New Diatom Project

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Charles
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New Diatom Project

#1 Post by Charles » Sat May 23, 2020 11:10 pm

I bought on eBay and have received diatomite from three US locations: Basalt, Nevada; Monterey, Calif; and Santa Monica, Calif. I will document from start to finish, processing these from raw diatomite to the finished type slide. First, the samples, The 5ml tube, I fill half way with diatomite and rest with distilled water to perform a series of freeze and thaw to break the material into a slurry:

Basalt, Nevada, Packaging, raw material, raw strew slide, material in a 5ml tube with distilled water:
Balsalt, Nevada Diatomite2.jpg
Balsalt, Nevada Diatomite2.jpg (98.06 KiB) Viewed 1525 times
Raw strew slide:
Nevada Uncleaned Strew.jpg
Nevada Uncleaned Strew.jpg (137.5 KiB) Viewed 1525 times
Uncleaned Strew Slide showing forms from the strew:
Nevada Uncleaned.jpg
Nevada Uncleaned.jpg (68.57 KiB) Viewed 1525 times

Charles
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Re: New Diatom Project

#2 Post by Charles » Sat May 23, 2020 11:17 pm

Here is the diatomite from Monterey, California:
Monterey, CA Diatomite.jpg
Monterey, CA Diatomite.jpg (122.98 KiB) Viewed 1519 times
Uncleaned strew:
Monteray CA Uncleaned Strew.jpg
Monteray CA Uncleaned Strew.jpg (182.88 KiB) Viewed 1519 times
Diatoms from raw strew:
Monteray CA Uncleaned.jpg
Monteray CA Uncleaned.jpg (69.38 KiB) Viewed 1519 times

Charles
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Re: New Diatom Project

#3 Post by Charles » Sat May 23, 2020 11:20 pm

Diatomite from Santa Monica, California:
Santa Monica, CA Diatomite.jpg
Santa Monica, CA Diatomite.jpg (107.77 KiB) Viewed 1519 times
Raw Uncleaned Strew slide:
Santa Monica Uncleaned Strew.jpg
Santa Monica Uncleaned Strew.jpg (142.88 KiB) Viewed 1519 times
Diatoms from Raw Strew slide:
Santa Monica Uncleaned.jpg
Santa Monica Uncleaned.jpg (69.02 KiB) Viewed 1519 times

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KurtM
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Re: New Diatom Project

#4 Post by KurtM » Sun May 24, 2020 12:07 am

I will document from start to finish, processing these from raw diatomite to the finished type slide.
Most excellent! I am already very much looking forward to each and every installment!
Cheers,
Kurt Maurer
League City, Texas
email: ngc704(at)aol(dot)com
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Hobbyst46
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Re: New Diatom Project

#5 Post by Hobbyst46 » Sun May 24, 2020 10:11 am

Very appealing post.
How many freeze/thaw cycles produced the raw strew slides shown above ?
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Charles
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Re: New Diatom Project

#6 Post by Charles » Sun May 24, 2020 12:49 pm

Thank you Kurt and Doron for your interest.
Hobbyst46 wrote:
Sun May 24, 2020 10:11 am
How many freeze/thaw cycles produced the raw strew slides shown above ?
The sample from the strew slide had not gone through the freeze/thaw cycle yet. The raw strew slide was made from the powder in the packaging mixed with a few drops of water on the slide. The raw diatomite is a bit crumbly. The whiter the material, the more crumbly it is. It should take between 15-20 freeze/thaw cycles to get the diatomite into a slurry.

The purpose of the raw strew slides was so I could see what to expect from each sample. It looks like the Nevada sample came from fresh water since it is predominately fresh water species and they are well distributed in the diatomite. The least promising is the Monterey sample but you never know until they have been cleaned and condensed.

The seller said he sold quite a bit to Stefano Barone of the Diatom Shop, and I see he is currently selling some nice diatoms from the Santa Monica deposit.

Wes
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Re: New Diatom Project

#7 Post by Wes » Mon May 25, 2020 6:04 am

I like your project.

