Re: DIYbio iGEM teams, DIYbio Safety Working Group, and a DIYbio symposium at iGEM 2009

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Jake

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Apr 11, 2009, 9:20:38 PM4/11/09
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Being a loose collective we can huff and puff all we want about
safety, but how would this actually be implemented? Right now it's
just an internet group. There's no way to enforce any of this and
even if we knew someone was violating the rules what could be done?
Ban that email address from the group? That's hardly a real threat.

Establishing safety guidelines is a worthy goal, but I don't think
it's going to do anything to allay any of the fears that people have.

-Jake

4phl...@gmail.com

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Apr 11, 2009, 9:24:38 PM4/11/09
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@Jake it really depends though. If diybio groups meet in person and keep in contact with other it would be (relatively) easier to enforce some sort of safety guideline. There's a huge difference between ignoring emails and ignoring someone speaking to you who knows you.
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-----Original Message-----
From: Jake <jake...@mail.com>

Date: Sat, 11 Apr 2009 18:20:38
To: DIYbio<diy...@googlegroups.com>
Subject: Re: DIYbio iGEM teams, DIYbio Safety Working Group, and a DIYbio symposium at iGEM 2009

Bryan Bishop

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Apr 11, 2009, 11:45:36 PM4/11/09
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The goal isn't to keep people calm- the goal is to not die. Keeping
people calm is a nice plus, of course. Here's how I've been thinking
of implementing assistance in safety guidelines in general.
Standaridzed protocols transmitted over the web-- such as my pcr.xml
example- have information about what tools and equipment is involved,
as well as various chemicals. Most chemicals that you use in a common
lab setting are going to have information in the MSDS database, which
stands for "Material Safety Datasheet". Material safety and equipment
safety is really just one aspect of safety, there are many others when
it comes to biological materials. But, in general, imagine the ability
to automatically print out documentation on what to do in case
something goes wrong, or documentation to show anybody that wants to
do a walk-through of a lab just what's going on or contigency plans,
or documentation just for yourself on how to carry out clean-ups of
common spills, etc. This information is vital. I don't think it's an
issue of making sure people are following some arbitrary set of rules,
but rather providing them with the tools to do better.

- Bryan
http://heybryan.org/
1 512 203 0507

ridgway

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Apr 16, 2009, 1:18:11 PM4/16/09
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Just so people know, http://2009.igem.org/Experimental_track has now
been updated. Participation requires $500+375/pp and some kind of
affiliation with a university, and gets you a 5 min presentation slot
and a poster at the iGEM Jamboree. If this maybe sounds interesting to
you, and you're in Alberta, drop me a note off-list
(rid...@dridgway.com).

doug.

