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aga
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[*] posted on 12-2-2018 at 14:11
Olive Trees


Anyone up for doing something that is actually useful ?

This bacterium :-
https://en.wikipedia.org/wiki/Xylella_fastidiosa

threatens to kill all the olive trees. Yes, All of them.

At the very least there could be no olive oil to be had, at all, for at least 15 years if it gets as far as Spain (we make about half of the global supply).

Italy is trying to fight it by ripping up acres and acres of ancient trees, then burning them to try to halt it's progress.

My initial thoughts are about a magnesium compound that could at least be tolerated by the plant, yet be toxic to the bacterium.

Detection of the bacteria is a biggie, otherwise there's no way of knowing if a tree is infected at an early stage.

Studies have shown that the bacterium basically blocks the sap channels, similar to human arteries getting blocked with fat/scar tissue.

Unfortunately the tree responds by shutting down the sap flow to the affected part, which means those parts die.
Basically the bacteria moves on down the tree and it all dies.

So, instead of random bollocks, is there a chance that anyone knows anything that could be applied to this Real Life problem, which is happening Now ?




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[*] posted on 12-2-2018 at 14:21


Great. Dutch elm disease for olive trees.

How about doing in or immunizing the insect vector?

If you are wanting to eat the olives/oil, you probably don't want a systemic poison.
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[*] posted on 12-2-2018 at 14:24


A systemic would be bad.

Chromium tainted Extra Virgin Olive Oil might not get thru the scanner at the airport.

Fortunately Olives are wind pollinated, however anything bad for Bees would not be good for them/us at this specific time.

Edit:

Attacking the vector might be good. Maybe attacking the bacteria's environment inside the vector would work.

Nice idea Bert.

[Edited on 12-2-2018 by aga]




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[*] posted on 13-2-2018 at 02:47


My first thought is contamination risk when getting smples to work with.
The ethics of posting such material internationally is questionable.

I'd start with boric acid as it kills veroa mites (for the bees)
and kills most insects, yet is considered generally non-toxic.




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[*] posted on 13-2-2018 at 06:34


Do you know if there are any species that are resistant or immune? What about other plants that are suseptible, have any of those shown species that are resistant or immune?

I know the only thing that seems to work for American Chestnut has been breeding with the resistant Asian chestnut which has produced something that is strikingly similar to the original American Chestnut but is resistant to the fungus blight.

As for Dutch Elm disease, it is also a fungus, spread by beetles, so like the Chestnut blight, both are caused by fungus, not bacteria like what is effecting the olive's and other plants by Xylella fastidiosa.

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.
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[*] posted on 13-2-2018 at 07:52


We have a vineyard here in California and Pierce's Disease has been an ongoing threat. This is caused by the same bacteria spread by the glassy-winged sharpshooter. Basically, the only defense that has been used is heavy pesticide use in conjunction with alerts. If a farmer identifies any sharpshooters, the word is sent out and farmers start spraying. Another similar problem is crown gall. That bacteria lives in the soil and infects through injuries in the plant stem caused by mechanical harvesting, mowing, pruning, etc. slowly choking off the plant until it dies. The only solution is to allow the vineyard to go fallow for several years before planting again. It's rough, we are dealing with that now.
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[*] posted on 13-2-2018 at 08:43


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.






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[*] posted on 13-2-2018 at 09:41


Human nature is the problem.

Like Dutch Elm and various other disease in the plant world, bio security is the hard part. I would think killing the bacteria would not be hard, whats hard is getting everyone in an area to do it, and then getting them to do the odd random tree growing semi wild that no one owns.

its likely in reality your going to have to have a firebreak area, its also likely that area wont produce for a couple of years. Even if its a bottle neck area, your up against the odd few who wont do it.

With some tree disease particularly up here in timber land, they use indicator and firebreak methods alot.
They leave a row (row sounds small, these are huge), then fell out everything behind the row until they reach a natural barrier. The barrier is normally a valley and river or a hill side with no trees.

They do the row on the side facing the known threat, they monitor it. After X time if they are not infected they back plant behind it. If it gets infected they fell and burn on the spot. It protects the millions of hectares behind the breaks.

If you can get EVERYONE with a olive tree on board you stand a chance with other methods.

[Edited on 13-2-2018 by NEMO-Chemistry]
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[*] posted on 13-2-2018 at 10:09


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.


Well I didn't mean to devalue or discredit anyone's abilities or resources and that it my fault. I'm not aware of what is needed to work with nano related substances other than ultra-small elements - so I just figured it might be out of reach for members.