From previous threads you linked to in my Oamaru post it looked like you are using Zrax and Klaus Kemp's adhesive. From what I read it seems like Zrax (which is probably just good grade Naphrax based on IR spectra) bubbles a lot less than Pleurax. I suspect the pleurax bubbling that some people report might be related to the higher vapour pressure of isopropanol vs toluene (pleurax vs zrax/naphrax solvents resp.).

Anyone care to share their experience with different mounting media and adhesives? What works well for you and such..

Hobbyst46
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Re: New Diatom Project

#8 Post by Hobbyst46 » Mon May 25, 2020 6:41 am

Wes wrote:
Mon May 25, 2020 6:04 am
I like your project.

From previous threads you linked to in my Oamaru post it looked like you are using Zrax and Klaus Kemp's adhesive. From what I read it seems like Zrax (which is probably just good grade Naphrax based on IR spectra) bubbles a lot less than Pleurax. I suspect the pleurax bubbling that some people report might be related to the higher vapour pressure of isopropanol vs toluene (pleurax vs zrax/naphrax solvents resp.).

Anyone care to share their experience with different mounting media and adhesives? What works well for you and such..
I can only testify for Pleurax. The manufacturer's instructions are to heat the slide very slowly until it reaches the target temperature. Indeed, rapid heating causes intensive bubbling upon evaporation of the IPA. Upon gradual heating, bubbling is less fierce and a fairly uniform layer of mountant spreads between the slide and coverslip. It is possible to avoid temperature overshoot.
Zeiss Standard GFL+Canon EOS-M10, Olympus VMZ stereo

Wes
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Re: New Diatom Project

#9 Post by Wes » Mon May 25, 2020 7:00 am

Hobbyst46 wrote:
Mon May 25, 2020 6:41 am
Wes wrote:
Mon May 25, 2020 6:04 am
I like your project.

From previous threads you linked to in my Oamaru post it looked like you are using Zrax and Klaus Kemp's adhesive. From what I read it seems like Zrax (which is probably just good grade Naphrax based on IR spectra) bubbles a lot less than Pleurax. I suspect the pleurax bubbling that some people report might be related to the higher vapour pressure of isopropanol vs toluene (pleurax vs zrax/naphrax solvents resp.).

Anyone care to share their experience with different mounting media and adhesives? What works well for you and such..
I can only testify for Pleurax. The manufacturer's instructions are to heat the slide very slowly until it reaches the target temperature. Indeed, rapid heating causes intensive bubbling upon evaporation of the IPA. Upon gradual heating, bubbling is less fierce and a fairly uniform layer of mountant spreads between the slide and coverslip. It is possible to avoid temperature overshoot.
What is the target temperature?

Hobbyst46
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Re: New Diatom Project

#10 Post by Hobbyst46 » Mon May 25, 2020 10:36 am

As far as I remember, heating the Pleurax mounted slide should be a slow ramp until about 180C, then 15 minutes at 180C.
Zeiss Standard GFL+Canon EOS-M10, Olympus VMZ stereo

MicroBob
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Re: New Diatom Project

#11 Post by MicroBob » Mon May 25, 2020 11:40 am

Hi together,
right before Cornona I prepared a group meeting on diatom strew slide making. The aim was to do a bit slide production from selected really nice material so everybody has some slides to take home. For this I built a small heat plate that heats a round cover slip which is then picked up with a pre warmed slide.
In my experiments in the preparation I had some cases where I didn't heat the slide enough to the warm Pleurax to spread fully. In these cases I warmed the cover slips a bit with a cigarette lighter (blue flame version). Here I recognized that in some cases "particles" formed in the mountant reducing the value of the slides considerably. The particles were visible by plain eye as a kind of misty look of the mountant. I haven't checked this in detail but there seems to be a temperature limit that has to adhered to.

