My research experience summer ’12

Here is the link to an abstract about the research I did during summer 2012 at the University of Minnesota.

http://www.mrsec.umn.edu/EHR/participants/2012Participants.php

It was work that represents how collaborative research can be. I was working in an Engineering and Materials Science lab, researching how pores which form in lipid membranes can be “sealed,” basically plugged. One might propose a reasonable question: what does biology concerning membranes have to do with materials science? The answer is that there are all sorts of questions concerning Biological problems which can be addressed using basic chemical principles. In this case, we used our understanding of the amphiphilic structure of a lipid to design synthetic polymer which had this same quality. It was our hope that due to similar character, it would mimic lipid behavior and aggregate in the same way a lipid would with the goal of filling developing pores in membranes. To study this, we used a device called a Langmuir Trough, which was essentially a small pool of water. We inserted a mixture of biomolecules found in the membrane of muscle tissue from rabbits into the trough and measured the density of lipids, or put another way amount of aggregation of the lipids in the monolayer formed. We then decreased the lipid density by making the outline of the trough wider, and then inserted our synthetic lipid. The idea was to see how the lipid density of the monolayer was affected with the addition of the synthetic polymer, hoping to see an increase in density and return to the density the monolayer was at before expanding the width of the trough. If this was the result, we could conclude some kind of “sealing” of the model membrane (in monolayer form) occurred. I gained a lot from the experience because of how collaborative it was. The grad student I worked with was a great mentor. However in hind sight, I think she often got frustrated because her background was not in Biochem. It was in Chemistry and chemical engineering, which was the typical background for her lab; the other people in her lab (all males btw) were not working with Biological material. I think had she had more understanding concerning how properties like polarity, molecular weight, size, and perhaps most importantly non-covalent bonding such as vanderwals can be applied to biology such as the impact on lipid aggregation, she might have had more variables to consider, and more general understanding to work off of.

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Thought experiment: imagine a time when all of this was yet to be determined! what would that feel like?

Screen Shot 2014-04-19 at 9.59.43 AM

Above is a screenshot of a collection of images portraying the different levels of understanding of the DNA structure, minus Rosalind’s groundbreaking X-Ray diffraction image. At left is what a single chromosome looks like unraveled. In the center are electron microscopy images of DNA and at right are computer designed theoretical images of A, B, and Z DNA helices. I include these images to emphasize how much we know now relative to how much Rosalind knew at the outset of her exploration. It is difficult to imagine what it would feel like not to know what the basis for life and differentiation looked like. It would just be that thing in the nucleus that somehow was consistently translated into life. If human life is an incredible/wonderful mystery today, in the sense that it is amazing that life is habitually created and maintained to form intricate while functional structures, how much of a mystery would it have been then? Its an interesting thought experiment to imagine a time when DNA double helix was not part of the public’s vocabulary, when it was just accepted that something in the nucleus worked its magic! In trying to imagine this scenario, it allows me to appreciate how momentous the DNA helix discovery must have been for those involved and the public who benefited from the knowledge.

 

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C15H31COOC30H61

In talking about lipids today, we also mentioned waxes. Now, I always think of honey when I hear wax probably because of this great field trip to a honey farm when I was younger. They had the most delicious honey and beautiful honey-wax candles.

It turns out beeswax is made up of several compounds (much like the oils we mentioned in class). It’s chemical formula is usually a close version of C15H31COOC30H61, where its main constituents are palmitate, palmitoleate, and oleate esters of of aliphatic alcohols.

Apparantly there are even saponification differences between the European and Oriental beeswax. While the saponification value (refers to how much base you need to add to make a soap) for European beeswax is between 3 and 5, that of Oriental beeswax is 8-9.

