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I had to show this to my wife

ImageSome symptoms of hypoglycemia include headaches, weakness, nervousness, trembling and unclear thinking. Another thing you might notice is when you are hypoglycemic, it’s not a good time to talk with you spouse about finances.

A recent article, published (ahead of print) in the Proceedings of the National Academy of the Sciences by Brad Bushman, et al used voodoo dolls and loud noise blasts to measure the aggression spouses felt at one another.

[E]ach evening participants stuck between 0 and 51 pins into a voodoo doll that represented their spouse, depending how angry they were with their spouse. To measure aggression, participants competed against their spouse on a 25-trial task in which the winner blasted the loser with loud noise through headphones. As expected, the lower the level of glucose in the blood, the greater number of pins participants stuck into the voodoo doll, and the higher intensity and longer duration of noise participants set for their spouse.

I’m relating to the feelings of aggression thing a bit lately. No against my wife – or against anyone in particular, but just a low level sense of irritability most likely attributable to the diet I recently adopted. I’ve been trying to exercise more lately, but the more I exercised, the more I found myself ‘grazing’ in the kitchen, looking for just anything.

As I continued exercising and eating more to compensate, I was getting more and more frustrated by any return on my exercise investment, so I finally gave in and admitted that I needed to do something about the other end of the calorie equation. I considered a couple of methods, but finally settled on the ‘Lose It’ app for my iPhone. Basically, this app serves as a food and exercise journal with a little goal-oriented motivation thrown in for good measure. one of the things I liked best about the app was its use of graphs to follow weight loss and project how long, if trends continue, it will take to achieve a weight loss goal.

Really, there’s nothing like a food diary to limit what you eat.

ImageBut it’s not just hypoglycemia. Other work suggests that just engaging in self-limiting behavior – exerting self-control – leads to increased aggression. “In one study people who choose an apple instead of a chocolate bar were more likely to choose movies with anger and revenge themes than milder movies.”

Well, according to the app, I only have to keep things under control for another 100 days. Another 100 days of movies to line up.

 
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Posted by on April 15, 2014 in Uncategorized

 

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Another Puzzle – about the interaction of host and pathogen

Ok, I realize that some of the past puzzles I’ve made either had errors or were simply too obscure in their clues (again, I’m a crossword novice). I tried to be a little more clear with this puzzle and also did my best to force as many clues into actually ‘crossing’ as possible.

Let me know what you think and if you suspect any errors. The topic is: the host-pathogen interaction, our first chapter on immunology.

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Clues

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Posted by on April 15, 2014 in Uncategorized

 

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Your Inner Fish Crawls off the Page

ImageI’ve been assigning Neil Shubin’s Your Inner Fish as a reading and discussion assignment in my General Biology classes for several years now. I believe that it’s a good introduction to understanding how the process of science works in the real world, it does a good job communicating the methods and findings of a number of complex experiments, and it also walks through the history of ideas and how new information changed these ideas over time.

If I can get students to think about all these things and perhaps do a little extra digging (into the research), then I’ve down my job.

Episode I of the adaptation of this book  just aired this week and I was very impressed by the way the material was put together- refining the story from the book a little- and coming up with a standard documentary supported by computer graphics that really add to the story rather than looking tacky of fake. In fact, I think the graphics really transform the material into a living experience.

The story is told in two converging arcs. In one, we follow Shubin’s field work, where he decided that he was interested in finding the remains of one of the earliest organisms to crawl out of the water and establish terrestrial life. Prior work suggested that the earliest tetrapod ancestor on land emerged from the Devonian Seas about 370 Million Years Ago. Shubin and colleagues identified an ancient river delta of about this age in the Canadian Arctic and set out to locate some fossils.

ImageThe other story walks us through the idea of relationship with other life on Earth. What suggests this relationship? What evidence is there for it? How long does it go back?

As I said above, I have liked this adaptation very much so far and I am already planning to bring at least parts of this video into my classroom to supplement our discussions.