I know I've read about advances in medicine where nano bots or particles are "programmed" or designed to seek out specific "invaders" or obstacles and destroy them.

I would think that antibiotic or antibacterial agents would be a good start to look at with focus on gram negative targeting agents. I'm wondering if there are any antibiotics that target anthrax could be manipulated as it is also a rod shaped bacteria. It seems that treatment for bacteria as powerful as antrax still relies upon the standard antibiotics fluoroquinolones (ciprofloxacin), doxycycline, erythromycin, vancomycin, or penicillin.

What is both interesting and scary is the number of hosts the disease has been found in. In the Wiki article it states that as of 2015, 309 hosts have been found but majority remain asymptomatic. This is good news because this suggests that there is something within these plants that makes it inhospitable for the bacteria to either thrive or take hold and produce the symptoms in the olive. While it could be that the asymptomatic plants are the normal, the olive may have an elevated level of something that acts as a "steroid" for the bacteria, or some other action that leads to the blocking of the xylem.

I'm wondering if this bacteria infects bamboo as I've seen some plants exhibit similar characteristics to the oleander scorch which is caused by this bacteria. I haven't found anything related to bamboo, but "heavenly bamboo" which has been found to have the strain of mulberry leaf scorch (of 8 isolated strains of the bacteria in Souther California).

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



[Edited on 2-13-2018 by RogueRose]
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[*] posted on 13-2-2018 at 10:18


Between invasive species, both plant & animal, and disease, it's amazing that agriculture has stood the test of time. We keep getting damn invasive's from Asia from fish, bugs, plants, etc. They wreak havoc on native species and humans. We have stink bugs that are terrible that just appeared en-mass one year and they have been prolific ever since.

At least there is always money to be made taming these new invaders and the person who does actually does good for their community/country and not make $$ of others misfortune, addiction, ignorance, etc. It also spurs deeper learning and understanding of many subjects if you have to learn how to battle these invaders. Just thought I'd throw that out there cuz it helps if you can at least see a little light in a dark subject.

[Edited on 2-13-2018 by RogueRose]

[Edited on 2-13-2018 by RogueRose]
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[*] posted on 13-2-2018 at 11:01


Quote: Originally posted by RogueRose  
... I know very little on this, but I figure any info may lead to something.

I know nothing at all, apart from that if there are no Ideas, nothing new can happen.

The bit about 309 species found infected yet resistant is very good news.

It might be as easy as planting swathes of those species around olive groves to 'deter' the buggers.

Thanks for coming up with ideas - someone looking for ideas might read this and have a light-bulb moment, and They might be in a position to take the idea further.




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[*] posted on 13-2-2018 at 11:35


I believe one of the most significant factors affecting these explosions of disease are warmer winters. Historically, the cold winters would kill off a substantial portion of the vectors. Now that more of them are surviving there is exponential growth of infestations like the bark beetle in Pacific Northwest timber.

Monoculture doesn't help. All you see in our area are vineyard after vineyard. While my family might be part of the problem, our vineyard is relatively small and we make an effort to farm sustainably and responsibly. Unfortunately it takes just one bad actor to start a chain reaction along the superhighway of crops with little genetic variation.
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[*] posted on 13-2-2018 at 11:39


Epidemiology, aside, I've been working with bacteriocins lately (antibacterial peptides produced by bacteria), and that brought me to a group isolating a lysogenic phage for Xylella spp.

Here's the grant report:

https://static.cdfa.ca.gov/PiercesDisease/proceedings/2008/2...

Iron uptake may be key to virulence in Xylella:

http://jb.asm.org/content/190/7/2368.full

"This suggests that iron sensing might be important in the early stages of plant colonization, to activate systems that allow efficient translocation throughout xylem vessels..."

And... that some isoform of colicin V can be made by certain strains. Given that these tend to be selective for related bacteria (the Xylella would be clearing its turf of other bacteria that would occupy its genetic niche), the expression of this bacteriocin in E. coli and use of the isolate as an antibacterial might have merit.

Colicin is a bacteriocin originally isolated from E. coli, hence the name.

This would be great, http://agris.fao.org/agris-search/search.do?recordID=US20130... , but the CDFA shit the bed and the .pdf link gets a 404.

The idea is given here (Colicin, although not exemplified via Xylella spp.):

https://pdfs.semanticscholar.org/3435/96bcfa8cb60f1275c89fbe...

And here (nisin + EDTA, the EDTA disrupts the peptidoglycan of gram negative bacteria allowing nisin to do its thing):

https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS.1998.82....

