institute postgraduate symposium” this year held at the James Hutton Institute (latest incarnation of the SCRI) at Invergowrie.



There were students from SRUC (Scottish Rural University Colleges), The Rowett Institute of Nutrition and Health, Moredun, BioSS, the James Hutton Institute and me representing RBGE postgraduate science. The common defining feature of these institutes is that their primary funding body is the Scottish Government.

It was a mixed bag of talk ranging from the use of novel techniques for in-situ measurement of root-reinforcement of mountain slopes to humane mechanical methods for killing poultry to nanomedicines in the treatment of Tuberculosis. There was also a mix of nationalities represented: Scots, English, Swedish, French and Dutch.

It was very heartening to see the breadth and quality of science being produced by early career scientists at Scottish research institutes. I felt quite proud to be there part of it.

The three, well deserved, talks that were judged to be best to go forward to the annual Science for Life Lecture at the Royal Society of Edinburgh later this month were:

• The role of the gut microbiota in inflammatory disease states - Catherine MacDonald.
• In virto fermentation of oats (Avena sativa) and barley (Hordeum vulgare) by faecal gut microbiota -Andrew Chappell
• Computational identification and functional characterisation of DNA binding effector in Phytophthora - Graham Motion.

You'll be glad to know I held my own and actually enjoyed presenting a full on science talk for a change.

As just a brief summary of some fo the things I talked about in my half hour slot.


The checklist diversity of Clematis in Nepal.


What my revision has done.


Looked at the genetic relationships of different groups and the timing that we believe that they began to diverge to become the "species" we know.


And of course acknowledge those who have supported and help me to this point.

Best question I received from a statistician was “Just what is the Scottish Rock Garden Club?”

[ichristie]

Very well done Alan we are proud of you and your efforts, cheers Ian the Christie kind

[alanelliott]

Very well done Alan we are proud of you and your efforts, cheers Ian the Christie kind

Cheers Ian. Its been a busy stressful wee while lately.

[ChrisB]

Alan, on your chart of clematis above third one along on the bottom line, is it C. koreana?

[alanelliott]

It's Clematis tibetana subsp. brevipes an geographic and morphological intermediate between ssp. tibetana and ssp. vernayi. Only occurs in central Nepal in the Transhimalaya the dry area behind the tops of the main Himalayan range. The name covers Grey-Wilson's names from his monography that were used for ssp. vernayi and its various forms in Nepal but only in Nepal.

[ChrisB]

Thanks very much.  I have a clematis with flowers that look similar but I got the seed as C koreana.

[alanelliott]

Thanks very much.  I have a clematis with flowers that look similar but I got the seed as C koreana.

Nice always curious to know what people are growing. This isnt the taxa from Nepal - foliage from what I can see in your pic is different. Would need to see other characters to pass judgement as to what it is.   

[Maggi Young]

It can take a while to pin an ID to some things - but eventually someone like Al, beavering away in a herbarium, will make a breakthrough ;

"New taxa for TheBotanics herbarium. 1889 Clematis collection from SE India sitting unidentified is Clematis heynei "

[Maggi Young]

Alan is just about to set off on another field trip  in pursuit of Clematis knowledge and we wish him all the very best for the expedition.

Meanwhile, take a look at this : Botanical Selfies - eXtreme botany at 3600m with Alan Elliott

http://drmgoeswild.com/extreme-botany-at-3600-m-alan-elliott/#comment-34449

[Maggi Young]

Alan is safely returned from his recent expedition: we look forward to reading more here in the fullness of time - the fellow is very busy, you know!

On the 28th September Alan will be giving a talk  for Plant Heritage Scotland (www.plantheritage.com) 



Julia Corden is also involved in this event -

The Royal Botanic Garden Edinburgh will be hosting Plant Heritage's All Scotland Meeting, to which non-members are most welcome. The focus of this year's event will be a celebration of the achievements of Scottish plant hunters past and present, exploring some of the less obvious ways used at RBGE to conserve their findings. Speakers include Julia Corden of the Plant Hunters Garden, Pitlochry and Alan Elliott of RBGE.


see full programme of the day and booking details below

  PlantHeritageProgramme28-9-14.doc (47.5 kB - downloaded 197 times.)   - when booking, you might like to mention you read about this event here.