Julian Liber
Julian Liber
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Yeast DNA extraction without phenol or chloform
A DNA extraction protocol for Lyticase-digestible yeasts, without the use of phenol or chloroform. Adapted from the Promega Wizard(TM) genomic DNA kit with homemade buffers. Cost per sample is ~$0.06 USD of kit-included materials.
Protocol: docs.google.com/document/d/1Z9SD5BLJzEOBMrtb-_WOGFWRiwrvxqpoKsaBL9ibRlI/edit?usp=sharing
Cost breakdown: docs.google.com/spreadsheets/d/1gUerbbwcpGj_ds0Pb8yOsnZoR3JR9VZjDg6rdjRXWz4/edit?usp=sharing
Edit: After a recent test, you can likely use half or less of the lyticase. I had complete lysis for 3 tested strains at ~8-16 uL of 672 U/mL = 18-36 U/mL suspension.
zhlédnutí: 510

Video

Total phyllosphere microbial load
zhlédnutí 224Před rokem
Total phyllosphere microbial load
Leaf sterilization for endophytes of Arabidopsis
zhlédnutí 292Před rokem
Protocol for how to surface-sterilize, homogenize, and quantitatively measure endophytic bacteria or fungi of Arabidopsis leaves. Protocol and demonstration by Hannah McMillan, and filming, narration, and editing by Julian Liber. 3D-printed stackable leaf washing cylinders: www.tinkercad.com/things/ibUnaMQfW3d
Arabidopsis Mesh Pots - He Lab Protocols
zhlédnutí 146Před rokem
A protocol for preparing Arabidopsis in mesh-top pots for dip inoculation. This a protocol from Sheng-Yang He's Lab at Duke University Department of Biology. Video filmed, written, produced, and narrated by Julian Liber.
Microbotryomycetes yeasts transformation with Agrobacterium
zhlédnutí 142Před rokem
Here I show a detailed protocol for transforming yeats in the class Microbotryomycetes (Pucciniomycota), also called red yeasts, using Agrobacterium tumefaciens. Video was written, filmed, narrated, and produced by Julian Liber, in Sheng-Yang He's Lab at Duke University. A detailed written protocol including citations, recipes, and volumes/amounts can be found here: drive.google.com/file/d/1sqI...
Confocal Laser Scanning Microscopy of Arabidopsis thaliana roots - Bonito Lab Training
zhlédnutí 463Před 2 lety
YOU MUST CONTACT THE TAKAHASHI LAB BEFORE USE! Instructional video of how to use the Olympus Fluoview FV10i confocal laser scanning microscope to image Arabidopsis thaliana roots. The protocol involves staining roots with wheat germ agglutinin and calcofluor white for imaging root endophytic fungi. Roots are mounted and visualized with the microscope. Filmed at Michigan State University by Juli...
Brachypodium distachyon Seed Starting - Bonito Lab Training
zhlédnutí 419Před 3 lety
Virtual training for how to prepare, sterilize, stratify, and germinate Brachypodium distachyon seeds in the Bonito Lab at Michigan State University. Produced, filmed, and narrated by Julian Liber.
Making Purple-Dyed Yarn from the Lichen Punctelia rudecta
zhlédnutí 34KPřed 3 lety
I demonstrate how to identify and collect Punctelia rudecta lichens, then make a purple dye and use it to create purple wool. Identification of Punctelia rudecta: lichenportal.org/cnalh/taxa/index.php?taxon=54597&clid=1121 Wool yarn used in video: www.wetbellyfibers.com/product/u-s-merino-worsted-weight-yarn/48?cs=true&cst=custom
Water Backups of Fungi - Bonito Lab Training
zhlédnutí 452Před 3 lety
Virtual training for how to long-term storage for filamentous fungi using water backups in the Bonito Lab at Michigan State University. Produced, filmed, and narrated by Julian Liber.
