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An ounce of prevention: A microbiology extra credit opportunity

Most flu shots are administered  I.M. (intra muscularly), therefore, at a 90 degree angle relative to the skin.

Most flu shots are administered I.M. (intra muscularly), therefore, at a 90 degree angle relative to the skin.

Bob and Sally go to get their annual Flu vaccine at the public clinic. Every year, the two go together and neither have contracted Influenza since they began five years ago.

This time, while he was getting his shot, he says to his nurse, “These shots are great. I haven’t been infected with the Flu for years, despite at least some of my co-workers getting sick every year.”

His nurse finishes his injection and then says, “Well, you might have gotten infected, but you’ve didn’t get sick.”

“What do you mean? Isn’t that the same thing?”

“Actually,” says the nurse, ” it’s not.”

Explain what the nurse means by ‘infection’ and ‘getting sick’ being different things. Include, in your explanation, why it is that a vaccine might not prevent organisms from getting into your body and even into your cells, but that they can still fail to make you ill. What cells and molecules are involved in protecting you in this way?

 
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Posted by on May 1, 2015 in Uncategorized

 

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Invitation to Submit Questions for Microbiology (Mini) Exam II

infectious_diseaseMy microbiology class is having a special mini-exam on the Tuesday after we come back from Spring Break. This exam will cover chapters 11 and 12 of the Cowen Microbiology text, which is basically ‘how do we kill microbes outside of the body’ and ‘how do we kill microbes inside the body?’ This exam will also have elements taken directly from Exam I presented as an opportunity to retain that material and be sure that we keep these core ideas in mind.

That said, I will be happy to entertain any questions proposed by students (or non-students) on these topics.

 
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Posted by on March 12, 2015 in Uncategorized

 

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A Pointer

For my Microbiology students….

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“I feel kinda sick”

As we finish up the year dividing out time between Immunology and Epidemiology, you may find it useful or just interesting to take a look at the online Epidemiology course offered at Coursera. It is a six-part course taught by Lorraine Alexander and Karin Yeatts of the University of North Carolina, Chapel Hill.

As all Coursera classes, this is 100% free unless you would like to receive a signed certificate of completion.

Enjoy.

 
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Posted by on November 21, 2014 in Uncategorized

 

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It’s a Wide World

Have you ever asked yourself, “how is it that our immune system can fight off almost everything?”33707699

It’s one of those things that is easily ignored.

 It works. That’s all I care about.

If that’s not a good enough answer, then read on…

The answer lies somewhere between biology and statistics. And I want to  start with an analogy.

Think of a website that makes you log in when you visit (Google’s gmail, for instance). You come up with a password when you join and then use it every time you log in. Some annoying websites make you cycle your passwords regularly for security purposes. (I’m not saying there’s anything wrong with that, but it can be taxing to those who don’t use a password storage program. – by the way, I use Dashlane  and love it)

But every time you use a password, it’s off the list – you can’t use it again. So after about three changes, you start to sweat because you think your head is filling with all those old passwords and you can’t remember the latest one any more. As an analogy for the immune system, imagine a simple program that creates random passwords for you and ensures that they’re not repeats of any that you’ve used before.

Your immune system has no idea what you’ll come up against in the world. All it can do is make a vast repertoire of immune cells with the hope that it will be sufficient to react to anything. For simplicity, let’s just consider how cells make antibodies. To do this, your cells have a way of randomizing the protein sequence responsible for making these proteins.

The problem with this system, if it’s just a random grab-bag, is that sometimes those antibodies might bind to your proteins causing big problems. So, after the random process that generates antibodies, there is a second, non-random selection process that eliminates any that bind to you.

In my analogy, imagine that a random password is generated (the antibody), but then it checks to be sure it’s not the same as a previous password (no self – reactivity).

If you do any programming you can imagine outlining your code:

(let’s say passwords are 4-digit numbers from 0-9)

 

  1. generate a random number from 0001 – 9999
  2. cycle through old passwords
    1. check that the new password is not equal to the old password.
    2. If it matches, discard that password and go back to step I
    3. If it does not match, cycle to next old password
    4. Repeat until all old passwords have been checked
    5. Present new password to user

Now that I look at it this way, it is very much like evolution by natural selection. Random process à non-random selection.

ImageTo illustrate how this works with the actual proteins, it’s best to go to good old Janeway:

The top two panels show something more like the actual structure of the antibody. The bottom panel shows a simplified cartoon, highlighting the variable region and the constant region of antibodies. Think of the constant region as the backbone of the molecule – it comes in a few models, but doesn’t change.

The variable region is where the antibody binds its target. This is the region that gets scrambled up so the antibody will have a unique binding region.

The variable region is actually composed of several parts (V, D and J) that get pieced together, one of each sort. This accounts for some variability, but could only result in a handful of different types.

In addition to this mix-and-match, the joining of segments is also imperfect. Recall that DNA is ‘read’ in three-base codons. Because of this, adding one extra base in joining the elements will result in a frame-shift that creates even greater diversity. It also admits the real possibility that the protein made will be entirely unstable and useless. To account for this, each cell is positively selected for only ones that make stable receptors. It has two shots* at making this work. Once for each of the two chromosomes (one from your mom, and one from your dad) bearing this gene. If it succeeds, it goes on developing**; if it fails, it commits cellular suicide: apoptosis.

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Another figure adapted from Janeway

The result is a pre-immune repertoire of about 1012 antibodies available to protect you from any nasty ‘bugs’ out there.

 

* There is data supporting additional receptor editing. 

**         Heavy Chain is rearranged and interrogated first, then Light Chain.

 

 
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Posted by on May 2, 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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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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“This blog is our last hope ”

“No, there is another.”

Exam I for Microbiology nears. Where will the extra credit questions come from? Will they all be found here? Perhaps. But there is A New Hope.

 
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Posted by on February 19, 2014 in Uncategorized

 

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