More on this later…

 
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Posted by on April 10, 2014 in Uncategorized

 

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Fifty

ImageThe fifty word story challenge.

Thanks for the inspiration, Regina.

It Came From Under the Bed

His breath held painfully as fretful fingers climbed the bedstand lamp for the switch. Below, old homework papers crunched slowly. Ominously.

“Skipper…?” The dog’s name was little more than a slow exhale.

“Please be Skipper.”

Pffffffffft

He gagged on the warm, unlikely relief of dog fart.

 
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Posted by on April 8, 2014 in Uncategorized

 

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Cosmos – on the nature of light

Spectroscopy

In this weekend’s Cosmos, a lot of attention was spent discussing the properties of light. For something so apparently simple, there is a lot beneath the surface.

I wanted to talk about two elements of this episode in particular and provide some examples to explain things a bit better.


 

The first idea is that white light (what we get from out sun) is composed of all the colors. What we see as colors is actually the various wavelengths of light. We see short wavelengths as colors toward the red end of the spectrum; longer wavelengths appear as colors toward the blue end.

We also know that shorted wavelengths carry more energy. I like to tell my students to imagine a shoreline where all the waves are exactly the same height. If the length of the wave is shorter (measure from the top of one wave to the top of the next), then more waves batter the shore per unit of time. Longer waves mean fewer waves hit the shore in a given period of time. So, is more energy transmitted to the shore from the longer or the shorter waves?

Another part of this ‘white light contains all wavelengths of light’ comes from the way a prism reflects and refracts light. Any wave will change its direction as it goes from one medium (like air) to another (like glass) – it actually changes speed, which suggests a good analogy that I’ll explain in a second. How much it bends depends on the wavelength of the light.

The analogy is that of a car driving on a street. Imagine the car veering of the street at an angle to the right. As it leaves the road, it hits mud. The right wheel hits the mud first and slows down pulling the car harder to the right until the left wheel hits the mud. When that happens, the car stops getting pulled to the right and goes off in a straight line again. (the moment when the car is getting pulled onto a new course I’ve drawn a dotted line) The important thing to note is that the car was pulled right by the icky mud clinging to the tires more than the road does.

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We can bend light by passing it through a glass (prism). The result is depicted in this album cover for Pink Floyd’s Dark Side of the Moon.

ImageWe can even bring the colors back together to produce white light again by using a second prism.

 

All this gets us to the idea that light can be dissected into a spectrum using a prism. This is the first type of spectrum described below.


 

The three types of spectra:

  1. continuous spectrum – emitted by a dense hot object
  2. emission line spectrum – the precise wavelengths of light emitted from a hot gas   (we can ignore this type of spectrum for the purpose of this discussion)
  3. continuous spectrum with absorption lines – the inverse of the emission line spectrum. When a cooler gas absorbs wavelengths of light from a hot source.

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In the example discussed in Cosmos this weekend, we learned about the third spectrum. This is what is produced when a hot star emits light in a continuous spectrum. The cooler atmosphere of the star then absorbs some wavelengths of the light as it passes through. This is how DeGrass Tyson was saying that we could determine the composition of a star’s atmosphere from its spectrum. All we need is to do some experiments in the lab and see what absorption lines we see from different elements’ gas.

As always, the theory is cleaner than the reality, but let’s take a look at the spectrum from the sun. This image highlights some major bands and indicates which elements they come from.

Below the solar spectrum are some of the spectra from the sun’s constituents with major bands that correspond to those seen in the solar spectrum marked with (*).

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Again, I apologize for this not being very exact, but it does at least communicate the idea of what was discussed on Cosmos in a little more detail.