On Apr 10, 4:07 pm, Mackenzie Cowell <m...@diybio.org> wrote:
> Several weeks ago the Director of iGEM (my old boss) asked me to drop by to
> chat.  He basically told me iGEM wasn't going to allow amateur teams for
> 2009, despite earlier statements to the contrary, for two reasons:
>
> 1. iGEM depends on the academic institution of each team to provide a safety
> framework for that team.  Because there is no formal safety framework or
> guidelines or precedent for amateur teams working outside of traditional
> labs, iGEM is afraid of the potential safety liability and doesn't want
> amateur teams to participate until there is some kind of framework (2010!).
>
> 2. Most of iGEM's funding comes from grants to support undergraduate
> education.  A host of amateurs who are not undergraduates would be supported
> by grants for undergraduate education, which could be a situation the
> grantors wouldn't like.  Randy didn't want to take that risk.
>
> Randy also said iGEM would clarify the situation by making a press release
> regarding these changes, or at least describe them in an organizational
> email to the iGEM-interest email list.  That didn't happen.  So in the
> meantime, I've been verbally explaining the situation to groups of people I
> think may be starting iGEM teams.
>
> There is some good news: if you want to participate in iGEM in an amateur
> capacity, you can still do so by collaborating with a local iGEM team.  This
> could help a lot with the fundraising for both the local diybio group and
> the iGEM team.  DIYbio-Boston and DIYbio-NYC are both exploring
> collaborations with local teams.
>
> As a community we need to start addressing the safety concerns society and
> the larger scientific establishment has with garage and coworking space
> wetlab work.  I'm sure there are a multitude of opinions on how and what to
> do, and even what not to do.  But I believe we need to organize some kind of
> formal statement anticipating and addressing these safety concerns,
> preferably with the help of objective experts.  If you are interested in
> helping figure out how to do this, email saf...@diybio.org.  I'm thinking we
> should establish a  DIYbio safety working group to be responsible for taking
> a leadership role on this developing real solutions.
>
> I spoke with Randy about organizing a 1-day DIYbio symposium at the same
> time and place as iGEM this year (which is at MIT on the weekend of October
> 31).  He was receptive to this idea.  I think it would be very valuable to
> bring as much of the community together as possible to meet and discuss
> these issues and to present a collective snapshot of their work and projects
> to the world.  There would be cross-pollination with many of the iGEM
> participants, and lastly, I'd like to use the symposium as a deadline by
> which some group or groups of people could formally present thoughts and
> work on our safety strategy to the community and to the rest of the world.
>
> Thoughts?
>
> Mac
>
> On Fri, Apr 10, 2009 at 5:03 PM, jocelyn zuckerman <jocelynz...@gmail.com>wrote:
>
>
>
> > i've actually been in touch with tan in regard to my story. seems like a
> > very nice guy. i'd suggest emailing him, though not sure how open they'll be
> > given the competition and all...
> > On Fri, Apr 10, 2009 at 4:01 PM, Eric Zhang <ericzh...@gmail.com> wrote:
>
> >> I don't know any of them but it wouldn't hurt to ask.
>
> >> On Fri, Apr 10, 2009 at 3:35 PM, Sung won Lim <4phle...@gmail.com> wrote:
>
> >>> NYU is going for iGEM competition this year. Here's the link<http://ung.igem.org/Team.cgi?id=276>to the team page.
> >>> Primary contact is listed as Ignatius Tan with three student members and
> >>> an advisor. Does anyone on this list keep in touch with any of them? I'd
> >>> like to talk to them about project ideas/material acquisitions and such, and
> >>> showing up out of the blue might be a little weird. I'm also hoping that
> >>> some of them would be interested in diybio nyc as well.
>
> --
> p: 231.313.9062
> e: m...@diybio.org
> tw: @macowell

Tom Knight

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Apr 16, 2009, 10:50:41 PM4/16/09
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Bryan Bishop

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Apr 16, 2009, 10:54:05 PM4/16/09
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On Thu, Apr 16, 2009 at 9:50 PM, Tom Knight <t...@mit.edu> wrote:
> http://bitesizebio.com/2009/04/13/low-tech-lab-gadgets-and-solutions-my-all-time-favs/

"""
For the record, as well as loving Red Dwarf, I’m a huge fan of
MacGyver, the TV secret agent who could build any device from everyday
items found in the room.

You name it…he could build it in 60 seconds or less using only the
chewing gum and dental floss found in his pocket, escape impending
demise, and have enough time left over to catch the bad guy as well.

As a result, one of my favorite things in the world is to be like
MacGyver and figure out a cheaper or faster way to make or do
something useful using everyday items.

So here is my top ten list of favorite lab MacGyverisms; ways to use
everyday items to make gadgets and low-tech solutions for the lab that
I’ve accumulated over my many years of working as a lab rat and
writing tech articles.

10. Scoops or Measuring Cups = no more weighing. Do you weigh out
yeast extract, NaCl, and agar for each bottle when preparing media?
Save time by weighing the amount of powder that fits in a measuring
cup or scoop and then adjust the volume of media in each of your
flasks.

Designate one scoop for each powder added and just put one scoop of
each per bottle. Weigh once…scoop forever after.

9. Straws = free pasteur pipettes. Plastic straws lifted from
fast-food chains can be used for dilutions and innoculations. This may
take some experimentation, but I have done this for making hundreds of
innoculations for a screening assay without ever having to buy
expensive plastic pipettes.

Of all the varieties I tested, McD straws are the best and will
actually survive autoclaving (wrapped in bunches of 20 inside aluminum
foil!).