Below is a picture of Triacontanyl palmitate, one of the major components of beeswax. Looking at the long carbon chains, it becomes quite apparent why wax may be involved in repelling water…

 

 

800px-Triacontanyl_palmitate

 

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Margarine vs. Butter

In class we talked briefly about the differences between margarine and butter, so I was curious about whether there were any health differences between the two. Originally, margarine contained high levels of trans fat, but after the FDA publicized the health problems associated with trans fats, most companies removed them. In general, margarine contains lower levels of saturated fats, but higher levels of unsaturated fats. Saturated fats have been linked to an increased risk of heart disease and type 2 diabetes, whereas unsaturated fats have been shown to decrease blood sugar levels, the risk of heart disease, and the risk of type 2 diabetes. Additionally, margarine does not contain carbohydrates, which are found in fairly high levels in butter.

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Fun with lipids!

One of my favorite things to play with growing up (maybe now still) were bubbles. The small air filled spheres that pop releasing a small spray of water- I loved them.

Learning about lipids and looking into the structure of detergents that are products of lipids, I discovered that they are the source of the joy that is bubbles! A bubble is basically a spherical bi-layer of detergent molecules kind of like the vesicles we looked at in class. However, the orientation of the detergent in a bubble is such that the hydrophillic heads are in the middle of the bi-layer and enclose a thin layer of water while the hydrophobic tails face the middle and the outside of bubble where they are in contact with air.

I can now review my understanding of biochemical concepts while relieving finals stress!

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Soap-making

I’m so excited to be trying the soap-making process again! I got to do this once in my high school organic chemistry class, and it was a long process, from what I remember, so I’m interested in seeing the differences between high school soap-making and this year’s. While I was looking for things to jog my memory about what we did in the high school class, I found this website, which I thought I’d share with you: http://www.millersoap.com/soapdesign.html

I thought it was nice because it breaks down the amounts of lye and things like that that go into soap (I didn’t look at our page yet, so I don’t know what process we’re using. I know in high school I was worried that I made my soap too basic, so I didn’t use it much after I made it). In addition, it lists what each fatty acid helps with–conditioning, good lather, etc, which I didn’t see in high school, but it’s nice to know! Good luck with soap making, everyone!

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Coconut oil

Earlier this week, we talked a little about using coconut oil for conditioner, and it got me thinking about the varied uses for oils and the biochemistry behind these oils. I’m one of those people who uses oils for everything: facial cleanser, moisturizer, conditioner, supplement, oil pulling, etc. My family used a lot of “alternative” medicines and beauty products growing up, many of which involved either ingesting or topically applying natural oils. So, in light of our class discussion, I thought I would look into the chemical makeup of coconut oil.

From Wikipedia, coconut oil is extracted from the kernel or meat of matured coconuts. It is a high saturated fat and is slow to oxidize, making it resistant to spoiling or becoming rancid. There are two pathways for extracting the oil: dry or wet processing. Dry processing involves drying out the coconut meat and then pressing or dissolving the dried meat with solvent, which is often hexane. Wet processing involves treating the raw coconut using a variety of techniques, including heat, cold, salts, enzymes, centrifuging, and electrolysis. Coconut oil has both linoleic and oleic acid, which are omega-6 and omega-9 unsaturated fatty acids, among other fatty acids.

Scrolling down to the “Personal uses” section, the entry also notes that coconut oil can reduce protein loss in hair, although the exact mechanism is unknown. This makes sense to me, as from personal use I can say that coconut oil can make your hair a little “crispy”. I prefer to mix a little coconut oil with argan oil for conditioner. Overall, I think this sort of everyday science is super interesting! I love cosmetic chemistry, and I’m finding this lipid unit full of interesting bits and pieces

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Think About It This Way: Artistic Science

(Disclaimer:The post starts on a tangent, but I promise there’s a point!)

I was trolling on Facebook the other day and came across a wonderfully moving series of photos, of musical instruments photographed from the inside…What!!

http://www.boredpanda.org/musical-instruments-photographed-from-inside/

Now sure exactly how these photographs were achieved or collected, but it’s a wonderful, thought-probing concept. How often have we looked at a violin, a cello, a guitar and marveled at its exterior beauty? Conversely, how often have we been able to look inside the instrument to marvel at the craftsmanship from another angle? This is a lesson in perspective, no doubt! I suppose it’s almost like looking at the MALDI-TOF or other boxy instruments and being impressed that it looks so sleek and large and science-y; but at the end of the day, the real magic of the MALDI-TOF (and other intimidating instruments) is in its interior parts that break down and help us analyze the protein sample; that’s what we should be ooh-ing and aah-ing about.   Perhaps one day someone will figure out how students like ourselves can sit inside the machine and watch the machine as it does its work – it’s a perspective we’ve been lacking!

