Rainy Day Therapy

If you ask most people around me it is miserable out... cold, rainy, dreary. If it were a bit colder it would be a wonderful snow storm and a good way to end the winter. But, it is raining, raining, raining. The wilderness instructor in me calls this "prime hyperthermia weather". However, I am not in the wilderness, and I do not have to worry about hyperthermia when indoors is always nearby, so I propose a radical notion... it is actually wonderful out. Don't believe me? Follow these steps on your next walk home in the cold rain and enjoy experiencing the elements, the feel of your cold damp skin, and appreciate your warm home when you get there.

1. Walk with a friend

2. Skip until you get warm

3. Stamp in every puddle you pass trying to get your friend wet, make sure they do the same to you

4. Laugh loudly, try to laugh so loudly that people hunched over near you look up and maybe appreciate the experience, just a little bit

Getting ahead of myself

The pacific ocean.

The view from our "guest office" at MBARI

I have been slacking in blog-land recently, but I have something to report. I want to move to California, at least for a couple of years... like for a post doc. Now all I have to do is finish my PhD. I spent the last week out in the Monteray area working with collaborators at the Monteray Bay Aquarium Research Institute. By "working with" I mean that I was being shown how to use a very complicated instrument that we will eventually get to play with in our lab and bring to sea. I am (mostly) confident that when said instrument arrives I can tinker with it without breaking it. Using this instrument is going to test both my molecular biology skills as well as force me to learn some basic computer programming. As usual, I am looking forward to the challenge.

This was my first school-sponsored trip in this grad program, and it was certainly exciting to learn about this cutting edge technology. I really did try to come up with a less cliche way of saying "cutting edge". My advisor gets serious points for deciding to send my science-partner-in-crime along with me for this training. It cost him some extra money, but the two brains being better than one will certainly hold true when the instrument arrives.

So... back to CA (ah... if only I could go back). The folks at MBARI seemed to really enjoy their work, and why wouldn't you when you got to have the above view from your office each day. I grew up in New England where we like to think that the weather makes us tough, and we are stronger for it. This leads to the mindset that "those Californians can't possibly appreciate all that nice weather, how could they get anything done?". I am certainly willing to go give it a try, and report back!

Molecular Biology Actually Works

Up until this past Friday I was semi-convinced that molecular biology doesn't really work. Or, at least, that it was never going to work for me. Since I transitioned into biology from the world of Geology and Environmental Science I have been playing catch up in terms of learning lab techniques, some of which are very finicky. I can now say that it is very exciting when these processes actually work.

We have been attempting to increase the volume of our extracted DNA using a Whole Genome Amplification (WGA) kit. In contrast to the more common PCR which amplifies a specific region of the DNA, the WGA process amplifies all of the DNA in a sample. This is great if you have very small amounts of DNA, but the downside is that if there is any non-sample DNA present that will amplify along with your sample.

My science partner and I spend about 2 weeks trying to work with our WGA kit. In order to make sure we were really amplifying our sample DNA and not a contaminant that we inadvertently introduced we used water as a negative control along side our sample. If we did things correctly we should have seen amplified DNA in our sample and no DNA in the water control when we were done. However, time after time we had more DNA in our water control than we did in the actual sample. This was very frustrating. We tried everything we could think of to be more sterile, and kept getting the same result. Finally we contacted the company and they sent us a new kit to work with. The first time we used it we got good results! There was no DNA in our water control, and plenty of DNA in the sample. It is really good to know the process works, and now we might actually be able to send some DNA out for sequencing. I am beginning to believe all the people who have told me that in molecular biology you do something over and over and over and over again... and then, finally, it works.

a new month and a new semester

One month ago I decided to do monthly goals and self-check-ins rather than make new years resolutions. It is time to see how I did with my January goals.

Overall I would say not too well. Of my 10 goals I partially accomplished 3 of them, partially failed at 2, and totally failed at the rest. As I expected, I did not have nearly as much time for myself as I thought I would. However, this was just month one, and the overall goal was to set more realistic goals. So, now it is time to decide what I will accomplish in February. I have made 7 goals for myself that should be doable. 2 have to do with family. 2 have to do with work. 1 is fitness related (sort of a 3-in-1 goal). 1 is to keep my room clean and organize stacks of papers that have accumulated over the last months, and the last is to write at least 6 blog posts. So far I like the monthly goal setting.