Pleurax diatom slide mounting works best upside down in my opinion:
- Cover slip with diatoms (powder can just be shoveled on, spread itself later)
- drop of Isopropanol
- 1-2 drops of Pleurax
- put coverslip on pre heated heat plate (180°C in my case)
- pick up cover slip with pre heated slide (montant spreads well)
- let cool upside down with no pressure on cover slip

I would like to check the "particles" problem first and then show my new equipment and process, will takes some time.

Bob

Charles
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Re: New Diatom Project

#12 Post by Charles » Mon May 25, 2020 1:49 pm

Wes wrote:
Mon May 25, 2020 6:04 am
I like your project.

From previous threads you linked to in my Oamaru post it looked like you are using Zrax and Klaus Kemp's adhesive. From what I read it seems like Zrax (which is probably just good grade Naphrax based on IR spectra) bubbles a lot less than Pleurax. I suspect the pleurax bubbling that some people report might be related to the higher vapour pressure of isopropanol vs toluene (pleurax vs zrax/naphrax solvents resp.).

Anyone care to share their experience with different mounting media and adhesives? What works well for you and such..
I do use Zrax, which uses Toluene as the solvent and it also bubbles violently when heated. I think any solvent will bubble a lot when heated to drive off the solvent. I also have Naphrax and Pleurax and will test each.

Charles
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Re: New Diatom Project

#13 Post by Charles » Thu May 28, 2020 4:44 pm

I've gone through about 25 freeze/ thaw cycles with the 5ml tubes and decided to process more material, while I await the arrival of my 250ml flasks to do the rest of the acid processing. So I put some raw material into a 10ml plastic tube for the freeze/thaw cycles. Got about 10 cycles and one of the tubes developed a crack and I just poured it into another tube. About 10 cycles later, it developed cracks again. I thought I left plenty of air gap in the tubes with samples and water but apparently the pressure of the freeze/thaw cycle was too much. Transferred the contents to another tube to finish the cycles
Cracked.jpg
Cracked.jpg (120.43 KiB) Viewed 1322 times

MicroBob
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Re: New Diatom Project

#14 Post by MicroBob » Thu May 28, 2020 7:13 pm

Hi Charles,
I wouldn't have expected that to happen with a PE or PP bottle. Perhaps you could use a silicone form for ice cubes or choclate making?

Bob

Hobbyst46
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Re: New Diatom Project

#15 Post by Hobbyst46 » Thu May 28, 2020 9:11 pm

Charles,
Are those Falcon tubes ?
I am asking because, Falcon tubes are made of PP or PS and are recommended for freezing and thawing.
On the other hand, standard Falcon tubes are nominally 15 ml or 50 ml, not 10 ml as those in the photo.
Zeiss Standard GFL+Canon EOS-M10, Olympus VMZ stereo

Charles
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Re: New Diatom Project

#16 Post by Charles » Thu May 28, 2020 9:40 pm

I don't know what brand they are but they were inexpensive. I noticed that even though I left an air gap for expansion, a couple of the samples actually expanded it's volume in the tube during the freeze/thaw cycle.

Hobbyst46
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Re: New Diatom Project

#17 Post by Hobbyst46 » Thu May 28, 2020 10:08 pm

In general (Wikipedia) PP tends to be brittle upon freezing...
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Charles
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Re: New Diatom Project

#18 Post by Charles » Thu May 28, 2020 10:21 pm

Hobbyst46 wrote:
Thu May 28, 2020 10:08 pm
In general (Wikipedia) PP tends to be brittle upon freezing...
Good thing I have lots of spares. Surprisingly the 5ml tubes have not cracked even after about 30 cycles.

Charles
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Re: New Diatom Project

#19 Post by Charles » Fri May 29, 2020 2:19 pm

MicroBob wrote:
Thu May 28, 2020 7:13 pm
Hi Charles,
I wouldn't have expected that to happen with a PE or PP bottle. Perhaps you could use a silicone form for ice cubes or choclate making?
Bob
Bob, Yes, I think using open topped containers like ice cube trays or just storage dishes would work better. It not only has lots of room to expand and contract, but also would not leak like the screw capped vials. The screw capped vials do not appear that tight and is pulling in water when I immerse them in warm water to get them to thaw faster.

