Jump to content
The Corroboree

Tripyamine

Members2
  • Content count

    127
  • Joined

  • Last visited

Seller statistics

  • 0
  • 0
  • 0

About Tripyamine

  • Rank
    Psychonaut

Profile Information

  • Country
    OZ

Previous Fields

  • Climate or location
    Tropical and Humid

Recent Profile Visitors

1,010 profile views
  1. Not much has really changed in the space, Illumina has a bigger machine and nanopore has released some new flow cells that are making Illumina and Pacbio quiver a bit methinks. I did a few algae genomes last year for $2k with nanopore kit, it's still a bit of a pain in Australia because there are no distributors so you need a specific Bicon permit and the shipping is killer. But long reads are amazing, just not accurate enough but great for resolving repeat sections in genomes, Illumina is still kinda unavoidable. SDN-1 is kinda funny, it has to be markerless to start with. From what I understand its no plasmid and no DNA. That means you need ribonucleoproteins ie the pure cas9 protein and a pure guide RNA that will randomly perform insertion or deletion and you don't even really know how many bases will get removed or inserted because it depends on what repair mechanisms are available in the organism you want to transform. This gets really tricky because you have only really one option, you have to fuck with a gene that will allow you to select a line that has your SDN-1 as well, this means it probably won't have it and just your selection in/del will be present. So there is still a lot of parallel replicates needed in order to get a line with what you actually want. You cant insert a gene, you can only remove its function or slightly modifies it. And yeah @Darklight the hardest thing about nanopore and Pacbio is the extraction, you need ultra-pure and unsheared DNA if you want to get long reads and the most out of your flowcell. Kinda funny but, there is a legend from ANU that has made a group on a website called protocols.io that has customized extractions people have perfected for heaps of different tissue. It took me the better part of 4 months to get my extractions clean and big/unsheared enough to run, I had to make up a whole custom protocol. Database access is still amazing, bioinformatics is mostly opensource still, between GitHub/NCBI/jgi/ebi basically everything is there, not everybody does it but you should put your raw data on the sequencing read archive (SRA) at the NCBI. So you can go on SRA make an account and reassemble peoples work with newer/better techniques/use it to beef your own sequencing up. Something I have been doing a lot of is metagenomics, which is heaps of fun. Take a sample with a complex mixture of organisms and sequence everything and see what's in the pool. Its a really cool diagnostic tool for anything from gut microbes to algae in a creek. I think Metagenomics is something lots of you guys might be interested in because its a way to look for pathogens (bacteria/fungi/virus/etc) with plants and is starting to get really approachable price-wise. I can do a 16/18s run on Illumina for ~$80 (but that's just prok/euk) and if you want to look at everything you just extract DNA and run it on a nanopore and blast as your sequencing, start to see everything in realtime which is cool for viruses and weird stuff.
  2. Ok so PVA is a carbon source, plenty of things can grow off it as their primary carbon or even sole carbon source I guess the thing is what else is available and is there nitrogen and phosphate to facilitate things to grow/a bit of other stuff to satisfy any auxotrophy? I'm sure if you put some yeast extract or a rich nutrient source like molasses or malt then it would degrade much faster. Also if you oxygenate the solution then there is gonna be way more activity so movement definitely helps, ferments happen way slower without O2 unless anaerobic PLA - polylactic acid and PHA - polyhydroxy alkanoates Are both organic/biodegradable plastics eventually bugs will eat them, at around the same kinda rate as PVA, in fact in water treatment you can have massive columns of prills of these plastics and biofilms will form over them and deplete water of N and P, these are pretty common in marine aquariums. Here is a paper with some nice graphs, https://www.researchgate.net/publication/259284154_An_Efficient_Biotreatment_Process_for_Polyvinyl_Alcohol_Containing_Textile_Wastewater
  3. Tripyamine

    All good

    Went a different route, feel free to delete
  4. Tripyamine

    Trich Eileen (90% sure on genetics) tips for sale.