The academic semester has started up and my schedule already seems much busier than last semester. This is primarily because there is lots of lab work to be done before our summer research cruise. I am struggling with the voodoo-like nature of molecular biology, and really hope that things start working out soon! Everyone tells me that this is just the way it goes... you mess up a bunch of times, and then, magically, it works. I am really looking forward to being able to say "it worked!". Some day soon, hopefully...

Super Exciting Microscopy (SEM)

The scanning electron microscope (SEM) is my new favorite toy. Ok fine, its not really mine, and I guess its not a toy, but I have to admit that I was just as giddy as a chile with a brand new Ticke Me Elmo (or whatever is cool these days) on Friday afternoon, when I got to play with one of these amazing tools. A light microscope is limited in resolution by its optics, but also fundamentally by the properties of light. The microscope uses light reflected off of the subject to see it and then the optics focus and magnify the image generated by that light. Basic physics proves that any object or feature that is smaller than the wavelength of visible light (380-750 nm) will not be detected by a light microscope. That is where the SEM comes in. An electron beam has a much smaller wavelength than visible light, and when it is used to scan an object the resulting image has much higher magnification than is possible with a light microscope.

The image below is the fungus Acremonium strictum.

This next image is a Stibella fungus growing on Manganese.

The next image is from the same sample (Stibella growing on Mn). I think we are looking at bacteria growing next to fungal hyphae (on the right side of the image) but I am not entirely sure. It is interesting that when looking at something familiar under a new level of magnification, it can be difficult to tell what you are actually looking at.

Below is another image of the fungus Acremonium strictum, but at lower magnification.

I am pretty sure that everyone in my group thought I was a total nerd when I excitedly exclaimed "yes!" upon hearing that one of our samples was dinoflagellates. These are some of my favorite marine plankton, and leave behind beautiful shells that accumulate in sediments and allow scientists to reconstruct past climate based on which species (or really morphotypes) are present. Here is one image that I thought was especially nice. The UFO shaped object is a dinoflagellate, but I dont know what species or type.

Here is an image from the same sample that I was able to make into a 3D image by taking a picture of the same thing on a stage tilted 3 degrees in either direction and then merged with a special program. Unfortunately unless you have 3D glasses, it wont be that exciting.

Fun with light microscopes

Composite image of bovine endothelial cells created with fluorescense microscopy.

I spent three days last week participating in a microscopy workshop organized through a microbial sciences initiative at my school. It was interesting to meet others who different aspect of the micro-world. While I work with specific types of environmental samples, most microbiologists work on a specific model organism trying to figure out a specific process or part of that organism's physiology. Microscopy provided a common tool of interest to all of us!

This is an image of filamentous algae taken out of a Winogradsky Column, which is a great way to grow a lot of bacteria and other microbes in one location with very little work. We looked at many samples (compost, fungi, cultured organisms) under light microscopes but this sample was the most interesting to me to me because it was easy to find lots of cool microbes to take pictures of.

This is another image from the same sample. Here there are at least two different types of organisms, but I don't know what they are. The green is an alga of some sort, and the red could be a colony of purple sulfur bacteria.

After playing around with the basics of light microscopes and trying to perfect our focus, we tried our hand at fluorescence microscopy. This technique uses specific wavelengths of light to excite certain molecules within cells that emit light when they are excited. It is typically used for looking at samples that have been pre-stained with fluorescent dye (like the one at the very beginning of this post), but many of the organisms in the Winogradsky were auto-fluorescent so we were able to get some cool images by looking at them under specific colors of light. This green image is the same image as the one above, but with the red filter on. The organisms absorb red light, and reemit green light.

I looked at this exact part of the sample under red, green, and blue light. Each light excited different organisms, or different parts of the same organism. When you capture an image of each and merge the image you get something pretty cool!

Here is another example, but this time looking at a filamentous algae (shown in red) and a round one (shown in blue).

Stay tuned for even more exciting images from a Scanning Electron Microscope (SEM)!

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