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Headcheese: super high output plant genetics prep with screen

gridding plantlets to find genetically transformed items
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(+6, -1)
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I thought of two super high output plant genetics prep with screen protocols

From working (student) at the barley genetics lab I remember slicing up presprouted barley; rinsing with agrobacter plus gene sequence bacteria, then arranging these on agar plates to genetically engineer barley; thirty or forty dots on a plate was typical afternoons effort; the rate of actual transfection was near 10 per 300 dots; the thing that was most effortful was slicing the barley at the germ (like wheatgerm) area. At the time I thought a headcheese approach might be better

The headcheese approach to mass producing genetically engineered plants from embryos: use a wheat germ machine to gather barley germs (embryos); put many hundreds of barley embryos with agar to make a rod; use a microtome to slice off 1mm sized dots to place on growth medium

now, the nifty thing is that at 1mm spacing you can make a million little dots of plant embryo head cheese on a meter square flat surface, which is basically just a big table with a liquid spill rim or a flat

then you spray or paint on the genetically modified agrobacter vector that transfers its genes along with visibilization genes to the barley embyo slices on the flat; when the genes are transferred the growing plant tissue, known as a callus, makes a BFP or GFP or YFP various fluorescent proteins that an optical detector can detect. To make the attempt at transfering multiple genes at the same time you overpaint the treated areas with differently modified agrobacter vectors. Resistance to herbicide was the usual screen, but here I use visibilization proteins as a screen.

you could do this as an artist with your hand or you could just use a plotter structure to literally draw every combination of the multiple genes you want to combine with different fluids at different concentrations, basically you just draw your million subject plant genetic engineering projects with its wide variety of concentrations as well as possible gene combinations on the tray

moving from 30 or 40 to a million plantlets per afternoons effort is tactic kind of reminiscent of gene chips; with automation it creates millions of screened plants every few hours

when scientists amplified or downmodulated each of numerous chemical pathways (genes) to make a new higher yield of canola oil it was two years, this approach could shrink that to days if you have an idea of which genes to pump up, downregulate or contribute

Id like it to create massive rapid development of new plants like duckweed that makes ethanol or sugar to make ethanol

The headcheese technique must be modified to genetically engineer duckweed unless turion nodule head cheese is effective

I like the milled edges idea as well as the sewing idea

with the milled edges idea the duckweed is stacked |||||||||||||| to create rods, frozen, as it can live through that, then the sides of the rod are milled like the edge of a dime; transfection occurs at the growth area of a plant thus milling gives a tranfective surface plus the highly favorable cluster multiply growth point; the duckweed is placed on a mesh fabric on a million unit grid; gene transfection agrobacter is painted or plotted on the flat then covered with another layer of mesh; nutrient fluid flows atop the mesh; optical detectors look to find the fluorescent proteins that singly or multiply identify transfected plants; wonderfully just 30ish hours passes to a mature plant that has fully shown its ability to generate the product

each million plantlets may generate 10k transfections; each 10k transfections may simultaneously generate 100 plantlets with two different transfected genes; then maybe there is one with all three genes at once; obviously one also has the opportunity to rank the 10k transfections group according to gene effect amount then grow a big batch of that prior to transfection two

hyperprocessing: fabric rolls because the duckweed is between two mesh layers the size of the tray could be the length of a fabric roll; it is possible to wind many meters around a core then immerse the thing rather like a 35mm film developer

Sewing method is much more casual; lay a million duckweed plants on a mesh; cover with another mesh; run through a sewing machine where the | has milled sides to create multiple transfection opportunities per jab; after the | has generally left two or three small multiply edged transfection punctures on each duckweed plantlet you paint or plot the agrobacter gene vector on the top of the mesh; optical detectors find the plantlets that have been transfected; I like the idea of the sewing machine using thread soaked with agrobacter where various spools of thread could represent different genes to try

given that during the 90s about a trillion USD of petroleum was used domestically per year (three trillion now, twelve trillion worldwide) creating an ethanol plant which is currently on a few year projected horizon might be just a few months plus the rate of improvement is hundreds of times more rapid

