Testing, Identification and Removal Of Pathogens HLV / HSV etc

[englishrick]

Hay guys,,,I just wanted to start a thread on this subject and get into the advanced aspects of this Hops Latent Viroid and Hops Stunt Viroid issue,,,

I was also wondering what other pathogens might be lurking in some of your growrooms and how wide spread they are nowadays

I have been relying on apical meristem culture techniques, pathogen inhibition and a hardcore initiation phase to save the day, I'm just wondering what you guys have done to tackle this issue besides kill off your plants,

Il explain my methods for pathogen inhibition and hardcore initiation as we get into it,,

Firstly I wanted to talk about testing apparatus, testing Reagents,,field equipment and the company's providing such essential materials,,,

What fo you think of this ""basic"" field test kit

https://mhverify.com/

 

[englishrick]

Emerging diseases of Cannabis sativa and sustainable management



https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8451794/#!po=4.50820

 

[englishrick]

Does anyone have any thoughts on using CO3 to clean indoor grow areas between cycles??

 

[therevverend]

It's strange how things work out, a few years ago everyone was freaked out about tobacco mosaic virus. Worried that even smoking tobacco could spread the disease. (turns out tobacco burns hot enough to kill the stuff but you maybe want to be careful handling tobacco then handling your plants) Turns out to be almost no cases compared to these hop viruses that 'hop' easily over to cannabis. I wonder if anyone stopped drinking beer in their garden? It's not surprising since hops and ganja are so closely related. I'm an outdoor grower and don't usually take clones from other growers so I don't worry much about it. Although I do have a hop vine in the garden. I don't know anything about testing but that kit is expensive enough it better work. Of course if you're running a big commercial grow you'd better be sure you don't have it.

Tomato spotted wilt caught my eye as well. It's not in my area, yet, but I don't need it. My plants always end up a thrip playground with no damage and I grow tomatoes so I'm going to be watching the spread.

Does anyone have any thoughts on using CO3 to clean indoor grow areas between cycles??

A buddy of mine uses CO2 to kill pests in his room. During any point in the cycle. Fills the room with the gas, waits 10 minutes, then cycles it out. (carefully) He says he's eliminated every pest that requires oxygen to breathe.

 

[englishrick]

I'm wondering if anyone here on icmag has tried using any PCR test kits for cannabis?? It's a really new style to be PCR testing your inbound clones like the thing might have Covid19

 

[f-e]

$40 a test isn't going to break the bank. It's having to buy 24 at $900 that stops me. That's not going to appeal to a home grower. They need to offer 'singles' to prove to people they have some worth. Not just a cost.

 

[englishrick]

I'd happily pay for them if I knew they were reliable!!! ,,,

do any of you guys think this kit is not functioning properly?, ,,,

forget the money for a second,,,is the test doing its job properly or is it just crap??

 

[f-e]

As the first kit on the market, it will be a scam in some sense. As long as it's real, the price will come down though. It looks like a bit of kit is provided that won't need replacing, so future tests are more like refills. You know lab kit. That box will be little more than a test tube stand and cost 800 of the 900$

 

[dramamine]

Emerging diseases of Cannabis sativa and sustainable management



https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8451794/#!po=4.50820

That's a really good one. Thanks Rick.

 

[f-e]

Similar looking thing here, but you can buy 5 https://orders.agdia.com/agdia-immunostrip-for-tmv-isk-57400

A search for tobamoviruses field tests produces quite a few results.

Looking at these viruses detected, they all seem to produce very pronounced symptoms. I can't imagine a plant could sit in quarantine for long without showing.

 

[TPFTFW]

I’ll have to find the company but there’s one that offers tests for 20$ a pop sending tissue samps in

 

[Rico Swazi]

New!

A Long-Amplicon Viability-qPCR Test for Quantifying Living Pathogens that Cause Bacterial Spot in Tomato Seed

A Long-Amplicon Viability-qPCR Test for Quantifying Living Pathogens that Cause Bacterial Spot in Tomato Seed - PubMed

Bacterial spot is one of the most serious diseases of tomato. It is caused by four species of <i>Xanthomonas: X. euvesicatoria</i>, <i>X. gardneri</i>, <i>X. perforans</i>, and <i>X. vesicatoria</i>. Contaminated or infected seed can be a major source of inoculum for this disease. The use of...

pubmed.ncbi.nlm.nih.gov

showing what is out there . Not an endorsement but the company has it all it seems.
Scroll down to see the various applications.

Real-Time PCR | Thermo Fisher Scientific - CA

Explore easy-to-use, application-specific real-time PCR solutions with optimized assays & reagents, advanced instruments, and robust training & support.

www.thermofisher.com

Great thread Rick!

 

[GMT]

I'm assuming that viral issues are ones of contagion rather than inheritance? Correct me there if I'm wrong please.