The trick is to use a consistent size test tube for dilutions and
adjust the volume so that, when the straw is placed into the tube,
almost exactly 0.5-1.0 ml ends up in the straw.

You then place your finger over the open end and transfer the liquid.
To release the payload, take your finger off the top.

In a similar vein, don’t forget about toothpicks or wooden stir sticks
for replica plating.

8. Spaghetti Colander = no more dropped gels. Instead of using a
spatula to move your gels from stain to rinse solutions and risk
dropping your gel on the floor (butter-side down, of course), use a
small plastic colander fitted inside of a bowl, and several bowls of
the same size for the washes. That way you can just pick up the
colander and move it to the next wash station.

7. Body wash or shampoo = cheap blot washes. Cheap liquid soap can be
used for washings. Shampoo contains Sodium Lauryl Sulfate and can
substitute for expensive wash solutions in many types of blots.

Don’t forget that you can use zip-loc baggies instead of a seal-a-meal
for hybs too. To get all the air bubbles out, place a hollow stir
straw in the corner and make sure all the bubbles go out the straw as
you zip it up. Then slide the straw out while you cinch up the last
little corner.

6. Instant Milk = long life blocking agent. Powdered milk or cream
liquor can be used as a casein-enriched blocking agent for your blots.
It may not be any cheaper to use Bailey’s Blotting Juice, but there is
an obvious added advantage, plus you never have any stale leftovers.

5. Petroleum Jelly = super-cheap hot start. ‘A little dab’ll do ya’ to
“hot start” your Polymerase Chain Reactions. [see Horton et al, 1994]

4. Coffee Grinder = personal minifuge. You can use an old coffee
grinder as a mini-centrifuge by modifying it to have rings for holding
two eppendorf tubes for quick spins. An old-fashioned hand crank mixer
or egg beater also works for this application.

If you use duct tape (not on the list since it is so obvious!) to hold
it on a C-clamp, you can screw it onto the lab bench in any convenient
location.

3. Toothpaste = DIY miniprep matrix. Some brands of toothpaste contain
diatomacieous earth (Celite) as an abrasive. I’ve not tried this
myself, but rumor has it that you can separate out the particles and
use them as a matrix for binding DNA in mini-preps.

2. Furniture polish = fresh-smelling and silanized plates. Instead of
using Rain-X for silanizing glass plates for polyacrylamide gels, use
furniture polish. Spray on, wipe off. You also gain points for doing
all the lab benches along the way, and extra credit for using the
lemon scented variety to freshen up the place.

And the number one low-tech gizmo of all-time is…

1. Record player = shaking incubator. Bob Horton’s homemade shaking
incubator was fashioned out of an old-time record player. The plans
were originally posted to the bionet methods and reagents bulletin
board and highlighted in my monthly column in TiBS under the subtitle
“Spin Doctor” [see Hengen, 1996].A classic MacGyverism.

So what ingenious low-tech solutions do you use in your lab?

References:

1. Horton RM, Hoppe BL, Conti-Tronconi BM. 1994. AmpliGrease: “hot
start” PCR using petroleum jelly. Biotechniques 16:42-43.

2. Hengen PN. 1996. Methods and reagents. Eliminating banding
artifacts from SDS-PAGE. Trends in Biochemical Sciences 21:191-193.

DS

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Apr 17, 2009, 8:25:55 AM4/17/09
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My experience assisting with biosafety and biosecurity practices at
labs in the developing world suggests that Bryan is correct. If you
make information on safety practices available to researchers and lab
personnel, they will use it because it is in their interest to do so.
Safety rules not only protect you from harm, they also limit the
chance of contaminating your experiments.

On Apr 11, 11:45 pm, Bryan Bishop <kanz...@gmail.com> wrote:
> - Bryanhttp://heybryan.org/
> 1 512 203 0507

Meredith L. Patterson

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Apr 17, 2009, 10:51:03 AM4/17/09
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On Fri, Apr 17, 2009 at 4:54 AM, Bryan Bishop <kan...@gmail.com> wrote:
> So what ingenious low-tech solutions do you use in your lab?

