Olive Trees

Quote: Originally posted by RogueRose

... Maybe we can figure something out with nano tech (not "us" in this forum) that could somehow be used to attack this and not harm the plant. I guess it is conceivable that they could also be used to clear blocked xylem, like a drain cleaner for the plants circulatory system.

Quote: Originally posted by aga

Quote: Originally posted by RogueRose   ... Maybe we can figure something out with nano tech (not "us" in this forum) that could somehow be used to attack this and not harm the plant. I guess it is conceivable that they could also be used to clear blocked xylem, like a drain cleaner for the plants circulatory system. Why not us ? We might not have an NMR in the garage, but Ideas such as your 'nano drain cleaner' can only be for the good. @OldNubbins: sounds like an awful situation there. There are zillions of cicadas here, so if they get infected, bye bye olives.

Quote: Originally posted by RogueRose

... I know very little on this, but I figure any info may lead to something.

Quote: Originally posted by aga

I read a news item recently (today ?) where someone said there are 1,000s of bacteria in the soil that we know nothing about, basically because they are not happy being 'cultured' in a lab environment. They took the view that the DNA could be harvested en-masse, so did that. Turns out they isolated gene sequences that were very effective against even MRSA, without identifying the source organism. The hypothesis was that bacteria have been battling virii, fungi, everything, and for millions of years more than humans have, so they (or some of them) are very much better at it than we can even hope to imagine.

This is very true.

The ocean until fairly recently was thought to contain no bacteria, few virus. It turned out we looked in the wrong place, if you look in the top 2mm of scum in sea water its full of it.

Natural marine bacteria not stuff we pump in. But phages are as old as bacteria. I dont no too much about them, they are a kind of virus. But the host is always a specific bacteria, sometimes not just a species but down to below sub species level.

Take e.coli 157, it has a phage. The phage can only exist with the 157 strain of bacteria. To me it makes sense there is a phage for every Bacteria, the ultimate weapon against bacteria. But isolating is the costly bit.

The olive trees is the kind of situation we as mankind tend to make worse, it really works against them that they are a cash crop.

Truth is there is money in misery, most will loose money and livings and a few will make alot of it. Bio security is like all security, its really effective until some twat leaves a door open.

Ash die back is a good example, you dont hear much about it now, most think its gone away and we have resistant strains of tree.
We had some 200 year old Ash trees here on the outskirts of our wood.

3 years or so ago we got signs of the fungus, we rang the number the forestry people have for it. First question was how many hectares of woodland you got?

We said around 6 maybe 7 at a push, they asked how much was Ash, we said no idea they are sprinkled around the edge, so maybe 1 acre, perhaps 2 if you add all the trees up.

Line went dead, no one ever showed up. No little vial arrived in the post. Mostly we have commercial pines and spruces, shot a grey squirrel last year.

Did the duty and called it in, 4 people following morning with traps arrived. We are called every 3-4 months to see if we seen any more. We have just about lost most the Ash trees now, a few are hollow with some outer growth, but most the big ones have fallen.

Maybe 4 young trees fairly strong, but i dont think die back is over. I think the lack of interest is going to bite again.
Ash isnt commercial in our part, but the commercial forests are rimmed with hardwoods. The hardwoods act like wind breaks, they seem to benefit the pines, so they plant them around the edge.

But mainly no one bothers unless its a spruce or pine threat. The locals laugh at the English Deer shooting, they pay alot of money to come up on the hills and bag a deer.

Yet the rangers pay the locals to shoot them by the dozen! 12 deer can clear 3 acres of new plant in a morning. We let our wood go wild, we wont be felling it for the wood, just the odd thin out as it grows out. Its now at the 28 year mark, so final thin coming up and then should be felled in around 12 years or so.

We wont be doing that, as some fall in storms, we back plant with hardwood or let stuff self seed. Not the most popular place in the area .

Reading about the Olive bacteria, you cant help but think its always been there. Maybe the problem is modern harvesting leaving more sites open on the tree.

