How do phenotypes arise from genome?

[Jarrad]

Can anyone link me to any research that explains how multicellular life coordinate to express phenotypes? 

I'm having difficulty understanding how cells know their position in relation to other cells in order to move into any discernible shape, and how that is encoded in dna?

Something like a Tardigrade, at least wikipedia says it has 40k cells and is eutelic, sounds manageable... but HOW?!

How do those cells know they are all accounted for and in the right places? I feel like it's going to be an answer of some kind of bonds at certain places on each cell membrane but no idea what to even search for to learn more.

[Cathal (phone)]

Look to Nematodes: more manageable still, and the deterministic layout of EVERY cell is known, as is its full ancestry and patterns of cell expression.

A lot of the magic happens at conception, where gradients are established at the earliest stages which help guide cell differentiation and the propagation of more intricate patterns later on. A lot of the way the patterns propagate resembles fractals, so understanding emergent patterns will help too.

--
Sent from my Android device with K-9 Mail. Please excuse my brevity.

[Avery louie]

if you want to read a good but dense paper, check out alan turings paper on morphogenesis.

lots of math, but if you can get past that it is good.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+un...@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/529064b5-11cc-432c-8346-f82629b2d5c7%40email.android.com.

For more options, visit https://groups.google.com/d/optout.

[Jarrad Hope]

ahh awesome, thanks, will check out nematodes and just grabbed the turing morphogenesis paper 

You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/tIc3MCEFaKA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to diybio+un...@googlegroups.com.

To post to this group, send email to diy...@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAL4KOmgNuwy6%2BNFQOH0jRs_JT6OQm0jQZFuOSkV8uABq6D87hA%40mail.gmail.com.

[Sebastian Cocioba]

You may also want to look into Jim Hasseloff's work on M. Polymorpha and plant morphogenesis here:

http://www.plantsci.cam.ac.uk/research/jimhaseloff

He gave a fantastic talk at the plant synthetic bio conference at MIT and if his work is pay walled, just send him an email. He is a very nice person too. Its all very fractalesque and reliant on the way the first initial cells grow. After that it has to do with promoter activation for tissue specific regions but in general, in plants, its the concentration and ratio of a hand full of plant hormones over time and space. I induce plant tissue to make plantlets out of leaves every day in tissue culture. With the right hormones you could technically make any tissue turn into or produce any organ needed. I've had some fun accidents where a tomato leaf I cultured went full term in vitro but was no larger than 2". Full term meaning shoot, root, leaves, stem, flower, fruit, and seed. A complete lifecycle. Plants are a great model organism for understanding morphogenesis since they cycle fast, are cheap, and a small setup can get you rolling fast.

Pardon the shameless plug for plant biology but this list needs more serious plant people. Its getting lonely... :P

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

---

From: Jarrad Hope
Sent: ‎5/‎26/‎2014 3:04 PM
To: diy...@googlegroups.com
Subject: Re: [DIYbio] How do phenotypes arise from genome?

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAJoVaffaXhbtFp4tZ2RT-n-59VyfLUx-gyVwYDX3MHKEum%2BX0w%40mail.gmail.com.

[Jarrad Hope]

"I induce plant tissue to make plantlets out of leaves every day in tissue culture. With the right hormones you could technically make any tissue turn into or produce any organ needed. I've had some fun accidents where a tomato leaf I cultured went full term in vitro but was no larger than 2". Full term meaning shoot, root, leaves, stem, flower, fruit, "

To me, you sound like a wizard! That is really cool Sebastian! Do you have any pics?

How can it go full term but stay small?

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/-3806725917805544478%40unknownmsgid.

