Re: [DIYbio] Magnetotactic microorganism culture - minimum equipment requirements?

[Jeswin]

I looked at the powerpoint. I must say that this is a very interesting
concept. I'll look into it.

This is the future of DIYbio. Good luck

On Sun, Sep 9, 2012 at 11:20 PM, Michael Turner
<michael.eu...@gmail.com> wrote:
>
> (Note: first post to this list.)
>
> I have responsibility for a proof-of-concept for microbial spacecraft
> components. A draft presentation can be found at the "Current Project" link
> at this website:
>
> http://www.projectpersephone.org
>
> (Note: pptx format; alternating English and Japanese.)
>
> Can anyone suggest the minimal equipment for culturing magnetotactic
> microbes -- most likely bacteria (magnetospirilli) but possibly microalgae?
> Magnetospirilli are available in pure culture. However, they require some
> control of the oxygen in solution -- too much is as bad as too little. (In
> fact magnetospirilli use their magnetosomes to help swim in the right
> direction, toward the optimal oxygen stratum.) Magnetotactic algae might be
> easier to culture. The problem would be where to get (or how to derive) the
> starter batch. The most recent publication I've seen on magnetotactic algae
> is from the late 1980s.
>
> Ideal equipment specs:
>
> - highly available without much red tape (note: Japanese biotech industry
> regulations may apply)
> - usable in a high-school wet lab, by high school students
> - so cheap that bulk purchases could form the basis for kits you could
> give away to schools
>
> Yes, I know: "good, cheap, soon -- pick any two." At this point, however,
> I'm not sure which two would be my priorities. I might need to take any two
> I can get.
>
> Regards,
> Michael Turner
> Project Persephone
> 1-25-33 Takadanobaba
> Shinjuku-ku Tokyo 169-0075
> (+81) 90-5203-8682
> tur...@projectpersephone.org
> http://www.projectpersephone.org/
>
> "Love does not consist in gazing at each other, but in looking outward
> together in the same direction." -- Antoine de Saint-Exupéry
>
> --
> You received this message because you are subscribed to the Google Groups
> "DIYbio" group.
> To post to this group, send email to diy...@googlegroups.com.
> To unsubscribe from this group, send email to
> diybio+un...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msg/diybio/-/VEN9N7a4dWUJ.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>

[Simon Quellen Field]

The cheapest and fastest way to control the oxygen environment for your

critters is to set up a gradient. The bottom of a tall jar has no oxygen, and

the top has plenty, and the critters will swim to the middle where they are happy.

-----

Get a free science project every week! "http://scitoys.com/newsletter.html"

[Cathal Garvey]

Provided, of course, that you have no magnetic/electric nearby to mess
up their idea of up/down. ;)

>> http://www.projectpersephone.**org/ <http://www.projectpersephone.org/>

>>
>> "Love does not consist in gazing at each other, but in looking outward together

>> in the same direction." -- Antoine de Saint-Exup�ry

>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "DIYbio" group.
>> To post to this group, send email to diy...@googlegroups.com.
>> To unsubscribe from this group, send email to
>> diybio+un...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msg/diybio/-/VEN9N7a4dWUJ.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>>
>

--
www.indiebiotech.com
twitter.com/onetruecathal
joindiaspora.com/u/cathalgarvey
PGP Public Key: http://bit.ly/CathalGKey

[Michael Turner]

On Tue, Sep 11, 2012 at 1:33 AM, Simon Quellen Field <sfi...@scitoys.com> wrote:
> The cheapest and fastest way to control the oxygen environment for your
> critters is to set up a gradient. The bottom of a tall jar has no oxygen,
> and
> the top has plenty, and the critters will swim to the middle where they are
> happy.

Thanks. Yes, with a tall enough jar, the right concentration of oxygen
will happen somewhere. I hadn't thought of that. But what if the
optimal level changes because of the effects of the bacteria living in
it (waste products, etc.)?

I'd like to be able to concentrate these bacteria as they are
continuously produced. Knowing the best elevation at which to
periodically tap the column of water would be useful.

I'm very leery of contaminating the culture, so I'd prefer an
arrangement that didn't require opening a culture container and
sampling concentrations at different depths. Maybe a vertical pipe
with stopcocks every few centimeters or so? I don't want the equipment
bill to add up to much, so anything that simplifies the system is
welcome.

--

[Simon Quellen Field]

Magnetotactic bacteria are easy to collect, because (wait for it...)

they follow magnetic fields.

Place one horizontal pipe halfway up the column the colony is living in.

Wrap a coil of wire around the horizontal pipe.

Send a current through the coil.