    PM'd keen as a bean
  5. oh lordy, moving around fastq files is a right pain thank the lord for nectar and aarnet filestore Beijing genomics institute just/is opening up in aus so sequencing might get a little cheaper here. At the moment its costing me about 3k to do the sequencing on say 12 different "things". I do transcriptomics so for me its 6 different treatments of a yeast and a replicate. Im a bit lucky and we have the illumina, iontorrent and pacbio rigs in the lab upstairs so its just the painstaking mRNA extraction and then library prep but, at that point it gets given to a tech and the magic happens. My research group (if its important) doesn't have to pay for sequencing, however, we have to pay for the kits and the flow cell for the machine so thats what the 3k is. Im lucky and can handle most of the bioinformatics myself so no need to pay for any of that which can get very exxy and ive seen it too many times in the past that they just flat out balls up the analysis and you get bad results, that should be fine but nobody ever double checks because they are 20gb and take a day to crunch at the least. It should be interesting to see how pacbio and nanopore drop the price, I cant wait to run something on a pacbio2 long reads is where its at for large plant genomes so much repeat that make it cooked to assemble.
  6. Tripyamine

    Ginger beer plant culture

    Yerh I've isolated my own but I'm really looking for an old culture that's been going for a long time I know a few people have em in aus
  7. Tripyamine

    Ginger beer plant culture

    Hi peeps Wanting to try brew some slick drinks up and am looking for a starter culture of ginger beer plant! I found cultures alive but no stock :/ Send me a PM maby I have something cool you may want! Willing to cover postage of course!
  8. shotgun assembly is shit...... (ie putting a genome together usually gigabases together from 150base reads) As darklight said it costs a lot to build a decent scaffold and get the contigs (long linear DNA) to a small number (closer to the number of chromosomes the better.) Usually you start with a transcriptome (mRNA) to get a feel for expression and whats going on Sometimes mitochondrial or chloroplast genome sequencing is a better idea. You don't really need to have the whole genome, the paper mu! posted is not whole genome sequencing it is plastid or plastome sequencing which is just little dsDNA circles that provied sub functions in the cell like cpDNA (chloroplast) (which is a type of plastid) This avoids the need do assembly as the short reads can be stitched together from previous assemblies (scaffolding) and its not that huge so you can run a few plastomes in parallel (how the paper got so many done) on the one illumina chip which is what the "cost" of sequencing is, other then the couple of 12hr+ days you need to do for library prep if you had a few plants you wanted done (10+) and someone who was good at not fucking pipetting up or contaminating PCR reactions then you could do all of the plastomes for the cost of one "sequencing event" or you could make a snpchip that did it for specific lineages (cactus might be possible), which is based off nucleotides in the dna that change from plant to plant but doesn't really mean much in terms of function
  9. Tripyamine

    LED grow lights...?

    Has anyone ever looked into Light emitting plasma? SOOOO SPENNO BUT
  10. Tripyamine

    LED grow lights...?

    And gas discharge has better peaks! Absolutely nothing wrong with Luxeon T mate (Or the arrays M and K) And seriously check out Bridgelux Vero COBs you will cream your pants, Drive them with LDD-1000's and you there
  11. Tripyamine

    LED grow lights...?

    The big thing with leds is their efficiency. for the most part a T5 fluro has about the same efficiency as chinese leds (epistar and the like) some are upwards of 100lu/watt - where epistar is around 85lu/watt (most t5's are 85lu/watt) If you want LEDs I think you are a fool not to get Phillips Luxeon M or L or K I really Like the K emitters some of these are 140lu/watt Im guessing most of you will use white from 3500k to 6500k for the most part COB's seem to be where it is at now and These little fuckers are the absolute ducks nuts http://www.bridgelux.com/products/vero-series 130lu/watt typical flux and they are in the best mounting package around! Kinda hard to get them in australia You might think I sound over the top here but really spending a little bit more at the start on good LED's will not only last years longer but will cost almost half to operate and put out the same amount of light, or really you should just buy a cheap dual T5 fixture on gumtree, I see 120cm fixtures all the time with ballasts for $5 and they always have hundreds from a job site or some shit Don't buy chinese LEDS they are shit and fluro tubes are better essential
  12. He's still waiting on the seed, be patient it's coming and worth it
  13. Ahhh kinda unrelated but good story none the less I was traveling in the philippines last year with my girlfriend and we were scuba diving around this little rock island a few km out from the mainland, we came back to the island for some lunch and to relax and we were eating some BBQ'd pork the guide had cooked for us while we were diving. Anyway my missus saw the guide feeding bits of pork to some of the little local puppys on the island so she immediately decided she was going to feed the dogs to... she held a bone up and one of the little puppys latched onto it and then jumped over a bit and bit her on the hand just the slightest bit but still drew a little blood. So at this point everyone on the island started freaking out about the possibility of one of the puppies carrying rabies, so one of the old pinoys minced up a few garlic cloves between his fingers and raked it into the bite then rubbed it off and rubbed more fresh garlic on, this went on for 20min and she was not happy about the stinging, he then taped a piece of garlic to her finger and sent us on the boat back to the mainland. In the proceeding 2 months she had about 15 needles just to make sure But when I looked on good old wiki, apparently it is the first port of call for a rabid bite
×