Thanks for your timely and informative replies.
The EZNA kit employs proteinase K which, as I understand it, acts in both lysis and protection from DNA degradation. Will you comment on that phillyj?
Another consideration to the EZNA kit is chloroform. That reagent is added to "remove much of the polysaccharides and proteins and improve spin-column performance." Regarding chloroform what I know is:
PVA gloves should be used in handling
As a gas it's exposure limit is 50ppm per 8 hour day.
It may decompose to phosgene in the presence of oxygen.
Stabilized by alcohol it has a shelf life of no more that 1 year.
Disposal is regulated
Anyone care to share their experience with chloroform?
My plan is to aliquot 500uL containers as that is the volume prescribed by the EZNA protocol. I'll do that under a fume hood in the lab. Having minimal aliquots should reduce the health and environmental risk given our amateur environment. Comments?
Arnold,
This is our original project idea at least regarding the brown marmorated stink bug, a recently invasive species from China. Otherwise I think it's reasonably conventional stuff as might be found in a high school AP biology class.
We'll be sure to post all of our details here and, hopefully, make a path for you to follow and improve.
Greetings,
My 12 year-old daughter wants to be a molecular biologist. Sounds like quality time to me. I'm all in.
The project is RFLP of stink bug genomic DNA (Halyomorpha halys). We not looking towards cutting edge research. We'll be stoked if we can isolate, restrict, electrophorese and visualize.
I've collected some nice equipment including an electrophoresis system, centrifuge, pipettor, UV spectrophotometer and precision balance. All that wasn't cheap but I really want this project to work because success will be inspirational to the lass.
Some questions to the community if I may?
I plan to use spin-column kits for DNA isolation. In particular I like the EZNA kit from Omega Bio-tek. Any comment on this choice?
Reagents are proving difficult to acquire. I understand why suppliers frustrate the process. But surely there is an avenue to quality reagents that is controlled yet accessible. Any advice on how to inform suppliers?
Finally, as we are beginners, any other advice on getting started will be appreciated.
Best regards,
--The Sticky Ends
Maryland, USA
Sebastian,
Thanks for the referral to OpenWetWare. Lots of information there.
We're going to try some manufactured kits first. Then we'll definitely want to discuss hacker spin columns.
I read you when it comes to chloroform. My guess is the Omega kit will suit our purposes even without applications of chloroform. So maybe we'll go that route. Anyone care to comment?
Everyone,
May I thank you once again for your replies. Great to have your advice and to find a community of like-minded folk.
May I raise another topic?
Preparations of insect tissue are ideally made by cryogenically freezing and then grinding samples. I can achieve that but prefer the lesser alternatives. Any success stories using other mechanical methods such as straight mortar / pestle, coffee grinders or Dounce homogenizers?
Note my samples are insects with sturdy exoskeletons.
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Greetings,
My 12 year-old daughter wants to be a molecular biologist. Sounds like quality time to me. I'm all in.
The project is RFLP of stink bug genomic DNA (Halyomorpha halys). We not looking towards cutting edge research. We'll be stoked if we can isolate, restrict, electrophorese and visualize.
I've collected some nice equipment including an electrophoresis system, centrifuge, pipettor, UV spectrophotometer and precision balance. All that wasn't cheap but I really want this project to work because success will be inspirational to the lass.
Some questions to the community if I may?
I plan to use spin-column kits for DNA isolation. In particular I like the EZNA kit from Omega Bio-tek. Any comment on this choice?
Reagents are proving difficult to acquire. I understand why suppliers frustrate the process. But surely there is an avenue to quality reagents that is controlled yet accessible. Any advice on how to inform suppliers?
Finally, as we are beginners, any other advice on getting started will be appreciated.
Best regards,
The Sticky Ends
Maryland, USA
Gents,
Thanks again for the great leads and advice. BUGSS looks like an awesome space. Too bad you have to be 18 to participate. My daughter is just 12. And this one is for her. Still, we'll contact them as in community.
As to chloroform I have some numbers for consideration. What volume of chloroform exceeds exposure limits when left to completely evaporate in a sealed 8x8x10 room?
(A) The absolute max permissible exposure limit according to OSHA is 240mg /m3. So that would require 3.3mL.
(B) The recommended threshold limit value according to ACGIH is 50mg /m3 in an 8 hour workday and 40 hours per week.. Here 0.78mL are required.
(C) Finally NIOSH has established 10mg /m3 as a recommended exposure limit over 1 hour. Just 0.148mL are required.
Good stuff yes. But it's use clearly demands caution, a chemical fume hood and proper disposal. So we'll be reading Mr. McCorkle's paper with interest.
Dakota,
You put a lot into that last reply and we wish to acknowledge that with gratitude.
You sold us. We recognize the Wizard kit as a better alternative. We'll give that a whirl if you'll pardon the pun.
We also appreciate your comments regarding safety and responsibility. These sort of opportunities will be closed the first time one of us acts irresponsibly. We'll do our part.
You bring a point I wish to explore, hopefully, without derailing this string. How should we dispose of our waste? May I share our plan for review?
1. Recordkeeping of reagent use and generated waste by weight.
2. All streams of waste containerized and labeled.
3. Containers bagged by group.
4. Bags stored in labeled steel drums filled by vermiculite and closed with snap-ring lids.
5. Quarterly disposal at a licensed facility.
Under that regimen we believe we qualify as "conditionally exempt small quantity generators of hazardous waste." Anyone care to comment on that?
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Everyone,
We were able to obtain chemicals including pure ethanol without much hassle. And yes, the ethanol cost a whopping $100 / liter. Our experience so far is suppliers require two basic responsibilities from their customers:
1. Statement of intended use.
2. Commercial shipping address.
All that makes perfect sense to us.
Suppliers have an obligation to protect their enterprise from liability by recording customer statements on use. Every supplier has called us directly to asses our intentions or knowledge of the products.
When they call you must answer their questions truthfully. Suppose you buy ethanol under the pretense of molecular biology and then divert that material to beverages. You have now committed mail / wire fraud, a serious crime.
Providing a commercial shipping address is a common-sense safety precaution that assures chain of custody in shipping hazardous goods. Suppose, as you are at work, the neighborhood delinquents snatch that box of reagents from the front porch.
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Nathan,
Having access to a commercial shipping address does not allow one to purchase tax free. To lawfully purchase tax free you must first make an application to the ALCOHOL AND TOBACCO TAX AND TRADE BUREAU (TTB). The application form is here:
http://www.ttb.gov/forms/f515022.pdf
Understand, however, that you will be granting TTB a right of entry to inspect goods and records. We don't know about you but we would rather pay the tax, about $15 per proof-gallon. A reasonable compromise between responsibility and privacy.
And who, may I ask, sells liters of 200-proof for $35 tax paid?