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The Corroboree

Darklight

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Posts posted by Darklight


  1.  

    I agree with Darklight's comment "The exxy bit is getting the sequence data analysed by someone who knows what they're doing."

     

    This is ongoing for Lophophora right now so I can greatly appreciate what that means.


     

     

    OMG omg omg Trucha, and thanks for sharing this. So excited you're doing this from scratch

     

    What trucha is describing folks is the current gold standard for starting from scratch. Whole genome sequencing analysis. Then comes the development of marker sets. Two separate processes. There is a lot of overlap in common parlance, and even some scientists will take the linguistic shortcut.

     

    There is a surprising degree of capriciousness within this picture so a disturbing part of what has been published is really no more solid than a house of cards. The bar really needs to be raised a notch imho.

     

    Yep that blew me out. I was looking at whole genome sequencing of Ganoderma in 2014, talking to a couple of genetics post-docs and aside from the initial expense I was blown out that results can even differ depending on which brand machine you use. There is no one-size-fits-all standard, or wasn't at the time. And the blinkenlights machines are exxy and are superseded every few years. Whole genome sequencing is frequently outsourced even in mid-size facilities where the exxy toys of +5 years ago aren't up for replacement and yet almost obsolete

    • Like 2

  2.  

    A T section cutting is made by cutting a 4cm section of stem, around 2cm either side of a young shoot. The section could be layered using moist coir and course sand and wrapped with a stocking to allow easy watering. I'm not sure how long you would leave the layer cutting before checking if roots have formed. Once the roots have formed the cutting can be removed.

     

    Thank you! I had done a bit of googling and there were a number of teks suggested for the term so I got confused.

     

    Yours is a beautiful, clear answer and I'll be able to follow all that easily

     

    I don't want a million cuttings, just a couple of backups. Seymour is doing splendidly growing in the bathroom but I do like multiple copies just in case something happens to the original

    • Like 1

  3. Sent you the link to the sequencing place Change. It's not a state secret, but dealing with them does require a degree of technical knowledge

     

    CRISPR is for inserting and knocking out genes, not mutating them AFAIK. Happy to be corrected on this. Are you as technically up to speed on all this as you think you are?

     

    Mate, if you are in the Hunter and are playing with CRISPR you prolly want to be working out of a registered PC2 facility. Not sure about knockouts and OGTR, but unless you want to make ugly front page news I'd do a thorough OGTR legislation check and print out and keep the relevant documents next to you laminated in case of incursion.

     

    What you're proposing sounds like a PhD at the very least. More likely six PhDs.

     

    • Like 2

  4. Another example is drought tolerance within a species.
     

    It may be known, for example, that the presence of certain genetic markers in that species has a high correlation with drought tolerance.

     

    You can use those markers to screen a large population of that species, and select individuals to test for drought tolerance to breed from

     

    etc


  5.  

    The exxy bit is getting the sequence data analysed by someone who knows what they're doing. I know a few such people socially and once they started to explain the process to me my head assploded.

     

     

    I was wrong. There are places in .au which will extract your DNA and run all kinds of cool tests for about $100. They can give you results in spreadsheet form which are easily understood by people with minimal experience. They can provide more help for more cost.

     

    The problem is that you need  genetic *markers* for whatever it is you are seeking. These are similar to the controls you run in any experimental setup.

     

    You need specific markers for your specific test. And if these markers don't already exist on some database, you need to develop them, and that's the exxy part.

     

    For example, if you need to determine whether your Acacia is species x or species y, you will need the genetic markers for one or both of those species, so you can tell whether your sample fits the profile. If there are no markers on public record, you will need to track down the part of the genetic code which is consistently different in either species. Apparently this can be a PITA, time consuming and exxy.

     

    However ( a separate example here ) if you need to determine whether your sample is a clone of Acacia x, or a seed grown individual, you will need different markers to those outlined in the example above. Again, if these markers do not exist on public record you will need to develop them.

     

    Plant species such as tobacco, rice, wheat, and that bloody tedious Arabidopsis thaliana have plenty of markers on record, often available to the public. Is less likely that your obscure ethnobotanicals will have such records on them. There are places to check, but no idea where to find them. One place to start looking is formal published genetics studies on your species of interest. Another are the databases.