Perhaps picking olives and not shaking fuck out the trees with a machine might help..... cant see a chemical answer, the vectors are too many and by the time the tree is badly infected.....

[Edited on 14-2-2018 by NEMO-Chemistry]

"Shaking the shit out of the trees" - That really made me think that that could be a trigger for the olives to give the bacteria a foothold. Think about a bruise on the body, maybe the same thing with the olives. Damaging the outer layer (xylem/phloem/bark) may rupture small cells that give the bacteria an access point to take root. From what I've read, almonds also suffer from the same disease and they are harvested the same way.

On another point, eating almonds is the most environmentally damaging thing you could do, as far as water consumption and drought issues in California. The amount of water it takes to make a single almond is outrageous! It is so much I don't even want to write it b/c it makes me so sad and the fact that one company ("The Wonderful Company" - makes me want to spit that it is named that) uses so much water while others (farmers) are loosing their shirt. Take a look at these articles to see the damage this one married couple has done to California over the last 2 decades.

https://www.alternet.org/story/149061/meet_the_billionaire_c...

http://www.seecalifornia.com/farms/almonds.html

I refuse to eat almonds in any mix and pick them out as my boycott and would rather throw them away in hopes of some positive karmatic return.
/rant

So, both olive & almonds are suffering from the same thing, both are harvested by grabbing the trunk and shaking/vibrating very violently (some very dry drought area's end up having root damage because they shake so hard). I also wonder how much the hydration level of the plant effects the behaviour of the bacteria, less water flow, bacteria moving through slower, or the xylem isn't as wide or possibly have the same pressure within the xylem or pressure within the individual cells. This could be something as simple as a nutrient deficiency which may allow for some "small" imbalance that can allow the bacteria to take hold.

NEMO: I hope you put all that ash to some good use, maybe put some on a lathe and make your own Louisville Slugger or at least maybe you/someone got some good firewood out of it - ash is great firewood. We have a good bit of "woods" that started off as planted evergreens allowed to go wild and over 70+ years there are some beautiful hardwoods as well as some nice fruit trees and original evergreens though those are getting few and far between as storms have taken their share. Having a diverse woods is awesome for animals and we have more living there than areas 10-15x the size as there are about 3 levels of ecosystem (4 if you include under ground) where different animals live.

Quote: Originally posted by RogueRose

On another point, eating almonds is the most environmentally damaging thing you could do, as far as water consumption and drought issues in California.

Quote: Originally posted by OldNubbins

Quote: Originally posted by RogueRose   On another point, eating almonds is the most environmentally damaging thing you could do, as far as water consumption and drought issues in California. Cattle farms, both for beef and dairy, use more water than almonds. Alfalfa grown for feed consumes much more water and is less efficient at using it. The only thing it has going for it is crops can go fallow in drought years while almond trees will die if not maintained.

Quote: Originally posted by RogueRose

I had heard that the almond was the most inefficient food energy wise when it comes to water consumption. I'll look at the video that references it and see what the numbers are for both. Either way, both are pretty heavy at water usage.

Quote: Originally posted by Ozone

Interestingly, it is often easiest to isolate the phage you want from the wild-type bacteria themselves. Shotgunning the sequences of the bacteria can reveal the presence of the viral DNA--which doesn't do much until the cell count reaches a certain point (quorum). Then, the bits activate, and the cells begin making the phage. Soon after, the culture dies. This is one (of several, all obnoxious) mechanisms by which an otherwise viable bacterial culture can spontaneously die in log-phase (red flag!). The trick is finding the spliced-up bacteria--which usually involves screening a ton of samples (which are, apparently, frighteningly abundant). This describes a standard method for phage selection (and discusses the limitations of several methods). I imagine that isolating a phage therapy for trees wouldn't be that different (but, getting it into the trees is a problem that remains--infected leaf hoppers?): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356574/ O3 [Edited on 14-2-2018 by Ozone]

There is a video that states it takes 41 gallons per almond. I thought that sounded ridiculous and looked and found that is per ounce. There are some stats that show 1.1 gallon per almond and that the 20 gallons is probably 1 oz of almonds with shell, and the 40 gallons per ounce is probably without shell as the shells about about 1/2 the weight of the nut. Walnuts are somewhat worse but they are much bigger in size, so they take more water per nut. Another source states 1,929 gallons per lb of almond or 120gal per oz.

https://www.huffingtonpost.com/2014/10/13/food-water-footpri...

http://www.businessinsider.com/amount-of-water-needed-to-gro...