The bacteria will swim down the horizontal pipe, even if the oxygen levels

there are not ideal.

An added bonus is that few other organisms will follow them, so you have

concentrated the species you are after.

-----

Get a free science project every week! "http://scitoys.com/newsletter.html"

[ByoWired]

On Wednesday, September 12, 2012 12:38:22 PM UTC-4, Simon Field wrote:

Magnetotactic bacteria are easy to collect, because (wait for it...)

they follow magnetic fields.

Are you sure you want to make a magnet this way? 

I've never worked with magnetotactic bacteria but I've heard they are notoriously difficult to isolate and culture.

Google "magnetotactic difficult" and see what pops up.  

[Simon Quellen Field]

Isolation and culture are different than collecting.

The original post seemed to assume a culture that was already pure,

and was concerned with oxygen starvation and oxygen poisoning.

Actually, magnetotactic bacteria are notoriously easy to collect from

uncultured sediments.

That paper basically uses exactly the method I proposed in my reply.

I wish I had seen it, I would have linked to it originally.

-----

Get a free science project every week! "http://scitoys.com/newsletter.html"

--

You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diy...@googlegroups.com.
To unsubscribe from this group, send email to diybio+un...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msg/diybio/-/1Xnat493w0cJ.

[Avery louie]

According to betsy dexter deyers book, magnets in a windogradsky column work well.

--A

[Michael Turner]

On Thu, Sep 13, 2012 at 12:29 PM, Avery louie <inact...@gmail.com> wrote:
> According to betsy dexter deyers book, magnets in a windogradsky column work
> well.

Yes! Thank you.

A Field Guide to Bacteria, Betsey Dexter Dyer, pp.102-104

I'm embarrassed about not running across this before.

Regards,
Michael Turner
Project Persephone
1-25-33 Takadanobaba
Shinjuku-ku Tokyo 169-0075
(+81) 90-5203-8682
tur...@projectpersephone.org
http://www.projectpersephone.org/

"Love does not consist in gazing at each other, but in looking outward
together in the same direction." -- Antoine de Saint-Exupéry

[Jeswin]

On Wed, Sep 12, 2012 at 11:29 PM, Avery louie <inact...@gmail.com> wrote:
> According to betsy dexter deyers book, magnets in a windogradsky column work
> well.
>
> --A
>

So is it possible for me to go out and collect some magnetotactic
bacteria with this method?

[ByoWired]

On Sunday, September 9, 2012 11:20:09 PM UTC-4, Michael Turner wrote:

(Note: first post to this list.)

...

Can anyone suggest the minimal equipment for culturing magnetotactic microbes ...

Have a look at the 2011 book, Metal Nanoparticles in Microbiology.  It has an entire chapter on growing magnetosomes.

Also there's a book called Magnetoreception and Magnetosomes in Bacteria, which ain't too shabby either.

I'm surprised the know-it-alls on this forum didn't point you to these books already.  Shocking.

[witold]

In this publication, they used a really simple method for culturing

http://www.google.fr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CCUQFjAA&url=http%3A%2F%2Fwww.impmc.jussieu.fr%2F~menguy%2FPDFs%2FArticles%2FIsambert_AmMin_2007.pdf&ei=3D1hULrxOZKk0AW6oIDABA&usg=AFQjCNELv6Uf8adRUYXYw38nG81-xn2YFA

You can use a powerful magnet to isolate them.

I've tried it but it seems like i waited too long, now I have a really interesting ecosystem in my bottle. Different kinds of algae, and a very large colony of red bacterias but i don't know what it is though...

Tell us about your progress.

Bye.

 

--
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diy...@googlegroups.com.
To unsubscribe from this group, send email to diybio+un...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msg/diybio/-/Xu-vxKVpBhgJ.

[Jeswin]

On Tue, Sep 25, 2012 at 1:20 AM, witold <alb...@gmail.com> wrote:
> In this publication, they used a really simple method for culturing
> http://www.google.fr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CCUQFjAA&url=http%3A%2F%2Fwww.impmc.jussieu.fr%2F~menguy%2FPDFs%2FArticles%2FIsambert_AmMin_2007.pdf&ei=3D1hULrxOZKk0AW6oIDABA&usg=AFQjCNELv6Uf8adRUYXYw38nG81-xn2YFA
> You can use a powerful magnet to isolate them.
> I've tried it but it seems like i waited too long, now I have a really
> interesting ecosystem in my bottle. Different kinds of algae, and a very
> large colony of red bacterias but i don't know what it is though...
> Tell us about your progress.
> Bye.

This is interesting stuff. Anyone know if the DIY web-cam microscopes
can be used to look at these bacteria. Maybe watch how magnets affect
them?

