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Re: cleaning diatoms

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  • Keith Shaw
    Hello Brian (and Alex), Now this bubbler/foam diatom isolation idea is very interesting! Brian, to save us doing some re-inventing the wheel experiments,
    Message 1 of 17 , May 1, 2011
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      Hello Brian (and Alex),

      Now this bubbler/foam diatom isolation idea is very interesting!

      Brian, to save us doing some "re-inventing the wheel" experiments, would you be willing to give us a more detailed description of your apparatus to get started?
      Like form of the container for the electrodes. Maybe a cylinder?
      Surface area of the electrodes and spacing?
      Etc., etc...

      Thank you in advance for any assistance.
      -Keith


      "urginia" wrote:
      > ...
      > I only tried the following once, many years ago, but it
      > worked a treat with a mixed marine plankton sample:
      > 4.5 volt battery with two aluminium electrodes.
      > Produced very fine bubbles...
    • urginia
      Hi Keith, I will try and reconstruct what I did from memory! I realise now that it must be well over 30 years ago that I tried this. Please note that I did
      Message 2 of 17 , May 1, 2011
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        Hi Keith,

        I will try and reconstruct what I did from memory! I realise now that it must be well over 30 years ago that I tried this. Please note that I did this with a live diatom-dominated marine plankton net sample.

        The volume of sample would have been between 500 and 1000 ml. As you surmised I did this in a cylinder ...probably a 1000ml measuring cylinder. Size of electrodes - I guess about 8 x 3 cm. I held them apart with some pieces of neoprene...perhaps 1cm apart, and the whole held together with elastic bands. I attached wires to the electrodes with paper clips.

        My recollection is that the cells were scavenged into a surface scum very quickly... definitely minutes rather than hours...say 30 mins. The removal of cells was almost total, leaving clear water below. The key to this (I think) was a) the very small bubbles that were formed and b) the colloidal (? magnesium) salt that trapped the cells.

        The general process of scavenging cells and organic matter from suspensions by ascending bubbles is widely used and known as "foam fractionation" or "protein skimming". The separation achieved depends partly on the hydrophobic nature of the material being separated... therefore it may well only work efficiently with living diatoms with intact cells.

        I only used this "electrolytic" method once when I was messing around, but I remember telling someone about it and they achieved a very high separation as well with diatom cultures and other algal cultures. I just parked the method in my head as something interesting to try again when i got some time.

        At best my "experiment" was a proof of concept - no more !

        Good luck if you try to develop this further !

        boa sorte
        Brian


        --- In diatom_forum@yahoogroups.com, "Keith Shaw" <scitech200@...> wrote:
        >
        > Hello Brian (and Alex),
        >
        > Now this bubbler/foam diatom isolation idea is very interesting!
        >
        > Brian, to save us doing some "re-inventing the wheel" experiments, would you be willing to give us a more detailed description of your apparatus to get started?
        > Like form of the container for the electrodes. Maybe a cylinder?
        > Surface area of the electrodes and spacing?
        > Etc., etc...
        >
        > Thank you in advance for any assistance.
        > -Keith
        >
        >
        > "urginia" wrote:
        > > ...
        > > I only tried the following once, many years ago, but it
        > > worked a treat with a mixed marine plankton sample:
        > > 4.5 volt battery with two aluminium electrodes.
        > > Produced very fine bubbles...
        >
      • Keith Shaw
        Hi Brian, Thank you very much for the outline of your proof-of-concept apparatus. Very small bubbles streaming off the electrodes is an interesting alternative
        Message 3 of 17 , May 2, 2011
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          Hi Brian,

          Thank you very much for the outline of your proof-of-concept apparatus.
          Very small bubbles streaming off the electrodes is an interesting alternative to the conventional porous "stone" with a compressed air feed, e.g. aquarium bubbler.
          In general, as also suggested by Alex, it just seems to make a lot of sense to be able to concentrate the marine diatoms in the foam, relatively easily and mostly free(?) of other organic matter...