[Sebastian Cocioba]

Nah its been a routine technology for over 40 years. Its called plant tissue and its quite simple if u can keep things clean. If you give a plant gibberellins it will induce early senescence thus flower and fruit in vitro. Dwarf mutations are the product of either natural or man made knockouts of the gibberellic acid pathway. Adding GA also elongates cells so if ur stem gets stunted u use it to stretch it out. U need a decent disparity between stem top and roots for plant to be healthy so if u only get leaves from tumor tissue it may be wise to add gibberellins to the media. Literally plant tissue manipulation. You need to develop some instincts much like cooking. Protocols are nice but they can't account for every possible outcome and life is never cookie cutter. Sometimes the plant just doesn't want to sprout shoots just yet, it needs coaxing. Lots of fun!

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

---

From: Jarrad Hope
Sent: ‎5/‎26/‎2014 4:07 PM

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAJoVafct1ov59%2Bv9yhdstVwT4dyPfY_xeUm%2B3uK-bFCKmNxd_A%40mail.gmail.com.

[Katherine Gordon]

You have stumbled upon the question that has stymied developmental biologists forever. How does an organism know how to arrange its cells and what factors are in play that predispose one to chaotic misplacement of tissue types/cell types..?

--

-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+un...@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/f3c94f2a-4b00-4107-aaa6-5590d1157d09%40googlegroups.com.

[Andrew Willoughby]

How effective is this on plants that take longer to mature, like fruit trees?

[Sebastian Cocioba]

If you find a paper citing a reliable protocol for the
micropropagation, or in my case transformation, of the species in
question then you are good to go. I've had to cook up my own protocols
for a number of species simply due to reliability issues or lack of
data on the plant in question. Take the papers with a grain of salt and
do an empirical hormone assay. Normally the RMOP medium is the rule of
thumb. Solanum family is a little tricky and needs extra care but it
should work well across the board. I've done citrus, papaya, and now
willow too and all yielded good results. A sapling by any other name
grows quickly in vitro. Its in soil where it slows down due to massive
lignin and cellulose demands as well as other factors that I am unaware
of currently.

Overall the process is very trial and error based. I've noticed drastic
hormone response differences between two cultivars of the same species
so it may require a little luck too. As I've mentioned several times,
Im an experimentalist by nature and take all published articles with a
medium to large grain of salt and use them as a reference. A good cook
reads a recipe and improvises based on experience. The same goes for
plant biotech. By all means do try to replicate the paper verbatim but
you will notice subtle to stark differences in results. One factor that
you can't learn from reading is tissue culture "craftsmanship". The way
you cut the tissue, when, where, and how large can have huge impacts on
end result. You can only develop these instincts with time and
practice. Luckily plant tissue culture is cheap.

It took me around 3-5 years to really understand the results and
manipulate the tissue accordingly. Im sure there are much brighter and
keener minds here on the list who could put my skills to shame in no
time and I highly encourage you all to try it. It would definitely put
some fire under my butt to maintain a higher standard of work. So far
I've gotten to the point where I don't even care about optical density,
age of culture, exposure time, yada yada when it comes ti agrobacterium
transformations. It works damn near every time, albeit with drastic
changes in efficiency. I don't have space so a few plants from each
experiment is all I can afford to maintain so the low efficiency is
much easier on the conscience than killing a few hundred happy healthy
transgenic plantlets. Im no tree hugger but dont really like snuffing
out life for no reason....except mosquitoes. Those should all die
promptly.

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC

Plant Biotech R&D From: Andrew Willoughby
Sent: ‎5/‎27/‎2014 12:01 PM
To: diy...@googlegroups.com
Subject: RE: [DIYbio] How do phenotypes arise from genome?

How effective is this on plants that take longer to mature, like fruit trees?

--
-- You received this message because you are subscribed to the Google
Groups DIYbio group. To post to this group, send email to
diy...@googlegroups.com. To unsubscribe from this group, send email to
diybio+un...@googlegroups.com. For more options, visit this
group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google
Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send
an email to diybio+un...@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio.
To view this discussion on the web visit

https://groups.google.com/d/msgid/diybio/a1d2d004-d5dd-4da7-99ca-da6088461b39%40googlegroups.com.