[Michael Turner]

I'd be particularly interested in that if it could result in a
compelling classroom demonstration.

[witold]

You can see them with your own eye when you collect them with this method.
https://www.youtube.com/watch?v=fCSOdQK5PIY
https://www.youtube.com/watch?v=I7PnRY4md4s

I don't know what is the power required by the magnet to attract them. I think it was my mistake during my first attempt.

> --
> You received this message because you are subscribed to the Google Groups "DIYbio" group.
> To post to this group, send email to diy...@googlegroups.com.
> To unsubscribe from this group, send email to diybio+un...@googlegroups.com.

[Simon Quellen Field]

Towards the end of the second video, they are trying to use a refrigerator

magnet to attract the cells.

Unlike the other magnets, refrigerator magnets are made by creating thin

stripes of alternating north and south poles. This allows the relatively weak

magnets (ferrite in a rubber matrix) to stick to the fridge. Unless the poles

are close together, the rubber magnets can't generate enough force to stick.

You can confirm this by rubbing the north pole of a strong NdFeB magnet

all around one side of the rubber magnet. That will make that side south,

and the other side north. It will no longer stick to the fridge.

The bacteria swim along the field lines. The magnetosomes are not actualy

being pulled by the magnet to drag the bugs around, the bugs just use them

as a compass to tell up from down (they don't care about north and south).

In higher latitudes, the Earth's magnetic field points down, and at the magnetic

pole, it points straight down. I would expect to find fewer magnetotactic

bacteria at the equator than near the magnetic poles, as the expense of

making the magnetosomes is only worthwhile if they can be used to find the

oxic-anoxic boundary (i.e. moving up and down is important, north and south

is not).

I would also expect bugs from south of the equator to swim in the opposite

direction from those north of the equator. One could use this as a test to see

if the bugs learn which way to go, or whether it is innate in their genes.

So with the fridge magnet, whose poles are less than a millimeter apart, you

won't see a lot of movement, since the bugs just move from one pole to the

other.

The Earth's magnetic field is very weak, so the strength of the magnet should

not matter much. You could try the modified rubber magnet, and it might work

as well as the strong NdFeB magnet. Some NdFeB magnets might be strong enough

to actually drag the bacteria around by their magnetosomes, as opposed to making

them swim in a particular direction. You could test this by reversing the magnet.

Swimmers should swim away. Dragged bugs would still be attracted.

-----

Get a free science project every week! "http://scitoys.com/newsletter.html"

[Cathal Garvey]

Webcam-scopes tend to have magnifications of between 200x and 400x. To
see bacteria at all, you generally need 600x-1000x, preferably better,
and preferably with oil-immersion to direct more light into the lens.

Short answer; seeing bacteria with a DIY Webcam microscope is unlikely,
sadly.

[Jeswin]

On Wed, Sep 26, 2012 at 10:29 AM, Cathal Garvey <cathal...@gmail.com> wrote:
> Webcam-scopes tend to have magnifications of between 200x and 400x. To
> see bacteria at all, you generally need 600x-1000x, preferably better,
> and preferably with oil-immersion to direct more light into the lens.
>

Is there any way to add a microscope lens to a webcam and get the
required magnification? Will that cause aberrations? Just looking for
a cheap DIY microscope.

[Cathal Garvey]

I'm pretty sure if you just shove a camera up to a microscope eyepiece
you can get half-decent pictures. I've done it a few times, but YMMV
according to camera quality and probably lens setup.

It's really more a question for Simon, I think he's the resident list
microscope expert..

[Simon Quellen Field]

Yes, there are inexpensive ways to get high resolution microscope photos

and video.

I have here on my desk a webcam whose lens I have replaced with a 40x

microscope objective. I also have an adapter I built from a cheap plastic

lens cap that allows me to put microscope objectives on my DSLR camera.

I will be including both of these in my microscope book.

A 40x microscope objective costs about $30, and can achieve resolutions

under half a micron fairly easily.

But to take video of magnetotactic bacteria changing direction when you change

the magnetic field polarity, you don't need much at all. 200x magnification will

show bacteria just fine if you set it up for dark field illumination. It is the same

illumination that allows your naked eye to see motes of dust in a sunbeam.

Anton Van Leeuenhoek saw bacteria with a single lens, similar to the one you

can make as shown here.

-----

Get a free science project every week! "http://scitoys.com/newsletter.html"

--
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diy...@googlegroups.com.
To unsubscribe from this group, send email to diybio+un...@googlegroups.com.

[Simon Quellen Field]

To see what Cathal was referring to, look here.

-----

Get a free science project every week! "http://scitoys.com/newsletter.html"