 

[Rico Swazi]

Glad you are here GMT. Appreciate your knowledge. Was a lurker years back when rick did his perfect state thread.
think he is on to something today with qPCR testing for not only viral but genetic stability which garners my interest
What are your thoughts on retrotransposons ? Seems they are the unseen mechanism of plant function and health

Gonna throw out a crazy thought-
is it possible to re-engineer free covid tests with different reagents to use in horticulture ?
tonne of them going unused

 

[GMT]

First, thanks for the compliment. Unfortunately, you are a month too early with this question for me. I'm about to start some personal research into elements of RNA concentrating on mRNA. I only recently realised how little I know about this subject, (often the way with stuff we don't know).
Transponsons and retrotransponsons, at first sight, do seem very scary, although that fact alone seems to excite biologists.
By profession, I'm an accountant, this is stuff I learn for fun. So there are huge holes in my knowledge base. You would be much better asking either @zif or @djonkoman about this. I'll come back and learn and pop an opinion or two in once I've got a grip on the subject.
Interesting topic though, since over a third of human DNA seems to have been made this way.

If someone has the biochemistry knowledge to create tests of that sort, they would do it from scratch rather than re-engineer what's out there now. It would be like deciding to write space invaders software by reverse engineering a chess program. Just more work than is necessary. Besides, there are lots of companies that will do it for you for a fraction of the price and time it would take a lone wolf.

I'll keep an eye on the thread, and hopefully someone will answer their bat signal I shone above.

 

[Rico Swazi]

Appreciate your knowledge and the humility brother. Accountant eh? counting beans has a different meaning these days I bet. lol. Was a machinist/fabricator in past life but now fill my days with research which exercises the mind and gardening which keeps the body physically entertained. Ongoing prostate and skin cancer makes me thirsty for knowledge on how DNA things go wonky and perhaps answer the question why me. Research on mRNA and retrotransposons has been top of the learning list for a few years now

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

Retrotransposons constitute a major source of genetic variation, and somatic retrotransposon insertions have been reported in cancer. Here, we applied TranspoSeq, a computational framework that identifies retrotransposon insertions from sequencing data, ...

www.ncbi.nlm.nih.gov

Retrotransposons are genomic elements that mobilize via an RNA intermediate in a copy-and-paste mechanism across the genome. Regarded as “drivers of genome evolution,” retrotransposons comprise nearly half of the human genome and are important vehicles of genomic diversity

Plants and animals are linked more closely than I ever imagined by those “drivers of genome evolution,” but not wanting to go too far off topic I want to say I am excited at the prospect of addressing the issue of dudding, viral load and other factors negatively affecting our beloved cannabis plant. The answers are there if we ask the right questions of who does what where and when. Would be a shame for all those free PCR tests go unused after we paid for them. Locked in a warehouse then into the garbage dump is the 'merican way don't ya know.

Lovin the bat signals and other perks with the new software. I'll admit with as much time as I spend thinkin about things, I fail to ask the right questions.

Looking forward to be standing on some shoulders so that I may see more clearly.

 

[GMT]

It seems it takes a hardship to force most to look beyond the normal scenery of life. I have a genetic immune condition that drives a lot of my research. Sorry to hear about your driving factors.
Hopefully we'll both get the chance to learn a bit more in this thread.

 

[djonkoman]

I wouldn't count on using covid tests for anything else.

the way that you show the presence of something with pcr is dependent on primers. these primers are little stretches of dna (~15-20 basepairs), which are designed such that they will only match the gene you are interested in. (you can design them basically anywhere btw, so you could capture the entire gene between your primers, or just a small part of the gene, or you could also target regions outside genes)
so, then these primers will stick to the dna at this specific spot that you designed them for (if you're unlucky, they'll stick at other places too, and you'll not get good results, but that's part of designing oood primers). and then after these primers are there the region in between the primers (you always have a reverse and a forward primer) gets amplified.

this amplification of something you can then eventually detect.
so if whatever gene you are interested in is not present> primers don't stick>no amplification>nothing to detect.

so, covid pcr tests will be using specific primers for that purpose

I also expect the sample for a covid test will have to go through another step, because it's rna. pcr works on dna. if you start off with rna, you first turn this rna into dna, and then do the pcr on the dna you made.

I think they actually use 3 different sets of primers for covid tests btw, as a backup. it was a lot in the news wth the 'S-dropout' that showed omicron. with omicron the specific spot where the primers targeting the spike gene (one of the 3 genes they test for) were suppodsed to stuck to was mutated so much that the primers wouldn't stick anymore. so you get results where the other 2 genes showed a positive but there was a negative for the spike gene.

regarding transposons, they're a cool mechanism, but I think you shouldn't focus too much on it as the sole/primary mechanism for evolution. transposons are just one of the ways in which mutations happen.
I think the mechanism to keep transposons suppressed during the growth of a new seed are really cool though (involves epigenetics)

btw, also bit offtopic, but you can do really crazy stuff with pcr. edna (environmental dna) is now a big thing with ecologists, and it's really amazing.

for example, this case I heard about where other people in a lab I worked at where working on: where they took the washwater from an apple growery (after harvest all the apples go through a big water bath) to run tests on. around these apple trees live bats. bats eat insects and shit. some of the shit ends up on the apples. this tiny bit of shit ends up in the washwater, but majorly diluted. then, but doing pcr on this water you can find out which insects were in the diet of the bat, and thus which pest insects are present among your apple trees.