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.
Переглядів: 556

Відео

Total phyllosphere microbial load
Переглядів 233Рік тому
Total phyllosphere microbial load
Leaf sterilization for endophytes of Arabidopsis
Переглядів 319Рік тому
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
Переглядів 163Рік тому
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
Переглядів 1512 роки тому
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
Переглядів 4782 роки тому
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
Переглядів 4303 роки тому
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
Переглядів 35 тис.3 роки тому
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
Переглядів 4553 роки тому
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
Переглядів 3273 роки тому
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
Переглядів 17 тис.3 роки тому
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
Переглядів 2293 роки тому
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
Переглядів 5473 роки тому
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
Переглядів 1833 роки тому
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
Переглядів 3,5 тис.3 роки тому
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
Переглядів 5433 роки тому
PCR Cleanup with ExoAP and Sanger Sequencing Submission
Agarose Gel Electrophoresis 1 - Bonito Lab Training
Переглядів 1813 роки тому
Agarose Gel Electrophoresis 1 - Bonito Lab Training
Agarose Gel Electrophoresis 2 - Bonito Lab Training
Переглядів 1643 роки тому
Agarose Gel Electrophoresis 2 - Bonito Lab Training
Endpoint PCR - Bonito Lab Training
Переглядів 1,1 тис.3 роки тому
Endpoint PCR - Bonito Lab Training
Making MEA+YE media (Malt Extract Agar + Yeast Extract) Part 1 - Bonito Lab Training
Переглядів 14 тис.4 роки тому
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
Переглядів 4,7 тис.4 роки тому
Making MEA YE media (Malt Extract Agar Yeast Extract) Part 2 - Bonito Lab Training

КОМЕНТАРІ

  • @erikawerner
    @erikawerner Місяць тому

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

  • @Gwenny89
    @Gwenny89 Місяць тому

    Will it stay purple after long years of sun exposure?

    • @julianliber4633
      @julianliber4633 Місяць тому

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

  • @user-ug5sb6qg1u
    @user-ug5sb6qg1u Місяць тому

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

  • @tawseefalaff9976
    @tawseefalaff9976 2 місяці тому

    Is the isopropanol ice cold or room temparatyre

    • @julianliber4633
      @julianliber4633 2 місяці тому

      @@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 2 місяці тому

      @@julianliber4633 Thank you so much

  • @modo5091
    @modo5091 2 місяці тому

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

  • @elizabethannegrey6285
    @elizabethannegrey6285 2 місяці тому

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

  • @cheezyasf
    @cheezyasf 2 місяці тому

    Does it need to be heated ?

    • @julianliber4633
      @julianliber4633 2 місяці тому

      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 3 місяці тому

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

    • @julianliber4633
      @julianliber4633 3 місяці тому

      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 3 місяці тому

      @@julianliber4633 I added it during fermentation

    • @julianliber4633
      @julianliber4633 3 місяці тому

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

    • @LK1zt
      @LK1zt 3 місяці тому

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

  • @hiteshipant7300
    @hiteshipant7300 3 місяці тому

    Thankyou sir ❤

  • @pietervandijk9480
    @pietervandijk9480 3 місяці тому

    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 3 місяці тому

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

  • @christineg8151
    @christineg8151 3 місяці тому

    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 4 місяці тому

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

  • @delynndehardt1859
    @delynndehardt1859 5 місяців тому

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

    • @julianliber4633
      @julianliber4633 5 місяців тому

      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 5 місяців тому

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

  • @naturalwitchery
    @naturalwitchery 6 місяців тому

    GREAT video!

  • @jatinhemnani6111
    @jatinhemnani6111 6 місяців тому

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

    • @merrivideo
      @merrivideo Місяць тому

      I'm having the same issue. How did you solve it?

  • @high.on.matcha
    @high.on.matcha 6 місяців тому

    great video

  • @caucasianrugs
    @caucasianrugs 6 місяців тому

    is it lightfast?