qPCR - Bonito Lab Training
zhlédnutí 323Před 3 lety
Virtual training for how to run qPCR assays in the Bonito Lab at Michigan State University. Includes mix reagents, filling plates, adding template, and running softwre. Produced, filmed, and narrated by Julian Liber.
CTAB - Chloroform DNA Extraction from Fungal Tissue - Bonito Lab Training
zhlédnutí 17KPřed 3 lety
Virtual training for how to isolate high-quality DNA from fungal tissue using the CTAB - chloroform method in the Bonito Lab at Michigan State University. Produced, filmed, and narrated by Julian Liber. *Correction: At 11:04, centrifugation time should be 60-90 seconds with 80% ethanol. The protocol is adapted from Doyle 1991. scholar.google.com/citations?view_op=view_citation&hl=en&user=pMyR8R...
Mortierellaceae Isolation Part 3 - Bonito Lab Training
zhlédnutí 222Před 3 lety
Virtual training for how to isolate Mortierellaceae in the Bonito Lab at Michigan State University. Includes isolating visible growing fungi obtained by techniques in previous videos. Produced, filmed, and narrated by Julian Liber.
Mortierellaceae Isolation Part 1 - Bonito Lab Training
zhlédnutí 532Před 3 lety
Virtual training for how to isolate Mortierellaceae in the Bonito Lab at Michigan State University. Includes techniques to culture fungi from soil or other substrates. Produced, filmed, and narrated by Julian Liber.
Mortierellaceae Isolation Part 2 - Bonito Lab Training
zhlédnutí 178Před 3 lety
Virtual training for how to isolate Mortierellaceae in the Bonito Lab at Michigan State University. Includes identifying and selecting colonies based on morphology. Produced, filmed, and narrated by Julian Liber.
Fast DNA Extraction of Fungal Tissue - Bonito Lab Training
zhlédnutí 3,3KPřed 3 lety
Virtual training for how to perform fast DNA extraction of fungal tissue using alkaline lysis in the Bonito Lab at Michigan State University. Produced, filmed, and narrated by Julian Liber.
PCR Cleanup with ExoAP and Sanger Sequencing Submission
zhlédnutí 508Před 3 lety
PCR Cleanup with ExoAP and Sanger Sequencing Submission
Agarose Gel Electrophoresis 1 - Bonito Lab Training
zhlédnutí 175Před 3 lety
Agarose Gel Electrophoresis 1 - Bonito Lab Training
Agarose Gel Electrophoresis 2 - Bonito Lab Training
zhlédnutí 160Před 3 lety
Agarose Gel Electrophoresis 2 - Bonito Lab Training
Endpoint PCR - Bonito Lab Training
zhlédnutí 1,1KPřed 3 lety
Endpoint PCR - Bonito Lab Training
Making MEA+YE media (Malt Extract Agar + Yeast Extract) Part 1 - Bonito Lab Training
zhlédnutí 14KPřed 3 lety
Making MEA YE media (Malt Extract Agar Yeast Extract) Part 1 - Bonito Lab Training
Making MEA+YE media (Malt Extract Agar + Yeast Extract) Part 2 - Bonito Lab Training
zhlédnutí 4,7KPřed 3 lety
Making MEA YE media (Malt Extract Agar Yeast Extract) Part 2 - Bonito Lab Training

Komentáře

  • @erikawerner
    @erikawerner Před 8 dny

    Thanks for the interesting video. Are you from the San Diego area? Your Name sounds familiar .

  • @Gwenny89
    @Gwenny89 Před 11 dny

    Will it stay purple after long years of sun exposure?

    • @julianliber4633
      @julianliber4633 Před 10 dny

      @@Gwenny89 it will fade gradually with sun exposure. Unfortunately most naturally-derived pigments are less colorfast than synthetic ones.

  • @user-ug5sb6qg1u
    @user-ug5sb6qg1u Před 12 dny

    I always knew this lichen was special. Although, ammonia is not something I like to mess with. Pokeberries make purple too.

