Mr. Microscope's Cube 2.1

[Felicia]

Sorry to here about the dino's Mr. M! I hope taking the sand bed out helps some and that you can find a good way to fight them. I don't know a lot about them in aquariums. How do you get them?

 

On the positive side, at least you got to do some microscopy. I liked the quick light microscopy video and am looking forward to some TEM and SEM images. I really should start analyzing stuff from my aquarium on our lab equipment. Unfortunately, I mostly work with a multi-angle light scattering system that can determine the molecular weight and radius of gyration of polymers and proteins, so it wouldn't be much fun or useful with aquarium samples. We do have brightfield, fluroescent, and confocal microscopes though.

 

I'm with you on thinking the sand bed is doing more harm than good. My sand bed was about an inch deep and at 2 years old, its what caused the crash I had in my tank. 2-year-old sand bed is just gross! The smell of mine when I took it out of my tank was horrible!

[Mr. Microscope]

/jelly

 

 

Freshwater dip everything, hope stuff survives.

Best of luck to you. I hope it works out.

Sorry to here about the dino's Mr. M! I hope taking the sand bed out helps some and that you can find a good way to fight them. I don't know a lot about them in aquariums. How do you get them?

 

I'm with you on thinking the sand bed is doing more harm than good. My sand bed was about an inch deep and at 2 years old, its what caused the crash I had in my tank. 2-year-old sand bed is just gross! The smell of mine when I took it out of my tank was horrible!

Thanks Felicia. It would seem at the very least that doing all these water changes is helping. I did like another 3-4 gallons yesterday while removing the back right corner. I only have the front right side left. Then, I'm planning to thoroughly siphon/scrub the rocks and then do another blackout. I hope that gets them or at least staves them off for a little while.

 

Yeah, the water along with the sand I'm siphoning out is like brown/green and also doesn't have the best smell. Not horrible and not sulfury as some people experience, but not great nonetheless. After dumping out the water, I throw the sand straight in the garbage and take it out right away so it doesn't stink up the house.

On the positive side, at least you got to do some microscopy. I liked the quick light microscopy video and am looking forward to some TEM and SEM images. I really should start analyzing stuff from my aquarium on our lab equipment. Unfortunately, I mostly work with a multi-angle light scattering system that can determine the molecular weight and radius of gyration of polymers and proteins, so it wouldn't be much fun or useful with aquarium samples. We do have brightfield, fluroescent, and confocal microscopes though.

Yes, I'm looking forward to seeing these things in action under the EM. I'm Critical Point Drying them today.

 

Very interesting stuff. Do you have any publications/co-authorships yet? Let me know if you want to do any collaboration. I'm very proficient with cryo-ultramicrotomy/EM of polymers with low Tg's if you ever need to see co-polymer transition boundaries or anything of that sort. I've also done a bit of protein EM via negative staining and plunge freezing.

[Felicia]

Best of luck to you. I hope it works out.

Thanks Felicia. It would seem at the very least that doing all these water changes is helping. I did like another 3-4 gallons yesterday while removing the back right corner. I only have the front right side left. Then, I'm planning to thoroughly siphon/scrub the rocks and then do another blackout. I hope that gets them or at least staves them off for a little while.

 

Yeah, the water along with the sand I'm siphoning out is like brown/green and also doesn't have the best smell. Not horrible and not sulfury as some people experience, but not great nonetheless. After dumping out the water, I throw the sand straight in the garbage and take it out right away so it doesn't stink up the house.

 

Yes, I'm looking forward to seeing these things in action under the EM. I'm Critical Point Drying them today.

 

Very interesting stuff. Do you have any publications/co-authorships yet? Let me know if you want to do any collaboration. I'm very proficient with cryo-ultramicrotomy/EM of polymers with low Tg's if you ever need to see co-polymer transition boundaries or anything of that sort. I've also done a bit of protein EM via negative staining and plunge freezing.

Sounds like you've got a good plan to try to beat the dinos. I wish you luck! Aquarium pests can be the worst

 

How'd the critical point drying go? When will you be imaging them?

 

I have one co-author publication and another in the works, but those are pretty unrelated to my thesis work. I should hopefully have a first author paper out for my thesis work sometime soon. I've also got a side project I'm working on that I hope to publish on in a few months. I forget if you're doing your PhD now or if you're postdocing? A collaboration would be awesome and I will definitely keep you in mind if I decide I need some EM characterization for my project. N-R is such a fun place to network So do you have a serious love/hate relationship with your EM's? I swear the multi-angle light scattering instrument I am in charge of running for my lab is the bane of my existence. My whole project depends on it and I just had to mail it off to the company who makes it yesterday for service because the laser that produces the scattering went out. Now I've got several weeks of hold up on my project while that gets repaired. Gotta love research!