          But right now I have to stay focused on sorting out a reproducible bleach protocol to routinely clean the marine/marshland diatoms I have been collecting. I'm starting to see some success and will prepare a series of images for the group.

          I have also, finally, figured out a way to roll a diatom in a critically adjusted water column (between slide and coverslip). It takes a lot of patience but the resulting, unambiguous valve and girdle images makes the effort worthwhile...

          -Keith



          "urginia" wrote:
          > Hi Keith,
          > I will try and reconstruct what I did from memory! I realise now that it must be well over 30 years ago that I tried this. Please note that I did this with a live diatom-dominated marine plankton net sample.
          >
          > The volume of sample would have been between 500 and 1000 ml. As you surmised I did this in a cylinder ...probably a 1000ml measuring cylinder. Size of electrodes - I guess about 8 x 3 cm. I held them apart with some pieces of neoprene...perhaps 1cm apart, and the whole held together with elastic bands. I attached wires to the electrodes with paper clips.
          >
          > My recollection is that the cells were scavenged into a surface scum very quickly... definitely minutes rather than hours...say 30 mins. The removal of cells was almost total, leaving clear water below. The key to this (I think) was a) the very small bubbles that were formed and b) the colloidal (? magnesium) salt that trapped the cells.
          >
          > The general process of scavenging cells and organic matter from suspensions by ascending bubbles is widely used and known as "foam fractionation" or "protein skimming". The separation achieved depends partly on the hydrophobic nature of the material being separated... therefore it may well only work efficiently with living diatoms with intact cells.
          >
          > I only used this "electrolytic" method once when I was messing around, but I remember telling someone about it and they achieved a very high separation as well with diatom cultures and other algal cultures. I just parked the method in my head as something interesting to try again when i got some time.
          >
          > At best my "experiment" was a proof of concept - no more !
          >
          > Good luck if you try to develop this further !
          >
          > boa sorte
          > Brian
        • charles
          Hello Mr. Dailey, I think there is a typo in item #3 of your method. You first mention heat H2SO4 and it is followed by the statement add oxidant to bleach .
          Message 4 of 17 , May 7, 2011
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            Hello Mr. Dailey,

            I think there is a typo in item #3 of your method. You first mention heat H2SO4 and it is followed by the statement "add oxidant to bleach". I think you ment - add oxident to H2SO4? Is this assumption on my part correct? My chemistry is weak at best but one is an acid and the other a base. Is this correct?