  • @tawseefalaff9976
    @tawseefalaff9976 Před 16 dny

    Is the isopropanol ice cold or room temparatyre

    • @julianliber4633
      @julianliber4633 Před 16 dny

      @@tawseefalaff9976 I typically chill it for this protocol, but if it's at room temperature then you can likely put it in the freezer for 1 or 2 minutes longer.

    • @tawseefalaff9976
      @tawseefalaff9976 Před 16 dny

      @@julianliber4633 Thank you so much

  • @modo5091
    @modo5091 Před 18 dny

    Hello thanks for your video, i am now fermenting my own! will this colour fade in sunlight?

  • @elizabethannegrey6285
    @elizabethannegrey6285 Před měsícem

    Absolutely mesmerised. Thank you for this video, and your dedication to keeping an ancient craft alive.

  • @cheezyasf
    @cheezyasf Před měsícem

    Does it need to be heated ?

    • @julianliber4633
      @julianliber4633 Před měsícem

      Yes, I believe so. It is possible that the dyeing will work offer a long time at low temperature, but I haven't tested that.

  • @LK1zt
    @LK1zt Před měsícem

    I added lime of milk. Does this affect the target product?

    • @julianliber4633
      @julianliber4633 Před měsícem

      Is that in addition to ammonia or instead of it? Raising the pH generally makes the color more purple but otherwise shouldn't effect the dyeing.

    • @LK1zt
      @LK1zt Před měsícem

      @@julianliber4633 I added it during fermentation

    • @julianliber4633
      @julianliber4633 Před měsícem

      @@LK1zt as long as there is plenty of ammonia and oxygen, it should be fine!

    • @LK1zt
      @LK1zt Před měsícem

      @@julianliber4633 Thank you for your feedback. Have a good day

  • @hiteshipant7300
    @hiteshipant7300 Před měsícem

    Thankyou sir ❤

  • @pietervandijk9480
    @pietervandijk9480 Před měsícem

    Is there a need to (pre)mordant, or is there enough tannins in the lichen? If there is a need for premordant, what would give the best effect for purple?

    • @julianliber4633
      @julianliber4633 Před měsícem

      No need to pre-mordant. Not sure of the exact reason, but the dye will bind without a mordant present.

  • @christineg8151
    @christineg8151 Před měsícem

    Gorgeous! My MIL was cleaning graves on Memorial Day this year and i asked her to save any lichen she found. I was expecting some of the xanthoria lichens because she described it as bright yellow-green, but instead she brought back nearly a quart of this! Looking forward to trying it out.

  • @user-fd3wl1pr7s
    @user-fd3wl1pr7s Před 2 měsíci

    you should have a rack under the glass jar - like they do with canning.

  • @delynndehardt1859
    @delynndehardt1859 Před 3 měsíci

    It is a beautiful color, but you'd have to collect & use a LOT of lichen for just 1 garment.

    • @julianliber4633
      @julianliber4633 Před 3 měsíci

      After a decent windstorm, I was able to collect enough lichen to fill a 1 L jar, which then provided dye for about 400 or 500 g of wool. It will take time, but the lichen gives more pigment than expected!

  • @jeanstevens2305
    @jeanstevens2305 Před 4 měsíci

    GREAT ! You show us pictures of the lichen and how to test it.

  • @naturalwitchery
    @naturalwitchery Před 4 měsíci

    GREAT video!

  • @jatinhemnani6111
    @jatinhemnani6111 Před 4 měsíci

    How do u prevent scraping agar while removing mycelium from plate The fungi im working on has very flat colony

  • @high.on.matcha
    @high.on.matcha Před 4 měsíci

    great video

  • @caucasianrugs
    @caucasianrugs Před 5 měsíci

    is it lightfast?

    • @julianliber4633
      @julianliber4633 Před 5 měsíci

      I've noticed fading after regular wear in sunny weather after about 6-8 weeks. The color becomes less intense, but retains its hue.

  • @ellenmorris6915
    @ellenmorris6915 Před 5 měsíci

    Last summer, I made this according to your directions and it worked great! Trying it again and after three weeks I have what looks like grape juice colored solution. My question is: How do I know when it's ready?