References:

  1. for a good explanation of spectra http://www.astro.washington.edu/users/anamunn/Astro101/Project1/stellar_spectroscopy_introduction.html
  2. for the periodic table of light http://www.alexpetty.com/index.php/2011/07/20/the-periodic-table-of-the-light/
  3. for the composition of the sun http://chemistry.about.com/gi/o.htm?zi=1/XJ&zTi=1&sdn=chemistry&cdn=education&tm=41&f=10&su=p284.13.342.ip_&tt=65&bt=0&bts=0&zu=http%3A//imagine.gsfc.nasa.gov/docs/ask_astro/answers/961112a.html

 

 
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Posted by on April 7, 2014 in Uncategorized

 

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A game for cramming micro students

Exam II in Microbiology happens this Tuesday. If only there was some less stressful way of studying for the exam. Perhaps a puzzle to kick back and contemplate …?

(As an aside, I really don’t like the way this puzzle turned out – for a crossword puzzle, there are very few words that cross. I may attempt to redo this later, but there’s an exam to write first)

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Clues:

Oh No!

Autocorrect strikes again – 1 Across = the DESTRUCTION of all microbial life.

I do apologize for my poor clue-writing. I’m only a recent adopter of crosswords and I’m not yet very good at writing them the way they should appear.

(I can only solve NYTimes’ Monday puzzles)

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Posted by on April 6, 2014 in Uncategorized

 

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A quick look at mRNA Splice Variants

-Beadle and Tatum Redux

-Beadle and Tatum Redux

In my microbiology class this past week, we were discussing how prokaryotes and eukaryotes differ in their handling of DNA, RNA and gene regulation. Mostly, we focused on how the presence of the nuclear membrane in eukaryotes separates the processes of transcription and translation and what this results in. Briefly, bacteria are prokaryotic life forms that lack a defined nucleus (among other differences). Because of this, when bacteria transcribe mRNA, it is immediately available for translation – the DNA, RNA polymerase and Ribosome all exist in shared space. Below is a classic image of a strand of DNA(stretching left to right) in E. coli being transcribed into RNA. The RNA molecules extend away from the DNA and appear to travel up or down away from the DNA in this micrograph. Along the length of the RNA, we see dense ribosomes which are busy synthesizing proteins.

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In Eukaryotes, the nucleus encases the DNA, the RNA polymerases and mRNA. mRNA can be completely synthesized and modified in a number of ways before they are exported from the nucleus to the cytoplasm, where ribosomes will translate the message into protein.

One of the modifications of Eukaryotic mRNA we spoke about was splicing. Splicing is a means of snipping segments of non-coding introns out of the mRNA leaving a mature mRNA with a continuous strand of exons. One interesting possibility this enables is the production of alternative sequences made from differential splicing of the immature mRNA. These alternative mRNAs are known as splice variants. At this point, I was asked for an example of a gene that is handled in this way and was caught flat-footed.

Hmm. Perhaps this is something that I’d heard so much about in classes but never in the ‘real world’. I’ll have to look.

One of the first things I found was this discussion of splice variants suggesting that this was not a biologically significant event. i.e., the RNA may be alternatively spliced, but do these splice variants actually result in functional proteins with different properties. The author poses a challenge to find examples of splice variants that are ‘real’. The ensuing discussion is a good one.

What would this looks like?

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Regardless, I found a paper with some good figures that may help students understand how this phenomenon (at least putatively) occurs.  Here’s the best figure presenting a diagram of the different mRNAs created and gels and sequence data indicating that these exist.

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The above Figure shows the presence of distinct RNA species, although that, alone, does not mean that these RNA are ever made into protein. To do that, western blots of protein extracted from various tissues is shown below.

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What is left to find is whether each of these two proteins actually does something. Are both forms required? Are their functions distinguishable?
My quick look through the literature did not uncover any evidence for this last question. If anyone out there knows the literature on this, I would love a push in the right direction. It doesn’t matter what gene we’re looking at, just that it is an example of alternative splicing and that each of the splice variants is actually made and has some identifiable and distinct function.
 
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Posted by on April 4, 2014 in Uncategorized

 

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