            Charles

            --- In diatom_forum@yahoogroups.com, "bill2penn" <dailey@...> wrote:
            >
            > Sparkleen 1 is a mixture of sodium carbonate and a alkylated phenol polymer. Be careful using too much since it is basic.
            >
            > So briefly my method:
            > 1. Freeze/thaw in water or use sodium acetate trihydrate (I have found that sodium acetate does a great job although is more expensive. You can find it on ebay for relatively cheap). Wash multiple times with dw.
            > 2. HCl boil for 20 min or so. I use about half water, half muriatic acid (conc HCl sold as wash for concrete, etc). Wash multiple times with dw.
            > 3. conc H2SO4 heating, when white fumes, add oxidant to bleach. I use sodium nitrate or potassium perchlorate. CAREFUL!!!! Cool, CAREFULLY dilute with water. Wash multiple times with water.
            > 4. Heat to simmer with Sparkleen 1. I use 0.5 tsp in 500 mL water and heat for 30 min to a couple hours. Wash multiple times with water. Repeat this step as necessary until there are clean forms.
            > 5. Separate fractions by "gold panning"
            > 6. Use sieves if needed.
            >
            > Bill
            >
            >
            > --- In diatom_forum@yahoogroups.com, Richard Carter <rcarter68502@> wrote:
            > >
            > > Bill,
            > >
            > > I'd sure like to hear more about your use of glassware cleaner.  I have a sample of a very interesting Early Miocene freshwater diatomite from western Nebraska that is a real bear to clean.  It disaggregates fairly easily with freeze/thaw, and contains good specimens of several extinct Pinnulariaspecies.  It also contains the nastiest little bits of clingy, flocculant crud I've ever seen, and repeated washings in DW just don't work to get rid of it!  Maybe glassware cleaner would do the trick--------?
            > >
            > > Dick
            > >
            > >
            > >
            > > ________________________________
            > > From: bill2penn <dailey@>
            > > To: diatom_forum@yahoogroups.com
            > > Sent: Friday, April 29, 2011 4:52 AM
            > > Subject: [diatom_forum] Re: cleaning diatoms
            > >
            > >
            > >  
            > > Hi Chuck,
            > > YES! Please share your procedures with the group. The more different ideas/methods we have the better. If you write it up, post it in the Files section.
            > > I have recently modified some of my cleaning methods for difficult fossil diatomites like Oamaru to include simmering the diatoms in a dilute solution of my glassware cleaning solution, Sparkleen 1. I figure diatoms are made of glass so it should work. It does a dandy job. I intend to write this up too at some point. Too many things to do though...
            > > Bill
            > >
            > > --- In diatom_forum@yahoogroups.com, Chuck Stapleton <stapleton.chuck@> wrote:
            > > >
            > > > Greetings All,
            > > >       As I read through the files to try and catch up with the subjects of interest, I noticed a PDF on cleaning diatoms, etc. I use a very inexpensive and gentle method to clean diatoms that leaves many whole frustules on the slides.
            > > >       I buy, from a local beauty supply store, cases of Clairoxide (about $7.00 US for a 470ml bottle) which contain 40% Hydrogen Peroxide (no other ingredients). Clairoxide is used by the distaff side of the house for bleaching hair.I put the Jars on a hot pad for two or three days depending on the amount of organics in the level of the core I'm processing (more time near the top, etc.).
            > > >       I have been working on this process for about ten years and it seems to work well. I'm just now finishing the write up for the proceedure. I'm a Zinc Bromide kind of guy that practices recycling and I use Zrax. I made promises to several colleagues to get the proceedure out and I finally stop tweaking and have written it down (sort of). Be glad to share. By the by, I'm a paleoecologist that uses diatoms as a tool and not a taxonomist. YET!
            > > > Chuck
            > > > 251-402-8018
            > > >
            > >
            >
          • bill2penn
            Hello Charles, You are correct that I was not clear in my description. I used the word bleach as a verb (meaning to decolorize), not as a noun (meaning
            Message 5 of 17 , May 7, 2011
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              Hello Charles,
              You are correct that I was not clear in my description. I used the word "bleach" as a verb (meaning to decolorize), not as a noun (meaning sodium hypochlorite solution). I add an oxidant (either solid sodium nitrate or sodium perchlorate) to oxidize the material.
              DONT ADD Sodium hypochlorite solution (aka bleach)!!!!
              I will try to be more precise in the future.
              Thanks for picking that up.
              Bill