     

    Got some sequencing done recently for a common species, there were markers on public record for it. All up the bill was cheap, with supplied analytical spreadsheet.

     

     

    • Like 5

  6. Am a huge fan of commercial Trichoderma spp blends as a liquid fertiliser addition to my home garden.

     

    The commercial products are usually sold as dry powders- spore mixes treated for storage.

     

    I have run right out of these and need some soon. I have Trichoderma spp cultures in my library, and I can easily do liquid cultures based on my standard fertiliser blend.

     

    Would the shock of throwing a growing but otherwise sterile culture, even at log phase, into the wild to compete with other organisms potentially any advantage?

     

    What sort of optical density of the LC Trichoderma would I need as a fertiliser base, to add as 10x, 100x or 1000x. Can I wing it or do I need to switch the spectrophotometer on?

     

    Anyone had any experience trying this?


  7. On 06/10/2016 at 11:00 AM, obtuse said:

    Today marks 10 years since i joined SAB, and i just want to say a very big thank you to the SAB community.

     

     

    Love you Ob, know how you feel. Was a gamechanger for me too, and I suspect for a few others as well.

     

    When T first spoke about starting it I gave it six months til SAB was shut down. I love being wrong sometimes :D

     

    As a result of serious drug education and discussion I find I take a startlingly large amount of less actual drugs- like about 99.9%, and have furthered my education and professional development. Back in the early days not a few of us went on to study science or continue other studies inspired by what we learned here. A side effect I had not considered at all. Whoda thunk?

    • Like 4

  8. My eyesight's not what it used to be, if that isn't a carpet snake in your blogpress pic, and it's night time, it's a night tiger/ brown tree snake ( Boiga irregularis )

     

    http://reptilesofaustralia.com/snakes/colubrids/birregularis.htm

     

    Scale colour and underside colour can really vary in the same species between locations. I had a night tiger turn up in the kitchen at midnight a few years back which looked so close to a black snake- uniformly deep chocolate colour top scales and crimson belly ( red belly blacks have a pale belly and the red bits can only be seen from the side- I know that now ).

     

    A mate who is a snake catcher came down and told me that locally 3 key ID points were

     

    • They turn up at night
    • Prefer not to be on the ground
    • Have the characteristic 'doll's eye' whiter marking behind their eyes

    Minimally toxic and maximally cruisey snakes, they're pretty shy

     

    There's snake people round on the forums and locally who would know all this way better than me and who could give you more info

    • Like 2

  9. 3 hours ago, niggles said:

     I was thinking of SES but maybe fire would be good. My skills are more medical but the whole idea would be to learn new stuff (and help)

     

    Medical certs + experience will be welcome pretty much anywhere, and either SES or RFS is a good place to start volunteering

     

    There's plenty of places to volunteer up here, people are really appreciative of the help too


  10. Also: this on general n00b rural advice:

     

    Water, fences, fire-proofing, wind breaks, and access roads

     

    There's a fair whack of basic info to tick off against your just-arrived checklist. You've prolly done most of it already. Apologies if it teaches you to suck eggs

     

    Right *now* one of the first things you should address is fire ( because the season can come on fast, sometimes even within a week here and it's permit season already ), then access ( including turning space and unloading area ), or maybe water security. Then fences and windbreaks.

     

    About the smartest thing you can do first time you move out from the city to a new bush spot is make yourself known to the local RFS/ CFA. It's signalling to the locals that yes, you are new to the bush, but no, you are not a complete dickhead, and are willing to at least listen to what they say about your place and your plans.

     

    As the fire season progresses. and if it ramps up, it may become harder to find time to chat randomly with the firies because they may be busy here or out of area.

     

    Find out who your local RFS is, and when they meet ( usually monthly ). Get there a bit early, find the captain or a deputy, and explain why you're there. They may have time to talk right then, or they may allocate a time and meet you somewhere else. Usually they will love you to bits for this because you are one less clueless person they will have to visit at dinner time unless invited.