    • @julianliber4633
      @julianliber4633 Před 5 měsíci

      Awesome! I think the longer you let it go, the deeper the color for a given amount of liquid. I'm also not sure at which point the lichen is exhausted.

    • @ellenmorris6915
      @ellenmorris6915 Před 5 měsíci

      (This is a new batch from lichen gathered over the summer.)

    • @julianliber4633
      @julianliber4633 Před 5 měsíci

      @@ellenmorris6915 if it's like a deep purple grape juice, then you're probably ready to go!

  • @linhtrang6456
    @linhtrang6456 Před 5 měsíci

    Thank you Julian

  • @hanavesela5884
    @hanavesela5884 Před 6 měsíci

    This is amazing. I never heard of this process. Thanks for sharing.

  • @svetlananana9609
    @svetlananana9609 Před 6 měsíci

    💜💜💜💜Yaaay I love the color purple and almost exclusively wear only that. Thank you:) am exciting to go through the process soon

  • @jefflangat6052
    @jefflangat6052 Před 6 měsíci

    No enzymatic digestion, no incubatiom on water bath. Just addind ctab and cloroform and thats it????. I doubt it

  • @kapilramar2253
    @kapilramar2253 Před 6 měsíci

    Which kind of malt extract use Diastatic or non diastatic

    • @julianliber4633
      @julianliber4633 Před 6 měsíci

      It's just being used for sugars and will be autoclaved, so it doesn't matter. However, I use dry bacteriological malt extract which is presumably non-diastatic due to heat treatment.

  • @SilencedByYoutube
    @SilencedByYoutube Před 7 měsíci

    I'm pouring in a still air box. Can I leave the lids off the same way until the agar cools or will there be a risk of contamination? I don't have a flow hood.

    • @julianliber4633
      @julianliber4633 Před 7 měsíci

      You should keep the lids on in that case. There will be more condensation, but it's not a problem.

    • @SilencedByYoutube
      @SilencedByYoutube Před 7 měsíci

      @@julianliber4633 thanks

  • @allison5446
    @allison5446 Před 7 měsíci

    I have looked everywhere for a "soup to nuts" method of using lichen as a die and you have done it! I also live on the east coast and I thought that the lichen that I had collected was the common Green Shield (Flavoparmelia caperata) but your instructions on using a drop of bleach verified what I had initially thought was Punctelia rudecta. Yay! Purples!!! I love your step by step directions from harvesting, removal from bark, and the beginning to the end of the dying process. Thank you so much for an incredibly informative video! A++ !

  • @lisascenic
    @lisascenic Před 7 měsíci

    What an astonishing color! Is it colorfast?

  • @shirinpayizova8768
    @shirinpayizova8768 Před 7 měsíci

    Awesome, thank you for informationz

  • @onceuponatablecloth
    @onceuponatablecloth Před 7 měsíci

    I have a question. I started fermenting lichen and now realize I have so much more than I need. Will it keep longer than 6 months if I leave it in the jar? If I want to keep it longer should I strain out the lichen and boil the dye before saving it for later. Thanks for the info in the video so far. My wood pile was covered in the stuff and I got a bit overexcited, which is why I now have way more dye than I need at a time.

    • @julianliber4633
      @julianliber4633 Před 7 měsíci

      I've had my jars for 3 years now, still works great!

    • @onceuponatablecloth
      @onceuponatablecloth Před 7 měsíci

      did you strain out the lichen, or just leave it as is? @@julianliber4633

  • @jorgecarrascof.2025
    @jorgecarrascof.2025 Před 8 měsíci

    Hi Julian. I have had failed DNA extractions. Using the lysis buffer composed 100 mM Tris, 250 mM KCl, and 10 mM disodium EDTA (pH 9.5). The samples in tube PCR to 95°C for 10 min and then mixed with 40 ul BSA 3%. I tested in a electrophoresis the DNA and apparently there is no DNA and in PCR I can´t see amplicons. The fungal tested in my case were Beauveria, Metarhizium, Diplodia and Clonostachys. Considering your experience what is the probably problem ??