Picture of the samples in the vials after about 30 freeze/thaw cycles. All the rock has turned into a fine slurry, except the one from Monterey is a bit coarser.
Diatom Samples.jpg
Diatom Samples.jpg (100.93 KiB) Viewed 1252 times
My 250ml flasks should arrive today for the next step of acid treatment.

Hobbyst46
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Re: New Diatom Project

#20 Post by Hobbyst46 » Fri May 29, 2020 2:46 pm

Charles,
I do not have financial relations with suppliers of Falcon tubes, and I do not remember their price, but for what its worth, they never leak. Neither the 15mls, nor the 50mls. And, although they are dispensable, I reuse them many many times. For my last field mission, the 50mls were great - tossed them (with their smelly muddy contents) into a plastic bag and never worried about leaks on my way home...
Only that I use the PP ones, not the transparent PS ones, since the stoppers of the latter are fragile and they are attacked by acetone.
Those tubes are usable upon heating up to ~60-70C.
Last edited by Hobbyst46 on Fri May 29, 2020 2:58 pm, edited 3 times in total.
Zeiss Standard GFL+Canon EOS-M10, Olympus VMZ stereo

Wes
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Re: New Diatom Project

#21 Post by Wes » Fri May 29, 2020 2:55 pm

Hobbyst46 wrote:
Fri May 29, 2020 2:46 pm
Charles,
I do not have financial relations with suppliers of Falcon tubes, and I do not remember their price, but for what its worth, they never leak. Neither the 15mls, nor the 50mls. And, although they are dispensable, I reuse them many many times. For my last field mission, the 50mls where great - toss them (with their smelly muddy contents) into a plastic bag and never worry about leaks on the way... Only that I use the PP ones, not the transparent PS ones, since the stoppers or the latter are fragile and they are attacked by acetone.
Those tubes are usable upon heating up to ~60-70C.
I tend to agree. I freeze antibody dilutions to recycle antibody (expensive stuff) and use 15 ml Falcons, so far none of them have leaked.

I did however overfill a 50 ml Falcon with water to freeze and use the frozen vial as a cooling body in an experiment generating plenty of heat but those cracked (I did not leave any space for volume expansion).

Charles
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Re: New Diatom Project

#22 Post by Charles » Sat May 30, 2020 12:25 pm

Thanks. I will look into the Falcon tubes.

I was going to start the acid processing and need to do it outside, since I don't have a fume hood, but the weather will not cooperate. It's suppose to rain most of the day.

I want to start with the HCl 30%, to get rid of any calcium carbonates and any metals. I'll heat it in boiling water bath, dilute and remove the HCl and then use Sulfuric acid heated again in a boiling water bath, dilute and remove. Personal protection will include chemical resistant gloves, eye/face protection, lots of water and sodium bicarb on hand and performed outside.

Hobbyst46
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Re: New Diatom Project

#23 Post by Hobbyst46 » Sat May 30, 2020 1:24 pm

Charles wrote:
Sat May 30, 2020 12:25 pm
Thanks. I will look into the Falcon tubes.

I was going to start the acid processing and need to do it outside, since I don't have a fume hood, but the weather will not cooperate. It's suppose to rain most of the day.

I want to start with the HCl 30%, to get rid of any calcium carbonates and any metals. I'll heat it in boiling water bath, dilute and remove the HCl and then use Sulfuric acid heated again in a boiling water bath, dilute and remove. Personal protection will include chemical resistant gloves, eye/face protection, lots of water and sodium bicarb on hand and performed outside.
Watching from a safe distance... :)
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Charles
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Re: New Diatom Project

#24 Post by Charles » Sat May 30, 2020 3:37 pm

Hobbyst46 wrote:
Sat May 30, 2020 1:24 pm
Watching from a safe distance... :)
Yes, I think you are at a safe distance!