I think the water use all depends upon the region in which the crop is grown as much is lost to transpiration in arid regions. I know may plants take much less than what is stated but I live in a very humid area during growing season. I'd say my plants take about 1/4 what some sites post as the average water usage.

Considering the diversity of strains gained, the fact some came from things like 2Fistula discharge" (that's nice), and the phage isolated from a pond and not purchased from a bank.......

You got to ask a simple question, why the hell isnt more money (read huge amounts), being pumped into this? In all honesty if your using knockout plates, then why not combine several phages that are effective? I honestly thought they were much more highly selective than they appear.

Ok they are highly selective, but I think it shows real promise. But when they are not researching this very much when antibiotics are close to being shot, then i dont think Olive Trees will be a priority. But seriously aga, wouldnt cost you much to set up and play with some Bovine fetal serum and bacteria.

Class2 hood, CO2 or similar negative pressure HEPA incubator (pretty cheap second hand on ebay). aga plays with Agar! I can see a series here....

As you have Olives, I would suggest your extremely strict with Bio security and technique, but i dont see why you couldnt do it.

ROSE

Swap you some that sunshine for our high class guaranteed rain if you like

[Edited on 16-2-2018 by NEMO-Chemistry]

Quote: Originally posted by aga

Unfortunately i'm not young enough to know all about all of this. Rain would be very helpful.

In your case, the hard bit is finding the phage. The rest is easier than most the chemistry you done.

The reason your best placed is Olives, we can buy Olive Trees in the local supermarket down the road here. But i often wonder why they sell them, every year we buy some and every winter they die.

Travel

I cant go jumping on planes looking at infected olive groves, thats where I would start. Find the infection and you will find the phage not far from it.

No guarantee but my logic goes like this.......

Look for a infected Grove, one that isnt totally dead but has been infected a good while. Ideal candidate will have water or boggy bits some parts the year.

The bacteria needs water, because of how it infects i would think it needs nutrients in good amount and water. As you pointed out sunshine would help alot. Because if you limit the water your going to deprive the nutrients for the bacteria.

So working backwards, older the site of infection the more chance phages have had time to develop. Most likely place to actually find a phage, and one the easiest ways to sample.

Is a water swab strait onto lawns of bacteria, or in a perfect world into liquid broth cultures. But if you travel by air then its plates and lawns.

Do enough samples in enough little pockets of water and the odds go your way.

From there there is little to know, ideally you would make the bacteria selective. Take something away from it that only you can then give.

But for that you need to mess with plasmids, so trying to keep it real.

Do without selection, be OCD with ascetic technique, plate the bacteria strains up and liquid culture. The liquid cultures are simply a source of bacteria for the plate lawns.

Then spot test the plates with the sample swabs, each swab you plate test, put into a tiny liquid culture of the bacteria.

The reason is, if that swab has the phage on, you want to amplify it. easiest way for a non pro is feed it.

If spots on the lawns die rapid, and its obvious you dont have some other bacterial infection killing it, then the chances are good its a phage.

The vial with the feed solution is then upgraded to a larger one, keep it fed and renew every 5 days. This is a candidate.

Ask people to send sample of the xylem from infected trees, actually ask a local uni near the site to grab a sample for you (first/second year work ). Test the candidate on the new sample, if that dies........

You start to get excited, not free beer excited, but close to it.

This is something you could handle, but needs attention to detail and travel.