[Polarcollision]

That being said, I'm continueing to remove my sandbed. I hadn't considered that it is also a source of denitrifying bacteria, but I can't believe how much crap is coming along with it as I siphon it out of my tank. I'm convinced that it has to be doing more harm than good at this point. .

 

its hard to tell from the picture, but it looks to me that your sand is a slightly larger grain size. A few months ago I did a bunch of research that concluded with tanks generally having more problems--nutrients, pests, etc-- when the sand grain is larger. The consensus seemed to be linked to trapped waste, with a solution being to use very fine grain sand which prevents more gunk from collecting and decaying in the bed. possibly an option if you go back to sand.

 

I'm using the fine sand. So far so good, though it's only about 1 yr old. Tons of spaghetti worms keep it cleaned up as well. I can send you a starter kit, LOL

 

P.S. the dinos in your video look a lot like what I have. http://www.nano-reef.com/topic/316682-polarcollisions-nuvo-8-temperate-6/?p=4375356 However mine are in balance/not invading. Wonder what is making the difference... ?

 

P.S. 2 I read somewhere that palytoxin in zoas is from dinos within the zoa (the last comment in your microscope thread says this too). I always assumed that the dinos came from a zoa in my tank--maybe fragging or expelling. Since zooxanthelle are dinoflagellates. I'm sleepy and might be remembering this wrong.

[Felicia]

Thar's interesting to hear about the sand grain size. I used super fine sand in my redo of my tank, so hopefully I won't have the same issues I had with the old sand bed. Granted, the super fine stuff kicks up easy and tends to drift with the flow.

[Mr. Microscope]

Sounds like you've got a good plan to try to beat the dinos. I wish you luck! Aquarium pests can be the worst

 

How'd the critical point drying go? When will you be imaging them?

 

I have one co-author publication and another in the works, but those are pretty unrelated to my thesis work. I should hopefully have a first author paper out for my thesis work sometime soon. I've also got a side project I'm working on that I hope to publish on in a few months. I forget if you're doing your PhD now or if you're postdocing? A collaboration would be awesome and I will definitely keep you in mind if I decide I need some EM characterization for my project. N-R is such a fun place to network So do you have a serious love/hate relationship with your EM's? I swear the multi-angle light scattering instrument I am in charge of running for my lab is the bane of my existence. My whole project depends on it and I just had to mail it off to the company who makes it yesterday for service because the laser that produces the scattering went out. Now I've got several weeks of hold up on my project while that gets repaired. Gotta love research!

Critical point drying went well. The algae matrix that the dinos are sitting on came out looking like buds. lol

 

Good luck with your thesis and publications! I'm actually on staff in an instrumentation center at NU. I'm the guy everyone comes to when they need a good figure/image or have difficult sample preparation they need help with. So, I'm somewhat of a professional collaborator. We currently have 5 SEM's, 3 TEM's, a dedicated STEM, and a FIB. In addition to this, I'm a member of two labs on campus and have some research going with both of them.

 

Sorry to hear about your equipment issues. Arrrgh! A friend of mine once said that 90% of science is just getting things to work. LOL. It's proven to be true. Though, I guess when you're pushing the boundaries of science, there's bound to be mishaps. We're having issues with some new instruments for cryo work right now and are working with the vendors to fix/replace them. I guess you could add maintenance to the list of things I do. Occasionally, I find my self laying on my back trying to fix a pump or something attached to one of our EM's.

 

its hard to tell from the picture, but it looks to me that your sand is a slightly larger grain size. A few months ago I did a bunch of research that concluded with tanks generally having more problems--nutrients, pests, etc-- when the sand grain is larger. The consensus seemed to be linked to trapped waste, with a solution being to use very fine grain sand which prevents more gunk from collecting and decaying in the bed. possibly an option if you go back to sand.

 

I'm using the fine sand. So far so good, though it's only about 1 yr old. Tons of spaghetti worms keep it cleaned up as well. I can send you a starter kit, LOL

Very interesting point and great observation! Yes, I'm using Tropic Eden Reef Flakes. It is on the courser side. It was recommended by a friend and I really like it for how incredibly clean it is and how it looks. From what I've pulled out of my tank, I'd say you're correct. That stuff was filthy!

P.S. the dinos in your video look a lot like what I have. http://www.nano-reef.com/topic/316682-polarcollisions-nuvo-8-temperate-6/?p=4375356 However mine are in balance/not invading. Wonder what is making the difference... ?

Awesome microscopy! How'd I miss that!?