              --- In diatom_forum@yahoogroups.com, "charles" <suslavage@...> wrote:
              >
              > Hello Mr. Dailey,
              >
              > I think there is a typo in item #3 of your method. You first mention heat H2SO4 and it is followed by the statement "add oxidant to bleach". I think you ment - add oxident to H2SO4? Is this assumption on my part correct? My chemistry is weak at best but one is an acid and the other a base. Is this correct?
              >
              > Charles
              >
              > --- In diatom_forum@yahoogroups.com, "bill2penn" <dailey@> wrote:
              > >
              > > Sparkleen 1 is a mixture of sodium carbonate and a alkylated phenol polymer. Be careful using too much since it is basic.
              > >
              > > So briefly my method:
              > > 1. Freeze/thaw in water or use sodium acetate trihydrate (I have found that sodium acetate does a great job although is more expensive. You can find it on ebay for relatively cheap). Wash multiple times with dw.
              > > 2. HCl boil for 20 min or so. I use about half water, half muriatic acid (conc HCl sold as wash for concrete, etc). Wash multiple times with dw.
              > > 3. conc H2SO4 heating, when white fumes, add oxidant to bleach. I use sodium nitrate or potassium perchlorate. CAREFUL!!!! Cool, CAREFULLY dilute with water. Wash multiple times with water.
              > > 4. Heat to simmer with Sparkleen 1. I use 0.5 tsp in 500 mL water and heat for 30 min to a couple hours. Wash multiple times with water. Repeat this step as necessary until there are clean forms.
              > > 5. Separate fractions by "gold panning"
              > > 6. Use sieves if needed.
              > >
              > > Bill
              > >
              > >
              > > --- In diatom_forum@yahoogroups.com, Richard Carter <rcarter68502@> wrote:
              > > >
              > > > Bill,
              > > >
              > > > I'd sure like to hear more about your use of glassware cleaner.  I have a sample of a very interesting Early Miocene freshwater diatomite from western Nebraska that is a real bear to clean.  It disaggregates fairly easily with freeze/thaw, and contains good specimens of several extinct Pinnulariaspecies.  It also contains the nastiest little bits of clingy, flocculant crud I've ever seen, and repeated washings in DW just don't work to get rid of it!  Maybe glassware cleaner would do the trick--------?
              > > >
              > > > Dick
              > > >
              > > >
              > > >
              > > > ________________________________
              > > > From: bill2penn <dailey@>
              > > > To: diatom_forum@yahoogroups.com
              > > > Sent: Friday, April 29, 2011 4:52 AM
              > > > Subject: [diatom_forum] Re: cleaning diatoms
              > > >
              > > >
              > > >  
              > > > Hi Chuck,
              > > > YES! Please share your procedures with the group. The more different ideas/methods we have the better. If you write it up, post it in the Files section.
              > > > I have recently modified some of my cleaning methods for difficult fossil diatomites like Oamaru to include simmering the diatoms in a dilute solution of my glassware cleaning solution, Sparkleen 1. I figure diatoms are made of glass so it should work. It does a dandy job. I intend to write this up too at some point. Too many things to do though...
              > > > Bill
              > > >
              > > > --- In diatom_forum@yahoogroups.com, Chuck Stapleton <stapleton.chuck@> wrote:
              > > > >
              > > > > Greetings All,
              > > > >       As I read through the files to try and catch up with the subjects of interest, I noticed a PDF on cleaning diatoms, etc. I use a very inexpensive and gentle method to clean diatoms that leaves many whole frustules on the slides.
              > > > >       I buy, from a local beauty supply store, cases of Clairoxide (about $7.00 US for a 470ml bottle) which contain 40% Hydrogen Peroxide (no other ingredients). Clairoxide is used by the distaff side of the house for bleaching hair.I put the Jars on a hot pad for two or three days depending on the amount of organics in the level of the core I'm processing (more time near the top, etc.).
              > > > >       I have been working on this process for about ten years and it seems to work well. I'm just now finishing the write up for the proceedure. I'm a Zinc Bromide kind of guy that practices recycling and I use Zrax. I made promises to several colleagues to get the proceedure out and I finally stop tweaking and have written it down (sort of). Be glad to share. By the by, I'm a paleoecologist that uses diatoms as a tool and not a taxonomist. YET!
              > > > > Chuck
              > > > > 251-402-8018
              > > > >
              > > >
              > >
              >
            • Klaus Kemp
              Keith In a previous posting I mentioned that it is best to try and collect the Diatoms as clean as possible in the first place, by scraping the surface of the
              Message 6 of 17 , Jun 7, 2011
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                Keith
                In a previous posting I mentioned that it is best to try and collect the Diatoms as clean as possible in the first place, by scraping the surface of the substrate with as little of the substrate as possible. Also by doing this you can place them in a dish at home and watching tides from the comfort of your home.
                On a lighter note regarding this, we have the second highest tides in the world in the Severn estuary 42 feet rise and fall (Yes we still use feet as a form of measuring)The Bay of Fundie reputedly has the highest, still 42 feet is going some and I understand that we hold the record for the longest surf board ride on the Severn Bore. This tidal movement causes at the end of the holiday season a large collection of 4X4 Landrovers and associated vehicles to be stranded and submerged in the mud flats at Weston-super-Mare and Berrow beach, to be dug up in the future by Archeologists, I would guess that if you were to contact the Insurance companies it would provide the information of those stranded that they belong to the following categories of drivers.
                Male, aged between 16-25 (where testerone overrides grey matter) accompanied by young impressionable females, with a touch of Lager involved. This is probably contentious but having watched in person these characters desperately trying to recover their fathers transport, I may just be right in my assumption.
                Klaus