[Mega [Andreas Stuermer]]

 Im no tree hugger but dont really like snuffing
out life for no reason....except mosquitoes. Those should all die
promptly.

 

You probably already came across this?

http://www.newscientist.com/article/dn25457-brazil-approves-use-of-genetically-modified-mosquitoes.html

 

I think I probably posted it already somewhere else :D 

[Jebus Jones]

Well as you may note no one here has been able to definitively answer your question - as indeed nor can I. But I can tell you one thing and that 'things are arranged the way they are due to biochemistry and evolution'. This might seem like a bland and empty statement, but it may not be as empty as you think. Things are arranged the way they are due to a 'happy accident'. Others here have argued for a Turing like map of biochemistry, but for me from a classical perspective this seems too 'purposeful', almost as though there is some overall actor (albeit unconscious perhaps) (or a script) governing the process. It is better in many ways I feel to consider every cell in your body to have arisen (and to be so organised) as a matter of pure chance. A liver cell can no more 'know' where it belongs than can a kidney cell, or a brain cell. It just so happens that the pressures and limitations exerted on evolution have resulted in this very particular conformation of tissues.

A better way to think about this perhaps is to consider how a bacterium might find its way towards a richer source of nutrients either when in culture, or in its natural environment. A great many bacteria use a methodology known as 'quorum sensing' (a form of random walk) to achieve this objective. Although this process may look purposeful, it is nonetheless a fundamentally chance process. The bacteria is in no way concious of it's need for nutrients, nor does it adjust it's course intentionally in pursuit of a favourable outcome. Rather the organism behaves entirely mechanistically in response to a biochemical stimulus - which itself (outside of the lab) is chance in nature. (Indeed all actors in this process are essentially random and/or subject to chance. The bacteria's tissues, its genome (which have simply been 'selected for') the substrate upon which it lives and the nutrient source upon which it depends. It is a matter of the presence (or lack thereof) of a certain type of biochemical gradient that may be unique in each case. Cells like people, also have the capacity to 'recognise' each other, via cell surface proteins and cell binding proteins that only other cells of a similar type can recognise. They can also speak to each other and even to different parts of the same cell, both over short and long distances via the endocrine, intracrine, autocrine, juxtacrine, paracrine (nervous system) signalling pathways. Again while this may appear purposeful, it is important to remind oneself that right down to each individual biochemical interaction taking place in the most minute detail, each one of these processes has arisen as a consequence of chance. Although these pathways may appear more sophisticated than those of the bacteria, it is still possible to recognise a link between this primitive signalling methodology and more recent/more advanced signalling methodologies.

It is very hard to look at this process and at more complex biological arrangements and not see some form of 'organisation' or 'intent'. But its fair to say that all processes like this and all processes where tissues may appear to spontaneously 'self organise' originated in a step by step process and that the ancient ancestor of most modern bacteria was pretty rubbish at sensing the presence of nutrient gradients in its environment. Rather it seems likely that this behaviour emerged only very gradually over countless aeons of time, as a result of endless natural experimentation, overpopulation, extinction, chance and good fortune, as the system that allowed bacteria to become more efficient at 'sensing' nutrients in its environment evolved. Higher organisms after all are not governed by different processes than those that have governed the evolution of bacteria. There is no supplementary 'directed' subtext that governs the evolution of higher life forms.

I know some people will say that since stem cells have the capacity to differentiate into any tissue type that this is evidence that there is some 'direction' in this process. But there is not, as plainly the genome is the source of much of the randomness (in conjunction with external factors) that has resulted in the present state of affairs. Tiny steps, chance and almost unlimited time is what has brought us to this point. If you wish to have a better model for how random systems may display a capacity to self-organise, a better fit would be chaos theory. A sub-branch of Chaos theory is of course fractal theory, although this isn't an area I have a great deal of experience of personally.