P.S. 2 I read somewhere that palytoxin in zoas is from dinos within the zoa (the last comment in your microscope thread says this too). I always assumed that the dinos came from a zoa in my tank--maybe fragging or expelling. Since zooxanthelle are dinoflagellates. I'm sleepy and might be remembering this wrong.

I've been thinking the same myself. I've been doing some looking into where this stuff actually comes from thinking that it might lead to some solutions.

[Mr. Microscope]

Hello All,

 

I finished siphoning out 99% of the sand in my aquarium the other day. I have to admit, I never thought I'd go bare bottom, but I'm really loving how clean it looks. The white acrylic from my stand shows though the bottom and I think it looks very nice. I also like how the 1/2" acrylic base of the pillar kinda elevates and separates the corals and rock from the rest of the negative space surround it. Finally, the arch at the bottom of the pillar really sticks out now and my dottyback seems to love it. Here's a FTS I took last night:

 

Here's a FTS from earlier this month for comparison.

 

I couldn't resist taking another one with just the blues on with all the popping color:

 

Dinos are still present, but at bay for the time being. I think I may initiate another three day black out to help take them back a step further. Since I've taken nutrients down considerably with all the water changes from siphoning out my sandbed (I estimate about 22 gallons within a week and a half), algae has also been beaten back and since most of the dinos were colonizing the GHA, I think that's helped as well.

 

Here's a few more shots I took just for fun:

 

 

I think I finally found a good spot for my platygyre behind the torch. You can sort of see it in the FTS's in the reflection of the left pannel of glass.

[Arkayology]

Awesome colors on that acan man.

[natalia_la_loca]

Awesome colors on that acan man.

 

+1....really spectacular

[gena]

That looks pretty cool BB. Love all those acans .

[Felicia]

Thanks for reminding me that you are staff for the instrumentation center! I know you'd mentioned that before and then I just couldn't remember if you were a student, post-doc, or staff. That's funny that you spend time laying on your back fixing pumps, because I do that sort of thing all the time. In our lab, we don't have staff running our instruments. So each grad student gets an instrument or two that they are completely in charge of, and most of them are so old that they're out of warranty and so we have to always try to fix them first before we resort to paying for service. I spend a lot of time doing maintenance stuff and I cannot even count how many times I've fixed vacuum pumps in our lab Gotta love the research setting! As frustrated as I am that my main piece of equipment is currently down, I'm just glad it was still under warranty so that I don't have to try to fix it!

 

I usually really don't like BB tanks, but that looks surprisingly nice! I think its that raised platform that makes it look good! So you're thinking you won't add sand back in? The acans really pop even more right now with the sand gone!

[Polarcollision]

Very interesting point and great observation! Yes, I'm using Tropic Eden Reef Flakes. It is on the courser side. It was recommended by a friend and I really like it for how incredibly clean it is and how it looks. From what I've pulled out of my tank, I'd say you're correct. That stuff was filthy!Awesome microscopy! How'd I miss that!?I've been thinking the same myself. I've been doing some looking into where this stuff actually comes from thinking that it might lead to some solutions.

 

For comparison, the fine sand I use is caribsea ocean direct. It's tiny, like salt or sugar sand. When I transfered tanks, the year-old sand was a little dirty, but looked like it was a healthy dirty. If that makes any sense? In the temperate aquarium the sand was coarser. More like what you describe. It was the kind of nasty that makes you want to wash hands in bleach and alcohol. Maybe that difference in nutrients really is what fuels dinos? Anyways, I love the bare bottom look on your tank. You'd never know by looking at it that there were any issues. You can mail that acan any time! Gorgeous!!

[Mr. Microscope]

Awesome colors on that acan man.

Thanks Ark! They dull out a little as fully grown, but the babies stay like that for a while.

 

+1....really spectacular

Thanks Natalia! I'm happiest with my tank that I've been in a while despite the dinos.

That looks pretty cool BB. Love all those acans .

Thanks Gena! I was also surprised by the BB look. Usually people have black bottoms which doesn't do much for me. I think the white makes all the difference.

Thanks for reminding me that you are staff for the instrumentation center! I know you'd mentioned that before and then I just couldn't remember if you were a student, post-doc, or staff. That's funny that you spend time laying on your back fixing pumps, because I do that sort of thing all the time. In our lab, we don't have staff running our instruments. So each grad student gets an instrument or two that they are completely in charge of, and most of them are so old that they're out of warranty and so we have to always try to fix them first before we resort to paying for service. I spend a lot of time doing maintenance stuff and I cannot even count how many times I've fixed vacuum pumps in our lab Gotta love the research setting! As frustrated as I am that my main piece of equipment is currently down, I'm just glad it was still under warranty so that I don't have to try to fix it!