                --- In diatom_forum@yahoogroups.com, "Keith Shaw" <scitech200@...> wrote:
                >
                > Hi Brian,
                >
                > Thank you very much for the outline of your proof-of-concept apparatus.
                > Very small bubbles streaming off the electrodes is an interesting alternative to the conventional porous "stone" with a compressed air feed, e.g. aquarium bubbler.
                > In general, as also suggested by Alex, it just seems to make a lot of sense to be able to concentrate the marine diatoms in the foam, relatively easily and mostly free(?) of other organic matter...
                >
                > But right now I have to stay focused on sorting out a reproducible bleach protocol to routinely clean the marine/marshland diatoms I have been collecting. I'm starting to see some success and will prepare a series of images for the group.
                >
                > I have also, finally, figured out a way to roll a diatom in a critically adjusted water column (between slide and coverslip). It takes a lot of patience but the resulting, unambiguous valve and girdle images makes the effort worthwhile...
                >
                > -Keith
                >
                >
                >
                > "urginia" wrote:
                > > Hi Keith,
                > > I will try and reconstruct what I did from memory! I realise now that it must be well over 30 years ago that I tried this. Please note that I did this with a live diatom-dominated marine plankton net sample.
                > >
                > > The volume of sample would have been between 500 and 1000 ml. As you surmised I did this in a cylinder ...probably a 1000ml measuring cylinder. Size of electrodes - I guess about 8 x 3 cm. I held them apart with some pieces of neoprene...perhaps 1cm apart, and the whole held together with elastic bands. I attached wires to the electrodes with paper clips.
                > >
                > > My recollection is that the cells were scavenged into a surface scum very quickly... definitely minutes rather than hours...say 30 mins. The removal of cells was almost total, leaving clear water below. The key to this (I think) was a) the very small bubbles that were formed and b) the colloidal (? magnesium) salt that trapped the cells.
                > >
                > > The general process of scavenging cells and organic matter from suspensions by ascending bubbles is widely used and known as "foam fractionation" or "protein skimming". The separation achieved depends partly on the hydrophobic nature of the material being separated... therefore it may well only work efficiently with living diatoms with intact cells.
                > >
                > > I only used this "electrolytic" method once when I was messing around, but I remember telling someone about it and they achieved a very high separation as well with diatom cultures and other algal cultures. I just parked the method in my head as something interesting to try again when i got some time.
                > >
                > > At best my "experiment" was a proof of concept - no more !
                > >
                > > Good luck if you try to develop this further !
                > >
                > > boa sorte
                > > Brian
                >
              • Keith Shaw
                Hello Klaus, Yes, I listened to your advice re collection technique! Most recently I tried using a turkey baster to suck a sample from the surface of the mud
                Message 7 of 17 , Jun 8, 2011
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                  Hello Klaus,

                  Yes, I listened to your advice re collection technique!