Nisin is produced by Lactococcus spp, lactis subsp. lactis, in particular.

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[*] posted on 13-2-2018 at 11:49


oo missed a word out! I meant killing it is not hard. If you look hard enough, even MRSA from a hospital is likely to have its very own phage. I think its Romania where at one point they used phage therapy alot.

The fabulous thing about phages is they are so host specific, this is also the down side. Sometimes still used in veterinary medicine.

Somewhere on the net is a video about it. From memory, the hospital in Romania had a open sewer outlet. The video is from the 1980's - 90s???

Anyway in the hospital, when someone got something like MRSA from the hospital, they would literally go fetch buckets of shite etc from the outflow. They would culture it against plates of the MRSA strain.

9 times out of 10 they hit on a phage, they would then isolate and culture the phage. This was mixed with water and sprayed about, also dressings were made and so on. The thing is the phage was deadly for that bacteria, a custom made highly specific killing machine.

It turns out most bacteria have a phage, the hard part can be finding the phage. But find a suitable phage and you have found a safe and highly effective method of dealing with the bacteria. You could treat and eat no problem.

So why are they not used more widely?? I think its the cost of finding and isolating, i dont really get the why, it isnt used more. To me its a no brain er, if someone has MRSA then go find the phage for it, but i think its not as simple as that.

Anyway, rather than chemicals i would go this kind of route, chemicals alter too many things. They are often too non specific, many bio controls have gone badly wrong in the past. I honestly think phages for something like this would work, and work well.

On a practical level, might be a good idea to start stocking up on clean olive cell cultures. Ok for a number of years things would be hard, but maybe slash and burn now to stop it. Good stocks of cells from the best trees, sounds awful but just maybe in the long run............

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[*] posted on 13-2-2018 at 13:08


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.




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[*] posted on 13-2-2018 at 20:35


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 :D.

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]
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[*] posted on 13-2-2018 at 21:54


"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.
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[*] posted on 14-2-2018 at 00:19


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.
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[*] posted on 14-2-2018 at 02:03


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.


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.
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[*] posted on 14-2-2018 at 06:51


I'm not sure about that, at least with the almond trees around here.

They are one of the few cash-plants that grow without water or maintenance - olive, prickly pear, almond and moscatel grape.

Oh, and Weeds - they grow really well with without any help at all.




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[*] posted on 14-2-2018 at 07:14


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]




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[*] posted on 14-2-2018 at 09:08


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.


Unfortunately, the anti-almond rhetoric doesn't put water use into proper context. Off the top of my head, if you look at water usage in terms of calories/nutrition provided per gallon of water used then at about 20 gallons per ounce, almonds rank right around asparagus and soy products. Chickpeas and lentils use over 70 gallons per ounce. Cattle farming consumes over 100 gallons per ounce. Also consider that 2 out of every 3 almonds in the world are grown in California, with the vast majority being exported - that's a lot of money. Perhaps even enough money to generate an agenda that might prompt a certain series of Mother Jones articles...
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[*] posted on 14-2-2018 at 12:07


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]


In an ideal world you would carry the pahge in on the vector. Short shelf life!

Effectively you are infecting every tree, but as you say the population should crash extremely fast, much faster than damage beyond repair.

The main issue is would the rna then be washed out over time? If not then you have a tree full of phage rna waiting for the bacteria to show up. As soon as it did again, then bang population crash of the bacteria and so on.

I have seen the description you give for cultures. Without the ability to screen for rna/DNA you left head scratching, but i have always thought every bacteria must have a phage associated with it.

Screening for the first batch of phages would be the problem. Its an area I would love to do work in, but its at the really spendy end of technology lol.

I am sure other more harmless bacteria could be adapted to be suitable hosts for the phage. I wouldnt mind a look at those papers.
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[*] posted on 15-2-2018 at 05:07


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...

crop water useLARGE.jpg - 151kB

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.
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Bert
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15-2-2018 at 06:54
mayko
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[*] posted on 16-2-2018 at 11:02


Coincidentally, we read an article about phage therapy at this week's journal club. This looked at the screening and directed evolution of bacteriophages targeting multidrug resistant P. aeruginosa. This bacterium survives by upregulating the expression of molecular pumps on its surface, which kick poisons out of the cell. The virus identified here exploits these pumps to gain access to the bacterial cyctoplasm, meaning that challenging the pathogens with chemical antibiotics and bacteriophages simultaneously creates an evolutionary dilemma: adaptation to the virus increases susceptibility to the antibiotic, and vice versa. Cool stuff!

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