     

    They will usually know about fire ( and other ) history in your area, fire behaviour on your property, things you can do to help lessen the damage if there is a fire at yours or close by. And things not to do ( like burn off on total fire ban days- you might not start an actual bush fire but if the firies get an "I see smoke..." phone call at least one very pissed off person will show up. No. We do not get paid. )

     

    It's also excellent networking. Yes, there are the usual cohorts of arseholes and rednecks you find everywhere. Many of these are also lovely and you will come to learn that even though there are many diverging attitudes out here, no-one gives a fuck about that when there is an emergency. Almost all the people there will be well networked and resourceful and usually even capable. They can and prolly will do a zillion things to help you settle in ( and reduce their workload in the process )

     

    Joining these days takes time and a bazzillion police/ security checks as well as some pretty stupid worksafe checks ( please indicate the nearest exit... etc ) and the process is complete bullshit. This is not our fault, not at the pointy end, except we should def have complained more and louder when the shiny arses started making micromanaged demands on our time and attention ah shit... excuse me.

     

    But yeah, for a rural n00b I'd recommend going to at least one meeting to introduce yourself- it shows good will and good taste. You will probably learn some useful history of your place which will be unbelievably relevant to planning on your site ( drainage/ access/ all sorts of obscure but really useful shit ). And I'd maybe even recommend doing the Basics training. At least kick in for a sausage sanger at the Xmas party and chuck in for the raffle :D

     

    Bookmark this: FIRES NEAR ME

     

    And use it any time you see smoke rising which worries you. It's a map app which will show you where firies are already responding- useful if you see smoke but can't determine source or direction. Download the app and add it to your phone too if you can. It's not always up to date to the very minute, but it's good to check before ringing and reporting fires which may already be under control or not of concern

     

    Also: if you are in or around Nimbin, join either the FB Nimbin Hook Ups or the related FB discussion board. Mostly full of shit, but handy, and the occasional gem

     

     

     

    • Like 4

  11. 14 hours ago, Halcyon Daze said:

    Don't burn all those bamboo sticks mate, You'll wish you kept them. They are soooo useful. I often cut them and store them until I find a use for them. Trim the side branches off but leave the first section still attached, those little 1 inch bits sticking out are very useful for tying them together or letting a vine climb it etc.

     

    Bamboo sticks are ridiculously expensive at bunnings these days.

     

    Keep them if they're the type which store well. Most bamboo spp are known for their use profile and some store/ weather better than others

     

    I put down a clumping variety which was claimed to be good for outdoor building. 20 years later it's heaps big, but I couldn't work out how anyone would use it for scaffolding like they do on some Asian sites. Local bamboo expert told me it was the wrong type and is an indoor bamboo, best for veneer, needs varnish even for that.

     

    Mine lasts outside about 6 months before it falls apart. Great for staking and tripods ( re-use the U-nails and hay bale string, saves a trip to Bunnings ) but shit for the furniture and construction stuff I wanted.

     

    Anyone got experience with an easy, sustainable way to treat bamboo for storage? Like, actual experience, not just web links?

     

    ( OMG I have turned into the old lady who saves string, kill me now... )

    • Like 3

  12. On 30/07/2016 at 7:15 PM, waterboy 2.0 said:

    https://source.wustl.edu/2016/06/genetically-modified-golden-rice-falls-short-lifesaving-promises/

     

    Theory is one thing....practice is another... and since I've recently seen "golden" rice held up as an actual beneficial thing right now....

     

     

    Nice one WB <3

     

    The GM debate has me frothing at the mouth. Always has. CRISPR has just added new dimensions to the froth.

     

    Protip: I've worked in GM at a registered facility. No plants were ever released into the outdoors on my projects. My views there were pretty well known, but I'm familiar with the finer points of the technology as it was used up until CRISPR came in.

     

    tl:dr: The GM debate is a classic example of fucked up politics. The public is lazy, and wants a bunch of sexy lab coated people to solve their problems for them.

     

    We've had some very workable solutions to world hunger for years. Don't be a cunt. Share your things. Stop breeding like idiots.

     

    But no, none of those debates have happened- and the elephant in the room is the question of overpopulation. It's a subject no government or religious organisation will sanction realistic discussions around. The debate has been, yet again, reduced to "Science will solve it".

     

    One of my former supervisors- who was a very rare and remarkable individual in that he was a brilliant scientist and manager and a general sterling human being, once asked me how we were supposed to feed the increasing number of people on the planet without GM.

     

    My response was that we have been tinkering with GM for nearly 40 years and it still isn't sufficiently functional to replace conventional agricultural output. In that time frame, all the money thrown at GM could have achieved quite dramatic results if it had been shuttled towards dealing with overpopulation and mis-allocation of economic and food resources. Those years are now lost to us. In that time the population has increased to stupid, and shows no signs of slowing.