Trying to HCl cook, hoping the rains will hold off.
Diatom Cooking HCl.jpg
Diatom Cooking HCl.jpg (300.76 KiB) Viewed 1158 times

MicroBob
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Re: New Diatom Project

#25 Post by MicroBob » Sat May 30, 2020 8:30 pm

Hi Charles,
when I collect diatoms silt and sand are usually my problem contents. I try to remove them by selecting after the speed in which they settle in a suspension. How do you remove stuff like silt and sand and when do you do it?

Bob

Zuul
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Re: New Diatom Project

#26 Post by Zuul » Sat May 30, 2020 9:19 pm

Charles wrote:
Sat May 30, 2020 12:25 pm
Thanks. I will look into the Falcon tubes.

I was going to start the acid processing and need to do it outside, since I don't have a fume hood, but the weather will not cooperate. It's suppose to rain most of the day.

I want to start with the HCl 30%, to get rid of any calcium carbonates and any metals. I'll heat it in boiling water bath, dilute and remove the HCl and then use Sulfuric acid heated again in a boiling water bath, dilute and remove. Personal protection will include chemical resistant gloves, eye/face protection, lots of water and sodium bicarb on hand and performed outside.
Is heating necessary, or simply a way to speed the process? I frequently use HCl to clear calcium carbonate from marine equipment, but even at room temperature the acid is aggressive. I’m also curious what the sulfuric dissolves that HCl doesn’t. It’s been a while since my last chem class. :D

Charles
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Re: New Diatom Project

#27 Post by Charles » Sat May 30, 2020 11:27 pm

Zuul wrote:
Sat May 30, 2020 9:19 pm
Is heating necessary, or simply a way to speed the process? I frequently use HCl to clear calcium carbonate from marine equipment, but even at room temperature the acid is aggressive. I’m also curious what the sulfuric dissolves that HCl doesn’t. It’s been a while since my last chem class. :D
Some don't heat and leave it for 24 hrs. Some (I) heat to move the process faster. HCl dissolve Calcareous matter and some metals. Sulfuric and or Nitric acid removes organics and cellulose.

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KurtM
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Re: New Diatom Project

#28 Post by KurtM » Sun May 31, 2020 12:41 am

Charles, can you add a word on where you obtain your chemicals? Muriatic acid I know to be available in home improvement/hardware stores, but any comment regarding concentration? I seem to remember there being some discussion of having to be careful to buy the 'strong stuff'. And where do you get sulfuric acid? I bought auto battery electrolyte some time back, but it sure didn't seem to do much.

Disclaimer: I operate under the handicap of not having had a single chemistry class in my life, and little, if any, intuition for it.

Thanks again for doing this, I am following this thread with utmost interest. :geek:
Cheers,
Kurt Maurer
League City, Texas
email: ngc704(at)aol(dot)com
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deBult
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Re: New Diatom Project

#29 Post by deBult » Sun May 31, 2020 5:49 am

The diatoms shop in Holland sells pre-cleaned diatom samples (Website in English) and Mountants and other gear you may need.

So no unknown dangerous acids to mess around with: https://www.diatoms.nl/index.php?seo_path=samples

Happy customer only,
Best, deBult.

Charles
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Re: New Diatom Project

#30 Post by Charles » Sun May 31, 2020 11:59 am

MicroBob wrote:
Sat May 30, 2020 8:30 pm
when I collect diatoms silt and sand are usually my problem contents. I try to remove them by selecting after the speed in which they settle in a suspension. How do you remove stuff like silt and sand and when do you do it?
Hi Bob, I do this after the material has been cleaned. Once it is cleaned and gone through it's rinse cycles (about 5-6), I will suspend everything by shaking and then wait about 10 seconds and pour off the rest to a clean test tube. I will add more distilled water and re-suspend again, wait and pour off to the other test tube. I keep the coarse material too to ensure I don't have diatoms in there. I learned that heavy sediment will contain diatoms viewtopic.php?f=10&t=4227&start=60, so never through away the wash water or sediment until have looked and are sure there are no diatoms in it. Also I will be picking out the diatoms from a strew of the sample to a clean 'Keeper' slide so, some sediment is not a problem for me.

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