There is a patent that covers some of duckweed genetic engineering, to make this fully public domain I'd have to create a new transfection method different than agrobacter or biolistics: here is such an idea create "splintery spaghetti" genetic transfection technology; this is where an item like a sewing machine | leaves splinters at the site; these splinters are made from a blend of starch polymer plus gene fragments or plasmids to transfer; it is the jabbing with an icicle version of biolistics thus should work as well or perhaps better as the polymer splinters could have pH buffers or beneficial to transfection chemicals like "competence" calcium chloride

I also think the idea of a | covered with a honeycomb of little chambers that carry plasmid containing fluid would function as well or better than biolistics, another method would be like velour plate colony transfer where rather than velour a wide field of ultra tiny silicon carbide |||| each honeycombed with plasmid fluid nooks could be pressed onto a duckweed bearing surface

anyway the headcheese is what makes the mass screen possible

beanangel, Jun 20 2008

animal tissue culture transfection array plates of a few hundred items http://www.origene....eGFC-ArraySP384.pdf
[beanangel, Jun 23 2008]

us patent 4910146 is similar but absent head cheese or array http://www.google.c...nts?id=LfIfAAAAEBAJ
[beanangel, Jun 23 2008]

people making ethanol from duckweed http://media.www.nc...oblem-3358649.shtml
[beanangel, Jun 23 2008]


       OK, I got through the first few paragraphs, but then lost patience. But, as far as I got, and as far as I decoded, the idea was basically "use a machine to array transfectable barley sections on a big plate, then mass-transfect by painting on the relevant vectors."   

       This is a good idea, but I can't help think that it's already done in high- throughput labs (where almost every technique is adapted to high throughput). I don't have much experience in plant genomics, but certainly for all other aspects of genomics (including mass transfections), it's already automated. When were you a student in this lab? If it was more than five years ago, things will have changed a lot.   

       I didn't read the rest of the idea - if it contains something different from the first few paras, perhaps a summary would be beneficial?
MaxwellBuchanan, Jun 22 2008

       I just read the title and then scrolled to the bottom to confirm my suspicions. Neutral.
david_scothern, Jun 23 2008

       Well, the first bit is OK once you decode it, although possibly baked. He does have the odd good idea, once you get through the verbal eccentricities. I may even give it a [+] by way of encouragement.
MaxwellBuchanan, Jun 23 2008

       //There is aptent that covers some of duckweed //
Is this some kind of conformal coating?
AbsintheWithoutLeave, Jun 23 2008

       I am thrilled to find that there are researchers making ethanol from duckweed[link]   

       the high efficiency plant tissue culture system as a head cheese array appears to be new; there are just two or three patents on plant tissue culture arrays   

       duckweed prior to genetic engineering is three times as productive as corn; just a few GE modifications to make duckweed triple its carbohydrate mass creates a crop ten times more cost effective than corn that doubles mass every twenty or thirty hours   

       my thought is that plump leaved plants like iceplant as well as plants with carbohydrate rich leaves like taro or sweet roots like sugarbeet are a GE area here   

       to reach ten times the efficiency of corn modifying which polysaccharides are produced might shift metabolism to accumulate carbohydrate if the duckweed plants enzymes to convert certain types of starches are variable   

       I think this idea, as well as the actual duckweed researchers efforts, is absent threat. If the duckweed made ethanol directly with yeast genes then that could cause environmental issues, starchier duckweed gone wild is likely to be harmless
beanangel, Jun 23 2008

       Producing plants which grow at ten times the rate of anything else is anything but "absent threat". It's environmental havoc on a massive scale. Have a look at Japanese Knotweed, for example.   

       On another note, what is the relevance of the word headcheese to this idea?
david_scothern, Jun 24 2008

       Am I right in thinking that you're saying that rather than spending a lot of effort doing something (in this case preparing transformant cultures) precicely, doing it roughly (randomly?) on a much larger scale might be a lot less effort?
Loris, Jun 25 2008


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