     

    There are many aspects of GM I have no problem with. Vat grown medicinal compounds which would otherwise be expensive or prohibitively complex to acquire- totally in favour of those. There are other examples.

     

    Up until CRISPR I believed no viable replicable GM cells should leave the lab. All potentially replicable GM crops should contain non-viable pollen and/ or Terminator genetics. It hasn't been a popular position, but situations of crop contamination from GM pollen should not be possible, and horizontal transfer of artificial genetic material via bacteria should not be allowed.

     

    Now we have CRISPR, and we're going to get ag GM in sideways fast, because nobody is going to say to little Janey or Tommy's mum that the cure to their child's crippling and possibly fatal genetic disease can't be dispensed to them because GM. CRISPR human trials are very much a thing- the public are going to increasingly accept- and rely- on GM tech. The discussion about possible inheritance of human CRISPR modifications won't happen, because blah blah nobody wants to talk about overpopulation. Thus agricultural GM- and industrial GM can wait quietly in the wings until the public is ready for that too. And isn't science great? So shiny.

     

    I am a total fan. But not for the reasons and the circumstances and ethical climate which we are exist. Also: if you give scientists shiny toys, we will want to play with them. Historically, by the time we have worked out whether or not they're any good, or even safe to give out, some PR droid has sent out a bunch of glossy press releases and the public CBF with the ethical debate the lab crews have worked up.

     

    The future will not be evenly distributed. Someone said that a while ago, and it holds true. Just because you can imagine problems being solved doesn't mean the solution won't be hijacked, confiscated, taken out of reach, or used for fucked. So yes, CRISPR and GM offer potential solutions, but who's going to be holding them out to whom? Is the media brouhaha about CRISPR and rare genetic disorders going to generate billions of dollars to solve the problems of a few rich people at the expense of solutions to existing problems which will benefit more people?

     

    Save your seeds people. And buy from those who will. It's not 100% guarantee against famine, or starvation of people in countries you've never been to. But neither is locking your windows and doors 100% proof against burglary. It's just a good idea.

     

    Interesting anecdote: A couple of mates who work in international aid programs were told by a village of subsistence farmers in the tropics that they were going back to their traditional varieties of rice, because it only took a small handful of their local rice to feed each person a day. Their local species was substantially more filling at each meal and thus they required less room to grow more rice. They also complained that the rice on offer from the major seed company in the area was prone to disease. So they learned, or re-learned how to save their own seed.

     

    It only takes a generation to lose these skills, and they are gone.

     

    Apologies for the randomness of my response, the larger GM debate is a sleight of hand and renders me incoherent.

     

     

     

    • Like 4

  13. On 16/07/2016 at 4:39 PM, darkzen15 said:

     I have noticed weeds and plants blooming that normally bloom in spring blooming in mid winter and I have noticed flies and butterflies that are normally dormant till spring appearing in little bursts every few weeks or so.

     

    Has anyone else around the world noticed this or am I just over analysing?

     

    Extrapolating from insufficient data perhaps? Doesn't mean you are wrong

     

    I've lived in the one place nearly 30 years, and early bud- break for many Spring blooming plants has been absolutely a feature of most winters- I first noted it over 25 years ago when working pruning stonefruit.

     

    Early blooming isn't regarded well in most orchards as there is a good chance a later frost will knock the blossom off, the plants will have to use their reserves to re-flower and the crop will yield slightly less.

     

    What I have noticed is that over the last 20 or so years I have been using progressively less firewood to keep warm in winter. That could be for a number of reasons- increasing tree cover round the house is reducing both heat loss and the flow of cold air down the hill to the house, I don't go out til 3am as often and don't work in orchards at 6am any more, and have switched to mostly car driving in the last 5 years, I'm single right now so roaming round the house looking like a complete dag isn't an issue, and I'm not as big a sook as I was when i first moved here. Etc.

     

    But yeah, I do believe anthropic generated climate change is a real thing. However if HAARP turns out to be an actual working thing right now I will grind up and eat my crash helmet.

    • Like 2

  14. The tl;dr version of this is:

     

    Why are you concentrating on macrofungi so early on?