When I'm working with facultative anaerobes, I create a CO2-rich
environment in a ziplock baggie. Here's how.

Equipment:
- 2L soda bottle, empty
- Latex balloon with a neck wide enough to stretch over the mouth of
the soda bottle
- Funnel, spoon or small lab-type spatula
- Vinegar
- Baking soda
- Quart-size ziplock baggie
- Jumbo paper clip or screw-type hose clamp
- Petri dish, already loaded with agar and inoculated with your specimen
- Incubator

HOWTO:
1. Pour somewhere between 250 and 500 mL of vinegar into the soda bottle.
2. Fill the latex balloon about half-full of baking soda. You can do
this by sticking the neck of the funnel into the balloon and pouring
baking soda in (you may need to ram it through with a pen or
something, since it's clumpy), or picking up baking soda with the
spoon/spatula and shoving it into the balloon (you will likely spill
baking soda, but it works).
3. Stretch the neck of the balloon over the mouth of the bottle so
that you get a good airtight seal.
4. Hold the body of the balloon upright and shake all the baking soda
into the bottle. The vinegar and baking soda react to evolve carbon
dioxide, and the balloon will fill up.
5. Clamp the neck of the balloon with the jumbo paper clip or hose
clamp, as far from the mouth of the balloon as possible. Leave it on
the bottle for now.
6. Put your petri dish into the ziplock baggie, upside-down, and set
it all on a flat surface. Flatten the baggie as much as possible.
7. Close the ziplock baggie except for a small opening, just wide
enough to admit the neck of the balloon.
8. Detach the inflated balloon from the bottle, taking care to keep it
tightly clamped.
9. Insert the mouth of the balloon as far into the ziplock baggie as you can.
10. Carefully remove the clamp from the balloon. You may not want to
unclamp it all the way. Hold the balloon in one hand and keep your
other hand on the baggie so that the gas doesn't force them apart.
11. When the baggie is completely inflated, quickly slip the balloon
out and close the little opening in the baggie. Make sure the baggie
is fully sealed.
12. Being careful to support the baggie from beneath so that the petri
dish doesn't come open, pick up the baggie/dish apparatus and place it
in your incubator.

I haven't tested this with obligate anaerobes yet, but with
facultative anaerobes, it works great! You will want to check it
periodically (once or twice a day) to make sure that the baggie hasn't
deflated.

Cheers,
--mlp

Dan

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Apr 17, 2009, 12:47:06 PM4/17/09
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Regarding toothpaste -> diatomaceous earth for DNA preps, I'm not sure
if it's worth the considerable trouble. Diatomaceous earth is sold
relatively commonly as a non-chemical insect control agent. (and from
what I've read, it's quite effective and the insects can't develop
resistance to it) I've never seen it in a local store but I just
found it online for 10 lbs/$14.

I remember seeing some old protocols for how to prep diatomaceous
earth for DNA preps - basically a lot of acid washes. I never did it
since it looked like a pain but all reports seem to indicate that it
was as effective a commercial kits when done carefully.

I'm not sure it it's worth the trouble for miniprep-scape DNA preps,
especially since you can regenerate those columns with acid, as
mentioned on this list. However, for really big DNA preps, such as
multi-milligram levels, I can see this approach being worth the time
and effort.

Dan

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Apr 17, 2009, 12:49:30 PM4/17/09
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@ meredith - this is pure conjecture but you mgiht have problems with
obligate anerobes with a ziplock over time as plastic has very high
gas permeability. Freezer bags might be better as they are specially
designed to prevent oxygen from diffusing through them (the cause of
freezer burn). Some experimentation might be in order.

On Apr 17, 7:51 am, "Meredith L. Patterson" <clonea...@gmail.com>
wrote:

Nathan McCorkle

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Apr 18, 2009, 12:00:33 AM4/18/09
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I agree about the plastic for obligate anaerobes... Glass is a DIY supply, mason jars??? getting nitrogen or other inert gas is as well, just gotta invest in a tank, which should be under $100 i think
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

Aaron Hicks

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Apr 18, 2009, 3:24:22 AM4/18/09
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Has anyone tested those chemical handwarmers to see how much oxygen they scavenge?