    • @julianliber4633
      @julianliber4633 6 місяців тому

      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 6 місяців тому

    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 6 місяців тому

      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 6 місяців тому

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

    • @julianliber4633
      @julianliber4633 6 місяців тому

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

  • @linhtrang6456
    @linhtrang6456 7 місяців тому

    Thank you Julian

  • @hanavesela5884
    @hanavesela5884 7 місяців тому

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

  • @svetlananana9609
    @svetlananana9609 7 місяців тому

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

  • @jefflangat6052
    @jefflangat6052 7 місяців тому

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

  • @kapilramar2253
    @kapilramar2253 8 місяців тому

    Which kind of malt extract use Diastatic or non diastatic

    • @julianliber4633
      @julianliber4633 8 місяців тому

      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 9 місяців тому

    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 9 місяців тому

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

    • @SilencedByYoutube
      @SilencedByYoutube 9 місяців тому

      @@julianliber4633 thanks

  • @allison5446
    @allison5446 9 місяців тому

    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 9 місяців тому

    What an astonishing color! Is it colorfast?

  • @shirinpayizova8768
    @shirinpayizova8768 9 місяців тому

    Awesome, thank you for informationz

  • @onceuponatablecloth
    @onceuponatablecloth 9 місяців тому

    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 9 місяців тому

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

    • @onceuponatablecloth
      @onceuponatablecloth 9 місяців тому

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

  • @jorgecarrascof.2025
    @jorgecarrascof.2025 9 місяців тому

    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 9 місяців тому

      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 10 місяців тому

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

    • @julianliber4633
      @julianliber4633 10 місяців тому

      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 10 місяців тому

      @@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 10 місяців тому

      @@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 10 місяців тому

      @@julianliber4633What was the pH of BSA?

  • @denisemottley22705
    @denisemottley22705 Рік тому

    Very beautiful shade. 💜

  • @Medietos
    @Medietos Рік тому

    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 Рік тому

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

  • @PromorteD
    @PromorteD Рік тому

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

  • @FranOnTheEdge
    @FranOnTheEdge Рік тому

    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 Рік тому

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

  • @momentobooks
    @momentobooks Рік тому

    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 Рік тому

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

    • @momentobooks
      @momentobooks Рік тому

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

    • @julianliber4633
      @julianliber4633 Рік тому

      @@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 Рік тому

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

  • @mdhasibulhossain6389
    @mdhasibulhossain6389 Рік тому

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

    • @julianliber4633
      @julianliber4633 Рік тому

      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 Рік тому

    Thank you for this tutorial! It was very fascinating!

  • @shirellejohnson1387
    @shirellejohnson1387 Рік тому

    I wonder if it would work as a hair tones

    • @julianliber4633
      @julianliber4633 Рік тому

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

  • @miwamo
    @miwamo Рік тому

    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 Рік тому

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

    • @julianliber4633
      @julianliber4633 Рік тому

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

  • @TrudySchwartzBurrill
    @TrudySchwartzBurrill Рік тому

    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 Рік тому

      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 Рік тому

      @@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 Рік тому

      @@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 Рік тому

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

  • @KOUADRI_Mohamed_Elamine
    @KOUADRI_Mohamed_Elamine Рік тому

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

  • @ryanbiggums1431
    @ryanbiggums1431 Рік тому

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

  • @kreideprinzye15
    @kreideprinzye15 Рік тому

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

  • @sabahhassan3140
    @sabahhassan3140 Рік тому

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

  • @sabahhassan3140
    @sabahhassan3140 Рік тому

    You are successful teacher

  • @bcpem1
    @bcpem1 Рік тому

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

  • @naumankhalid8322
    @naumankhalid8322 Рік тому

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

    • @julianliber4633
      @julianliber4633 Рік тому

      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 Рік тому

    How to prevent the colour by fading?

    • @julianliber4633
      @julianliber4633 Рік тому

      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.