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Tripyamine

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Posts posted by Tripyamine

  4. Posted

    @Darklight spirulina can get to 2-2.5g/L and other stuff like nannochloropsis will only get to 1g/L (more if thin-film reactors). Also thats bone dry.

    I personally prefer nanno both taste-wise and nutritional content-wise, its an omega3 (EPA) production powerhouse, you can expect to see 25% lipid and of that ~50% EPA

    Both have good amino acid profiles too but iirc nanno is more complete being a eukaryote and not a bacteria like spirulina 

     

    5g a day of nanno gets you an RDI of lots of stuff, but it's more an adjunct than a meal replacement. one day we will get there but I couldn't only eat nori (tastes like) soylent green is soon

     

    with nanno you can grow out (from 1/5) to a dense culture in 4-5days, and if you harvest 80% so you can regrow straight away then your collecting 15+g a 20L bag/5 days.

     

    ~200L standing bags are the way to go, if you only yielded 100g it would be enough for a week. 

  5. Posted

    Hmmmmm I have a nice starter if anyone wants it le PM me 

     

    I really like bags to grow in for a small scale, it's very popular in the industry too. 

    If you get a bad infection/contamination you can burn your bags and reroll otherwise you can just keep reusing them.

    We use Polypropylene bag rolls and seal them ourselves to the size we need, and then sterilize with 70% ethanol and UV

     

    It's a good rule of thumb to always do a 1:5 inoculation with any algae (1:10 if you can't help it) 

     

    I'll grow up a 5mll culture from a stock or a plate, scale that up to 25ml, then to 100ml, then 500ml, then 2.5lt and then start a bag culture with 10L and gradually increase the volume to 20L.

    Then its too a big 100-200L bag like the one pictured and then to ponds/pools all the way up to 400kL

    image.thumb.png.d028c6539dbff277863f23b000536c07.pngPhotobioreactors — PureBiomass Inc

    Photobioreactors — PureBiomass Inc

    ^^^these are easy to make ill get some photos of our ghetto ones

     

    arthrospira (spirulina) likes to grow under basic conditions up to like a pH of 10 so lots of media reflect this as its useful for keeping lots of the contam/bugs out.

    Some good info on making the standard media here but you might struggle with some of the chems, also good culture info too. 

    http://sagdb.uni-goettingen.de/culture_media/02 Spirulina Medium.pdf

     

    Another good media to use that you can purchase heaps of for cheap as is Cell-Hi JW (should be around $40 for a kg that will make close to 1000L), you will have to google around to find a supplier as we make our own and haven't had to buy for a while. 

     

    At the end of the day if you scale up slowly and use appropriate media it's pretty easy to do, Spira harvests very easy compared to some other alga, but chitosan always makes it better! 

    Sparge with lots of air and give em plenty of light (outdoors is better than LED but cheap eBay grow LEDs will work fine just gets expensive >100L)

     

     

    image.thumb.png.d028c6539dbff277863f23b000536c07.png

    image.thumb.png.d028c6539dbff277863f23b000536c07.png

    • Like 4

  10. Posted

    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. 

     

     

    • Like 1

  11. Posted

    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

     

     

     

     

    • Like 1
    • Thanks 1

  14. Posted

    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.

    • Like 2

  16. Posted · Edited by Tripyamine

    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!

  17. Posted · Edited by Tripyamine

    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

    • Like 2

  19. Posted · Edited by Tripyamine

    And gas discharge has better peaks!

    there are already a lot of threads on horticultural lighting i have worked in the industry since i was 14 .

    LED lights are crap when philips starts putting out led grow lights use them .But you cant beat a hps

    some leds make claims but a lot of them are mono cromatic so you dont get a heathly spectrum of light

    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

  20. Posted

    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

    • Like 1

  24. Posted

    Ahhh kinda unrelated but good story none the less :P

    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 :o

    • Like 1

  25. Posted

    I use a $20usd (shipped) blue plastic probe from Aliexpress, this is wired up to a simple pH circuit and fed into an ADC and to an Arduino monitored via the serial out

    This sits in a saltwater frag tank all day and the data gets logged to a xively feed; when the lights come on there is a nice shift from the photosynthesis kicking in, and it's all exactly the same as the colorimetric 7 to 8.9 test kit that I have which is highly regarded (sailfert)

    As for probe calibration, Im sure you're aware that 99% of calib is done by cleaning the probe/keeping it clean

    I use a 12 bit ADC and this generates a value between 0-4096 which is directly proportional to pH

    The main calibration factor used is drift, which is the measure of how different the probe's reading is to a "new" probe if that makes sense

    • Like 1
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