    • @julianliber4633
      @julianliber4633 Před 7 měsíci

      Hi, you can't usually see the DNA on a gel prior to PCR due to the low concentration. How do you do your PCR? I have success using 0.5 ul of template in a 10 ul rxn, with GoTaq green master mix, primers ITS1f & LR3 at 500 nM, and a cycle of 95C/3min, 35x(95C/30s, 57C/30s, 72C/90s), 72C/7min. I've seen that too few cycles can result in failure to see PCR products.

  • @jeancastro1600
    @jeancastro1600 Před 8 měsíci

    Thanks for the protocol. Could you mention the code of the BSA solution you used or did you prepare it from powder?

    • @julianliber4633
      @julianliber4633 Před 8 měsíci

      I prepared from powder, and the protocol has worked in both labs I have worked in so the supplier probably isn't important.

    • @jeancastro1600
      @jeancastro1600 Před 8 měsíci

      @@julianliber4633 Thanks for the quick reply, could you please indicate whether you used PBS? did you sterilize the solution and how; did you use previously sterilized PBS and then dissolve the BSA? Thanks

    • @julianliber4633
      @julianliber4633 Před 8 měsíci

      @@jeancastro1600 because the first solution is buffered, I dissolve the BSA in PCR-grade water then filter sterilize with a low-binding 0.22 um filter.

    • @matiasguerrap.5456
      @matiasguerrap.5456 Před 8 měsíci

      @@julianliber4633What was the pH of BSA?

  • @denisemotley6639
    @denisemotley6639 Před 11 měsíci

    Very beautiful shade. 💜

  • @Medietos
    @Medietos Před 11 měsíci

    Beautiful! Is it the Stone-Lichen I used to make a beautiful rich reddish-Brown colour, with chemicals Alun and vinsten (Sw)? For this fine purple: No further chemicals needed for permanence?

    • @julianliber4633
      @julianliber4633 Před 11 měsíci

      No mordant is needed! You can get the color with the lichen dye alone.

  • @PromorteD
    @PromorteD Před rokem

    Very useful thank you. Confirmed that all of my seeds were indeed unviable!!

  • @FranOnTheEdge
    @FranOnTheEdge Před rokem

    Would it be possible to make ink with lichen like this? And if so must it smell of ammonia? How would you turn it into an ink?

    • @julianliber4633
      @julianliber4633 Před rokem

      It seems like French Purple is made this way. There's a comment that explains more.

  • @momentobooks
    @momentobooks Před rokem

    I collected lots of lichen on fallen trees on my propety, and it had been soaking in water and ammonia for 2 months now, and no sign of purple at the moment. The liquid is dark brown with some dark red hues, but it yields some uninteresting brownish dirty tone. Do you think it will really turn purple in a couple more months or it should have already started to look like purple is on the way?

    • @julianliber4633
      @julianliber4633 Před rokem

      It's possible that it will turn purple, which happens faster with oxidation. Do you open the jar for air?

    • @momentobooks
      @momentobooks Před rokem

      @@julianliber4633 Yes, once in a while but I will do it more often to see if it changes anything. Thanks!

    • @julianliber4633
      @julianliber4633 Před rokem

      @@momentobooks it's also possible that it might not be a lecanoric acid containing lichen. If you have some more of it you can try to scratch off the outer layer to reveal the white cortex, then put a drop of concentrated bleach on that spot. If it turns red, it probably is a lichen that will work to make the dye.

    • @momentobooks
      @momentobooks Před rokem

      @@julianliber4633 Oh! this would explain it! I put a couple different lichen in the jar.

  • @mdhasibulhossain6389

    Can you please share any reference of this protocol? I want to cite this method. Thanks.

    • @julianliber4633
      @julianliber4633 Před rokem

      You can cite this paper: peerj.com/articles/12701 Liber JA, Minier DH, Stouffer-Hopkins A, Van Wyk J, Longley R, Bonito G. Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities. PeerJ. 2022 Jan 27;10:e12701. doi: 10.7717/peerj.12701. PMID: 35127279; PMCID: PMC8801177.