     

    Personally I'd monitor your control area soil micro-organism health and contaminant levels vs your rehab patches at +0 days baseline.

     

    Then throw some micro-organisms onto different patches. Recheck at different time points. Take photos, notice any vegetation changes in transect grids.

     

    Soil Food Web people at http://soilfoodweb.com.au can assist with monitoring, tho their focus is largely agricultural. Their analysis should give you some good ideas as to what's missing.

     

    Contaminant monitoring can be done at EAL Lismore for a reasonable cost. http://scu.edu.au/eal/

     

    Nutri-tech have some cool micro-organism products, if it's specifically native regen you're looking at you might be able to talk with their technical team. If you have baseline readings for soild diversity and contam levels they will have a better idea of what they're addressing  http://www.nutri-tech.com.au

     

    A blend of micro-organisms is more likely to be adaptable than a single macrofungus- they will self select. Macro species can be added alongside, at any time point.

     

    Fruiting macrofungus of various species are a good environmental health indicator overall. But they are notoriously unreliable in their appearance and you'd be wanting data taken over years IMO

     

     

    • Like 5

  15. Cool project :)

     

    1 hour ago, shortly said:

    I am posting this in the hope of receiving feedback, comments or any input really.

     

    Ok so a little background. I am in the process of rehabilitating a site in Seq that has been logged & flogged for decades,

     

    So, to the project. I'm thinking if i select a number of likely candidates starting with Lepista sp. Agaricus spp. Calvatia sp, Ganoderma sp. from locations where glyphosate has been regularly used & breed from these individuals. If each subsequent generation is fed a media with slightly higher glyphosate concentrations. What is the likelihood that i will either breed either glyphosate resistant mushrooms? Or mushrooms that can

    metabolize the glyphosate and actively seek it out?

     

    What level of detail are you looking at wrt glyphosate monitoring? Are you doing actual chem analysis? Or looking at results on petries and extrapolating?

     

    Yes, selective transfers up a concentration gradient over time could give you what you are looking for on a macro level wrt a single compound, but they may not play out so well when competing with other organisms ex vitro.

     

    Quote

    The site appears to have relatively few fungi compared to other sites with similar habitats nearby. So we have been

    (re)introducing a variety of fungi from the local area to each patch as we go with mixed results.

     

     

    How are you determining results? How long has your rehab project been running? If you're determining results from visible fruiting over one or two seasons only, or in comparison to uncontaminated control areas over a year or two only you'll get very different results than if you were, say, monitoring for fungal colonisation of your target species in inoculated mulch.

     

    Are you running several patches, each with different treatments, against an uncontaminated control patch? Are you monitoring for an increased fungal diversity overall as a measure of rehab success?

     

    Determining which measurements accurately reflects the results you're chasing is best established early on.

     

    Apologies for sounding brusque, I get like that when something catches my attention :) PM'd you.

    • Like 2

  16. On 02/06/2016 at 3:18 PM, Anodyne said:

    dood, I think it's Nutri Tech Solutions (?)

     

    You're right, them. The tech dept was really nice when I had to contact them about stuff a few years back


  17. On 27/05/2016 at 4:30 AM, Ethnotramp said:

    Just curious as to whether anyone out there has any experience with this fungus? It is easily grown on various substrates (YM, PDA, PDY)  and forms  mutualistic symbiotic relationships with a wide variety of plants. It is reported to increase disease resistance, salt tolerance, drought tolerance, and phosphorus uptake. It cant help but feel this could be of interest to a lot of people here, but have seen no mention of it?  I have found cultures for sale only at ATCC.org for $354.00 US for an ampoule.  I want to get my hands on a culture, but at that price I'll be wanting for quite a while.:) If this fungus is as great as they claim, I would love to see this shared around with members of this great site:lol: and benefit all our growing endeavors.

     

     

    Tricho growers unite!

     

    I'm lazy, but is it available in Australia or found in Australia?

     

    ATCC is a pain to buy from, you need an account with the Australian distributors. A quarantine permit is usually compulsory, the distributors arrange it. It's a few weeks of hassle- longer if Biosecurity can't get their heads around it ( even if it has been previously imported )

     

    Try local vendors like Nutra-Life ( or whatever their name is these days ) and similar outlets. Email them and ask if it isn't in their catalogue.

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