                  Most recently I tried using a turkey baster to suck a sample from the surface of the mud (amongst some plant roots within which the blighters seem to like to hide out) and brought it home in a bottle. I have posted a few pics from such a sample to give you an idea of where I'm at right now...

                  I was very interested to read your comment on big tides in the UK. The road from Cherryfield runs out to Bar Harbor on the coast in the Gulf of Maine, and this is not so far from the Bay of Fundy. However, I think these tides run more like 20-25 feet as there is not the same "channeling" effect. But still way higher than I see further south in Gloucester!

                  The vehicles becoming stranded is so funny - I well remember "a somewhat difficult situation" as a teenager out on the sand with a tide rapidly coming in, more than a few years back... Dad was not a happy camper, at all.

                  Best regards,
                  Keith


                  "Klaus Kemp" wrote:
                  > Keith
                  > In a previous posting I mentioned that it is best to try and collect the Diatoms as clean as possible in the first place,...
                  <SNIP>
                  > On a lighter note regarding this, we have the second highest
                  > tides in the world in the Severn estuary 42 feet rise and
                  > fall (Yes we still use feet as a form of measuring)
                  > The Bay of Fundie reputedly has the highest,...
                  <SNIP>
                  > This tidal movement causes at the end of the holiday season
                  > a large collection of 4X4 Landrovers and associated vehicles
                  > to be stranded and submerged in the mud flats...
                  <SNIP>
                • David Richman
                  Keith, While no where near as spectacular as the Bay of Fundy, the Gulf of California can be just as treacherous. The maximum and minimum tides are +6 to -6
                  Message 8 of 17 , Jun 8, 2011
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                    Keith,

                    While no where near as spectacular as the Bay of Fundy, the Gulf of California can be just as treacherous.  The maximum and minimum tides are +6 to -6 feet on the same day  - a total of 12 feet.  The result at Cholla Bay, Sonora, in the north part of the Gulf  is that the bay, which is shallow, will completely empty at times.  I have in fact walked across the bay (being careful to avoid sting rays, which seem to be in every puddle).  Unfortunately this was before my interest in diatoms - I was a teaching assistant for Invertebrate Zoology at the University of Arizona at the time - but I could easily see how people could be trapped by the tide.

                    David Richman


                    On Jun 8, 2011, at 6:29 AM, Keith Shaw wrote:

                    Hello Klaus,

                    Yes, I listened to your advice re collection technique!

                    Most recently I tried using a turkey baster to suck a sample from the surface of the mud (amongst some plant roots within which the blighters seem to like to hide out) and brought it home in a bottle. I have posted a few pics from such a sample to give you an idea of where I'm at right now...

                    I was very interested to read your comment on big tides in the UK. The road from Cherryfield runs out to Bar Harbor on the coast in the Gulf of Maine, and this is not so far from the Bay of Fundy. However, I think these tides run more like 20-25 feet as there is not the same "channeling" effect. But still way higher than I see further south in Gloucester!

                    The vehicles becoming stranded is so funny - I well remember "a somewhat difficult situation" as a teenager out on the sand with a tide rapidly coming in, more than a few years back... Dad was not a happy camper, at all.

                    Best regards,
                    Keith

                    "Klaus Kemp" wrote:
                    > Keith
                    > In a previous posting I mentioned that it is best to try and collect the Diatoms as clean as possible in the first place,...
                    <SNIP>
                    > On a lighter note regarding this, we have the second highest
                    > tides in the world in the Severn estuary 42 feet rise and 
                    > fall (Yes we still use feet as a form of measuring)
                    > The Bay of Fundie reputedly has the highest,...
                    <SNIP> 
                    > This tidal movement causes at the end of the holiday season
                    > a large collection of 4X4 Landrovers and associated vehicles
                    > to be stranded and submerged in the mud flats...
                    <SNIP>


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