It's possible that an active handwarmer in a chamber might be enough to drop the oxygen concentration; if not, something like metal chips + salt water should do- magnesium, aluminum, iron, etc. (which are the active components in chemical handwarmers anyway).

They probably don't get down to low ppm concentrations of oxygen very fast, but it's possible a homebrew version could work more swiftly. This company's ATCO product is nothing more than iron powder, salt, and zeolite (available at aquarium stores for ammonia removal):

http://www.cwaller.de/english.htm?oxygen.htm~information

-AJ

Meredith L. Patterson

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Apr 18, 2009, 9:33:19 AM4/18/09
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Working from memory here, I seem to recall freezer bags working better
than regular ziplock bags, so yeah, I think you're right.

Cheers,
--mlp

Mackenzie Cowell

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Apr 23, 2009, 1:45:09 PM4/23/09
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I talked with Randy Rettberg (Director of iGEM) yesterday and he explicitly told me that DIYbio community members that have some kind of "affiliation" with a university can participate in the experimental track.  He's currently expecting like 10 participants for the track.

Mac

William Heath

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Apr 23, 2009, 1:47:05 PM4/23/09
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Anyone have an "affiliation" in the bay area I can affiliate with?

-Tim

P.S.

I shall affiliate.

Mackenzie Cowell

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Apr 23, 2009, 1:53:51 PM4/23/09
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Tim, I encourage you to make contact with the Bay Area Regenerative Science Institute.  They have hosted an iGEM team the last few years and I think you / other DIYBio-SF people would get along well with their advisor.  http://www.regensci.org/RSI/education/rsi-interns/2009-rsi-igem-program.html

Mac

William Heath

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Apr 23, 2009, 2:02:48 PM4/23/09
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I live in Palo Alto, right next to Stanford.  I wish I could find something closer to me.  Any ideas?  

-Tim

Parcon

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Apr 23, 2009, 9:19:07 PM4/23/09
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Any ideas of who I can affiliate with near Charlotte, NC?

- Parc

On Apr 23, 2:02 pm, William Heath <wghe...@gmail.com> wrote:
> I live in Palo Alto, right next to Stanford.  I wish I could find something
> closer to me.  Any ideas?
> -Tim
>
> On Thu, Apr 23, 2009 at 10:53 AM, Mackenzie Cowell <m...@diybio.org> wrote:
> > Tim, I encourage you to make contact with the Bay Area Regenerative Science
> > Institute.  They have hosted an iGEM team the last few years and I think you
> > / other DIYBio-SF people would get along well with their advisor.
> >http://www.regensci.org/RSI/education/rsi-interns/2009-rsi-igem-progr...
> > Mac
>
> > On Thu, Apr 23, 2009 at 1:47 PM, William Heath <wghe...@gmail.com> wrote:
>
> >> Anyone have an "affiliation" in the bay area I can affiliate with?
> >> -Tim
>
> >> P.S.
>
> >> I shall affiliate.
>
> >> On Thu, Apr 23, 2009 at 10:45 AM, Mackenzie Cowell <m...@diybio.org>wrote:
>
> >>> I talked with Randy Rettberg (Director of iGEM) yesterday and he
> >>> explicitly told me that DIYbio community members that have some kind of
> >>> "affiliation" with a university can participate in the experimental track.
> >>>  He's currently expecting like 10 participants for the track.
> >>> Mac
>
> >>> On Thu, Apr 16, 2009 at 1:18 PM, ridgway <ridg...@dridgway.com> wrote:
>
> >>>> Just so people know,http://2009.igem.org/Experimental_trackhas now
> >>>> been updated. Participation requires $500+375/pp and some kind of
> >>>> affiliation with a university, and gets you a 5 min presentation slot
> >>>> and a poster at the iGEM Jamboree. If this maybe sounds interesting to
> >>>> you, and you're in Alberta, drop me a note off-list
> >>>> (ridg...@dridgway.com).

Mackenzie Cowell

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Apr 23, 2009, 9:21:53 PM4/23/09
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Yes!  Google for Davidson College + iGEM.

Mac
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