  • @ZygoArachnid
    @ZygoArachnid Před rokem

    Thank you for this tutorial! It was very fascinating!

  • @shirellejohnson1387

    I wonder if it would work as a hair tones

    • @julianliber4633
      @julianliber4633 Před rokem

      L'Oreal has a patent, so probably! patents.google.com/patent/FR2907005A1/en

  • @miwamo
    @miwamo Před rokem

    Thank you for this video! I‘ve never seen such a interesting color dyeing idea from lichen. Also it’s interesting that you use to gather lichen chopsticks and a tofu package and cook it with a rice cooker😊

  • @nz-nz
    @nz-nz Před rokem

    How interesting! Would be great to know how this dye was “discovered” (I.e. using the ammonia to extract the pigment).

    • @julianliber4633
      @julianliber4633 Před rokem

      It's been around for a while! First urine was used, then ammonia later. en.m.wikipedia.org/wiki/Orcein

  • @TrudySchwartzBurrill

    If you use any acid like citric acid it will be pink or red, is that what you said? I couldn’t hear exactly. Thanks.

    • @julianliber4633
      @julianliber4633 Před rokem

      Yes, you could use citric acid or vinegar to lower the pH and get a red to pink color. The color changes if you wash the fiber in a different pH solution.

    • @TrudySchwartzBurrill
      @TrudySchwartzBurrill Před rokem

      @@julianliber4633 Is that the same chemically as a plant like a hydrangea bush can grow blue flowers in low PH soil the same plant if put with high PH soil will grow pink flowers?

    • @julianliber4633
      @julianliber4633 Před rokem

      @@TrudySchwartzBurrill it's similar, in that pH affects color, but the compound is different. Many pigments (natural and synthetic) are pH sensitive, and can be used as indicators. en.m.wikipedia.org/wiki/PH_indicator

    • @TrudySchwartzBurrill
      @TrudySchwartzBurrill Před rokem

      @@julianliber4633 thank you for the link and information. 👍

  • @aminemohamed70
    @aminemohamed70 Před rokem

    i have a request please, can you show us how to extract DNA from plants infected with obligatory fungi like Rust and Smut ??

    • @julianliber4633
      @julianliber4633 Před rokem

      I don't work with these fungi, but I'll see what protocols I can find.

    • @aminemohamed70
      @aminemohamed70 Před rokem

      @@julianliber4633 thank you so much

  • @ryanbiggums1431
    @ryanbiggums1431 Před rokem

    Can i use this receipe to make liquid culture medium by doing the same thing minus the agar?

  • @kreideprinzye15
    @kreideprinzye15 Před rokem

    You are Godsend. Thank you so much. By the way, do you have a citation for your source of protocol? thank you

  • @sabahhassan3140
    @sabahhassan3140 Před rokem

    This is my first time to understand I failed and failed and failed all times to grow mushroom thanks a lot

  • @sabahhassan3140
    @sabahhassan3140 Před rokem

    You are successful teacher

  • @bcpem1
    @bcpem1 Před rokem

    After all this I think I would rather buy some purple yarn at the store! 😅

  • @naumankhalid8322
    @naumankhalid8322 Před rokem

    thanks for the video. why did you make a single cutlet at the end when the whole plate is still used?

    • @julianliber4633
      @julianliber4633 Před rokem

      The cutlet on the plate's lid is used to help remove bacteria from the fungal isolate. The fungus will start on the cutlet, then jump the gap to the top of the plate where it can usually be isolated without any bacterial contamination.

  • @sudharaisherpa4031
    @sudharaisherpa4031 Před rokem

    How to prevent the colour by fading?

    • @julianliber4633
      @julianliber4633 Před rokem

      Unfortunately I don't believe there is a way to prevent fading as part of the dyeing process. Dyed fiber will fade with exposure to sunlight.