Decent scope ~£1,100 second hand

incubator with HEPA filtration, gas and vac line ~£120 -£550 second hand (I got a couple recently that were £50 each). The ones I got recently were from a uni. Excellent condition and extremely cheap.

Fume hood, you cant/shouldnt make a class2 hood. Secondhand ~£500 - ~£1,500 should do it but get a ducted one, you got Olives so you put a formalin burner output into the square thing ontop the hood where the ducting connects.

When the hood runs you run the fomalin burner, IF anything gets past the filters, its killed by the fumes. this isnt common as far as I know in a lab. But labs got the £ to change the filters like socks and I dont.

Plates aga and culture dishes etc ....... £ bit of string - £ long piece of rope.

But 100% someone like you could do this. Infact in many ways your ideal.

Its seriously such a cool project, if I could do the travel and grow.... Actually I could grow olive trees to a certain extent, i could grow cell cultured ones.

That would give me test sites, your case use cutting and keep them in the lab!! But testing cuttings comes later, alot later.

At the very least aga, you could pass the suspected phage to a uni looking into the disease. They can always take it to the next level.

[Edited on 16-2-2018 by NEMO-Chemistry]

Quote: Originally posted by Reboot

Systemic distribution of a phage would be a huge challenge. They can't really diffuse through membranes, they won't be actively transported, and in animals the immune system might go crazy when it sees them. So that's the more profound problem: How do you get the phage to your bacteria? I think a much more likely strategy would be to target the insect vector (perhaps with something akin to the BT toxins that are engineered into some crops to kill certain insects.) Otherwise, you're left with the traditional approaches of spraying pesticides or developing a strain of resistant olive tree. In the long term, I could imagine immune cells engineered to carry and deliver a phage warhead, although that may not have much advantage over a normal immune response for most cases.

Why not simply infect the olive trees with the bacteria? Inoculate the bacteria with phage just before infecting.

Or infect day X with bacteria then a few days later spray and infect with bacteria carrying the phage? When the phage has done its bit the rna should be left to some extent waiting for the bacteria to show up again?

I have done some pics of the matrix system i use, these are what I keep prospects in, as you will see they hold slim 1.3ml tubes. The incubating blocs have lids and working blocs dont.

Space wise they are a little small than my galaxy note 2 phone, each bloc holds 96 tubes. they also stack, at the moment i have some in the incubator with test cells from the electroporation experiments.

No idea how many blocs would fit in an incubator, i have had 19 and that hardly took up any room.

Also the vials have screw tops on.


[Edited on 21-2-2018 by NEMO-Chemistry]

[Edited on 21-2-2018 by NEMO-Chemistry]

Quote: Originally posted by mayko

RNA by itself isn't infectious, and is somewhat fragile in ambient conditions. The infectious unit of a virus is called a virion; it contains the virus genome (which may be DNA or RNA) bundled in a protein shell called a capsid. Virion stability varies widely.

Quote: Originally posted by aga

A good reason for me NOT to experiment would be the serious risk of transmitting the disease from A to B simply because i do not know what i'm doing. The best location for any research involving the active pathogen will be a biochem university in southern Italy, Naples for example. I'll see if i can find a contact and email them a link to this thread. It might be a waste of time, but you never know.

well I think I've a passive method to save the olive trees, if you have 1 million € free of taxes contact me

also if you want to produce megalots of lemons in bare sand...

the method is so simple...

Quote: Originally posted by mayko

RNA by itself isn't infectious,

Quote: Originally posted by Neal

For elemental metals, copper is the only anti-bacterial by a long shot.

Quote: Originally posted by Neal

Some various quotes from this thread: Quote: My initial thoughts are about a magnesium compound that could at least be tolerated by the plant, yet be toxic to the bacterium. Quote: I'd start with boric acid as it kills veroa mites (for the bees) For elemental metals, copper is the only anti-bacterial by a long shot. But for plants selectivity, use 3% hydrogen peroxide, kills bacteria and such with minimal harm to plants.