Extrapolating this further, I was trying to find some more artistic depictions of lipids and plasma membranes from various perspectives.  Traditionally, diagrams and schematics have  helped me understand just how the plasma membrane works, but it wasn’t until I saw a few videos by Nature or aesthetically pleasing pictures (below) of the membrane “landscape” (that is to say, a 3D-ish depiction that was NOT in a textbook!) that I began to appreciate how beautiful and brilliant the membrane is. From this perspective, I could get a big picture idea, start to imagine the plasma membrane not as a dividing line but as  a very dynamic landscape, and I think that has made all the difference.   I had some trouble finding lots of WOW-worthy artistic depictions of the plasma membrane, but I know there must be things out there, so I will keep looking and update this post as I see fit. I know there must be more lurking out there besides the one posted below!

(Source: Nature.com)

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Trans-fat

Lipids have always been one of the most interesting biomolecules. It is not a polymer like the other three large classes of biomolecules and at the same time it is so abundant in our bodies. Particularly interesting is something known as trans-fat. All the health articles are always describing how bad trans-fats are for our bodies and how they are linked to heart disease, high cholesterol, etc. I thought that it would be interesting to include an article that has compiled 22 foods that are high in trans-fat. As you scroll through it, you may notice how many of these foods are easily accessibly by us whenever we enter the dining halls. Yes, it is good to try to eliminate these foods that are high in trans-fat, but it possible to eliminate it completely: they are tasty, cheap, and students seem to love them. Are there other healthy and cheap alternatives that the school can use and to just tweak the menus in the dining halls to benefit us all?

Link: http://www.health.com/health/gallery/0,,20533295_16,00.html

 

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Sick and Tired of Being Sick!

So you might have all noticed that I left class early today. I’ve had nausea and other unhappy GI symptoms for about a month now, and, while the doc’s aren’t sure what’s causing my symptoms, it all boils down to biochemistry!

GI system is really interesting to me because it’s so inclusive: it’s composed of little foreign bacteria (your microbiome), which can affect the nutrients you up-take, your immune system functioning, your organs, your muscles, and your mind — it’s crazy how much these unrelated bacteria can do (and can literally make you crazy)! When we get sick, sometimes we lose all the healthy bacteria we need, allowing bad bacteria to take over. An overpopulation of bacteria H. pylori often causes GI problems, so I’m having a blood test for antibodies against that pesky beast. Prebiotics, taken as supplements or as RAW garlic, onions, and chicory root (with >60% prebiotic content), help feed and repopulate good bacteria, as do probiotics, like unpasteurized yogurt, which has good bacteria growing in it. Interestingly, however, we cannot digest prebiotics (only our microbes can), so taken in large quantities, they can actually make us sick!

In addition to our gut flora, our hormones (e.g., from the thyroid and pancreas) and our livers, which break down sugars and remove toxins, can play a huge role in GI health and well-being. To test for all these things, I’ve had blood work and samples taken, but so far nothing’s come back positive.

As I’m waiting to figure out what’s wrong, I’m on a restricted diet of essentially plain toast, plain meat (no sauces) and plain lettuce. Oddly, I’m not allowed to have dairy because my sickness seems to have removed all the lactase (lactose-digesting enzyme) from my system. Bad bacteria seem to be metabolizing the lactose I’m consuming to cause even more nausea, cramping, etc.

As miserable as I feel now, I am all the more appreciative for the flawlessness in our guts when we’re healthy. It’s truly spectacular how effectively our bodies communicate between organs and bacteria to keep everything in line and in proper concentrations. With a little push from allopathic medicine, hopefully my gut and I can get back on balance again!

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