Justin's Microbiology Journal
Wednesday, April 28, 2004
I can't seem to stain bacterial samples well. I attempted the very standard double gram staining technique today on my marine anaerobic bacteria sample. Fix sample, apply crystal violet, rinse, iodine, decolor via acetone-alcohol mixture, counterstain with saffranin.
After I was done, I really couldn't see any bacteria at all to speak of, and certainly not the existing colonies that were there before. Perhaps I did not fix the bacteria well enough to the slide. That is done by passing the slide through a low flame. I'll try again tomorrow with a new sample.
Now that I'm done with studying microorganisms via phylogenetic differentiation, I'm now studying the metabolic diversity of microorganisms and the svarious biochemical processes that allow such diversity.
Just finished anoxygenic photosynthesis, including electron flow cycles, photophosphorylation, the existence of superoperons to allow precise formation of the protein complexes in the membrane, and various different reduction power syntheses. On to oxygenic photosynthesis.
Off topic: My sister's redesigned her and her husband's restaraunt's website. It's the River House Tavern, great food in Westport.
I made it through all major Baltimore classifications of virii. A virus stretches the definition of what life is, because it does not have the means to replicate itself without a cellular host, notably any form of ribosome. Virii contain either DNA or RNA, and some contain RNA/DNA polymerase as well.
Interestingly hepatitis B has its own parasite, the delta agent. The delta agent is known as a sub-virus because the proteins for its coat are only expressed on the hepatitis B virus. So it requires both cell host and the cell host to be infected with hepatitis B to replicate.
I took a small video through my microscope of the bacteria yesterday. Link is here, 76meg though. You can see both coccoid and filamentous bacteria forming colonies, and quite a few spirillum shaped free swimmers.
Tuesday, April 27, 2004
Well, my culture of bacteria from the dead crab in salt water proved pretty awful. Lots of bacteria, but such an awful smell that I'm basically banned from the house from doing similar cultures. The worst smells come from clostridium, and I'm sure I hit the jackpot with it. It creates such wonderful chemicals as cadaverine, putrescine, ammonia, butyric acid, and hydrogen sulfide. So the smell of rotting corpses filled my house. My wife is still not talking to me.
I'm guessing once I finish staining the slide I'll find some vibrio hemolyticus, whose habitat is marine animals and can jump to humans. It's a major cause of gastroenteritis in Japan. A bigger danger is vibrio cholerae, the cause of cholera, but I'm pretty sure its environment is fresh, not marine water.
So I got a bit worried I wasn't as sterile as I should be, so I triple sealed the samples in plastic containers, ziplocs, and garbage bags and used alcohol and lysol to rub down everything I was in contact with and all lab surfaces.
Time to go work in a real lab I think.
Sunday, April 25, 2004
Perks to being an active blogger: Got my Gmail account today. Yay. I'm already active on orkut, use froogle, and read my news from the google news summary, I'd say google has replaced Microsoft as the factory for indispensable computer tools.
Wednesday, April 21, 2004
Here is another picture of the cat colon red blood cells. cat colon
Here's a shot of the spyrogyra from Monterey. spyrogyra
Alrighty. Got my camera mount adapter, so I'm off and running taking microphotographs. So far I've not yet figured out how to get the best focus, I'll continue to work on that. I'll post some pictures though taken with my phase contrast microscope. Warning, largish pictures coming.
Spent yesterday down in Monterey, where we went to the Aquarium. I also got samples of the marine water off Pacific Grove and the fresh water at the Camino Aguajito lake where we used to live.
So far, I've found nothing interesting in the marine water, but that's not too surprising. There are generally only 10^6 cells/ml in open ocean which is far fewer than you'll find in fresh water. Was a nice bloom of phyoplanktonic algae in the water at the lake, which turned out to be a species of spyrogyra. Generally I've found different algae in the backyard, I'll post pictures for comparison.
There were a few bacteria as well, but I haven't gone through the steps to classify them yet. No large colonies, just generally single coccoid and rod shaped bacteria with either a single flagellum or peretrichious flagellae.
Studying is going well. I've done all Bacteria, all Archaea, and all single celled Eukarya. I'm now into eukaryotic genetic modification, as there are a few more options than with bacteria.
Thursday, April 15, 2004
Tax season is done, finally. Getting back to focus on microbiology. I'm still slogging through all the phyla of bacteria, then on to archaea.
Phase contrast is invaluable in seeing unstained slides. So far I've observed bacillus subtillis (natto), lactobacillus casei strain shirota (yakult), and red blood cells,neutrophils, and eosinophils (had to stain those to see with methelyne blue). I need to go get some thinner cover slips. I'm unable to focus at 1000x through the thick glass, even with immersion oil.
Thursday, April 08, 2004
Hey, it's finally here. My Motic BA 450 microscope. On eosin stained and prepared slides, the results are just awesome. I'm not having as good luck with my slide preparation, I think it's a real art. Oh, and just need one more piece and I can start posting pictures on the web. Well, I couldn't wait. I had to take a picture, hand held above the camera opening. Picture is of a prepared slide of cat colon stained with eosin, phase contrast with 1000x magnification. The red circles are of course red blood cells.
Tuesday, April 06, 2004
Memorization, memorization, memorization. Studying every single group of bacteria currently. From Aquifex to Thermotoga to Green Non-sulfur Bacteria. Their morphology, specific trophicity, metabolic cycles and end products, culture requirements. Rough going.
Well, my Microscope salesman quit his company. No wonder I haven't gotten my scope yet. Sigh. The company promises to get me my scope by Wednesday.
On the up side, my staining and fixing chemicals have come in.
Methelyne blue: for nuclei and nucleic acids, and useful for identifying diptheria.
Eosin: for cytoplasmic staining and anything generally alkaline in nature. Useful for alkaliphilic bacteria like Bacillus halodurans.
Iodine tincture: for glycogen and complex carbohydrates
Carmine: generic protein stain
Crystal Violet and Saffranin: for gram-positive and gram-negative bacterial identification, as well as molds, protozoa, and fungi.
It will be interesting to compare phase contrast microscope identification with bright field staining techniques. Especially since I shelled out the bucks for the phase contrast capability :)
