bullet blender usage with zymobiomics dan mini prep kit

[grace-ac]

Sample type: 0.45um filters (product: here) - will be processing 1/2 filter at a time (cutting into small strips)

Kit: ZymoBIOMICS DNA MiniPrep Kit --> comes with own lysis beads in 2.0ml tubes

Bead beater in Roberts Lab: Bullet Blender Gold +

I have used this kit before for eDNA samples for eelgrass wasting disease pathogen DNA in water samples for the same filter type.

FHL has a bead beater listed in Appendix D in the ZymoBIOMICS DNA Miniprep kit manual:
_d4300t_d4300_d4304_zymobiomics_dna_miniprep_kit.pdf
1min run, 5 min rest, 5 times.

I just chatted with support from Zymo Research about using the Bullet Blender Gold + as the bead beater, and he just said make sure that I use the tube adapter for the 2ml and that since it looks like it's a high speed blender, do the 1 min run, 5 mins rest 5 times.

The main issue is that Zymo has not validated or tried using this bead beater method... thoughts on my trying it anyway?

Also, I have watched some videos on using the Bullet Blender and understand that it requires dry ice to pre-cool it and to keep it cool during the run.

[kubu4]

The main issue is that Zymo has not validated or tried using this bead beater method... thoughts on my trying it anyway?

What's the alternative, if you don't use it?

Regardless, you have past samples to compare extractions to, so you might as well go for it and see how it compares to your previous extractions.

Please be sure to review the Bullet Blender usage in the Handbook, as well. The Bullet Blender website also has a large number of example settings/bead types for various tissues. May want to glance at that and/or give them a ring.

[grace-ac]

Alternative would be I wait until I can get up to FHL, which would have to be after my qualifying exam of early May... but results are needed sooner.

These samples will be for qPCR for a different pathogen, so it won't be directly comparable, but I suppose since I'll be using only half of the filter for each sample, I have backup if the qPCR come up empty.

And yes, good point! I'll look more into the bullet blender usage/contact them.

[grace-ac]

Just chatted with folks from Next Advance about using zymo beads and tubes and they said it should all work great as long I use the proper adaptors for that tube size - so i shall proceed!

[grace-ac]

NY company, so they aren't picking up phone... but I'm trying to figure out what the different speed settings on the bullet blender equate to.

The bead beater i used at FHL was set to max speed - which was 3,450 oscillations per minute

been googling and looking through protocols, but asking here in case you have come across what the numbered speed settings on bullet blender correlate to in terms of oscillations per min @kubu4 :)

[grace-ac]

i'm thinking i might pick the highest number.... people i talked to on phone from zymo said run 1 min and 5 min rest 5x through... total of 5 mins of bead beating... i think highest setting should be fine?

[grace-ac]

i took a look at other protocols of what people are using and see that 8-12 is typical for tougher-to-lyse samples

[grace-ac]

ok - gonna do 1 min at 12, 5 min rest, 5times