 

I usually really don't like BB tanks, but that looks surprisingly nice! I think its that raised platform that makes it look good! So you're thinking you won't add sand back in? The acans really pop even more right now with the sand gone!

No worries.

Yeah, equipment can be a PITA.

 

Yes, I've decided to keep it BB for the time being. I will probably have to move in about two months and it's going to be loads easier if I don't have to worry about sand. I agree it seems to make everything pop a little more.

 

For comparison, the fine sand I use is caribsea ocean direct. It's tiny, like salt or sugar sand. When I transfered tanks, the year-old sand was a little dirty, but looked like it was a healthy dirty. If that makes any sense? In the temperate aquarium the sand was coarser. More like what you describe. It was the kind of nasty that makes you want to wash hands in bleach and alcohol. Maybe that difference in nutrients really is what fuels dinos? Anyways, I love the bare bottom look on your tank. You'd never know by looking at it that there were any issues. You can mail that acan any time! Gorgeous!!

Hmm.. Perhaps I'll have to give the finer stuff a chance later down the road.

Thanks PC!

[FlowerMama]

I'm surprised how much I like your tank bare bottom. I think it emphasizes your acans even more.

[Mr. Microscope]

I'm surprised how much I like your tank bare bottom. I think it emphasizes your acans even more.

Thanks 1st! I agree.

[FlowerMama]

Thanks 1st! I agree.

 

I know I'm young in this hobby yet but usually it looks too sterile for me, but oddly enough, not in your tank. I think it's just because it's taller than longer, not a rectangular tank, and my emphasis is still on your corals and not an icy looking bottom.

[spazizz]

Now you have more room for corals, cover the bottom with your dreams.

[Nigripes]

I run all the tanks I have ever had (apart from the first one) bb as I don't like the look of sand. My new build is bb too. It is too late now but I think you could have removed the sand all in one go and things would have been fine.

I say keep it bb for at least 6 months so you get a true comparison. I will wager your algae issues will tail off somewhat, as will the dino/cyno.

 

Good luck.

[RollaJase]

Dem canz .

[Mr. Microscope]

Pic for the day:

A. Saramentosa

[Justind823]

I'm not one for bare bottom tanks either but that looks pretty clean!

[Mr. Microscope]

Now you have more room for corals, cover the bottom with your dreams.

Thanks spazizz, but I'm actually planning to get rid of some to make room for growth (after I get rid of the dinos of course). The exception being all my nems for the top of the pillar. The weather is slowly getting better. So, my shipment might come next week.

Dem canz .

Thanks Rolla!

I'm not one for bare bottom tanks either but that looks pretty clean!

Thanks Justin!

I run all the tanks I have ever had (apart from the first one) bb as I don't like the look of sand. My new build is bb too. It is too late now but I think you could have removed the sand all in one go and things would have been fine. I say keep it bb for at least 6 months so you get a true comparison. I will wager your algae issues will tail off somewhat, as will the dino/cyno. Good luck.

Thank you for your input Nigripes! Yes, I didn't have any issues removing the sand as far as stuff getting kicked up while I was siphoning it, but it took about five gallons of water to about 20% of my sandbed. I only had the patience to do one of those at a time. I hope they do go away. I've initiated another three day black out to try and take them back another notch. I noticed a cool ball-nem tonight with the lights out. Check it out!

 

This, of course lead to a series of flash photography.

Clowns!

 

I love how you can see their iridescent blue scales here.

 

"Don't hate me 'cause I'm beautiful."

[FlowerMama]

I like ball nems. I had a couple in my Evolve. At first I thought they were some kind some kind of snail eggs but then I realized they never grew.

[Mr. Microscope]

Today is the last day of the blackout. So, I decided to do another water change. Here's the build up i had after three days and blowing off my rocks. I can't imagine what two years of this stuff must have looked like in my sandbed.

 

Here's the bucket afterwards.

 

and..since everyone has been sharing their cats lately, here's mine. Her name is Julia and she's 7 lbs. of fur and claws!

 

[Felicia]

Awesome photos! I love all the details you managed to capture. Those are some very pretty clowns.

 

Yeah, the holding tank I was using was bare bottom and it amazed me how much gunk built up in just a few days. Then thinking about the sand bed that I never cleaned for two years and I am not remotely surprised it caused the tank crash. Yuck! I am definitely siphoning detritus off the top of my new sandbed now.

 

Awww, Julia is a cutie! She looks like a little sweetheart. My cat, Lily, is a small cat too at only 8 pounds.