Archive for ‘Lyme disease’

November 7, 2015

Just call me Dr. Jones. Some day. Maybe.

by Janie Jones

So, today was a hallmark date.

I officially began my graduate school application process.  It took the better part of the day.  I had to dig up unofficial transcripts from high school and 4 different colleges I’ve attended over the years.  I had to fill out a ton of forms, write an essay about why I want to get my PhD, another about what qualities I would bring to the graduate school, and I had to send letters to people asking for recommendations.  Before I can complete my application I need to get my GRE scores and I need to get confirmation that the people who I ask for recommendations are willing to give them.  Then, I send $75.  If the graduate school thinks I am worthy, then I have to get all official transcripts from my high school and all the 4 colleges I’ve attended sent in.  After that, if my official transcripts confirm I’m still worthy, by April I should know if I will be allowed to torture myself for another 3-5 years in pursuit of my PhD.

It is sort of daunting.  I have to admit, there have been a lot of days in the past year or so when I have doubted whether I want to commit to more time in school.  I don’t really know what I’m getting myself into.  Most people say it’s tough.  Then again, calculus was tough.  Physics was tough.  I’ve been on the tough circuit this past couple of years.  I haven’t always performed as brilliantly as I’d have hoped, and I am quite tired.  As Forrest Gump would say, “I’m kinda tired.  I think I’ll go home now.”  But I have no home to go to, so I guess I might as well keep on running this race and, in just a few more years I could hold the ultimate academic title.  Knowing I am this close, I don’t think I could be satisfied with not going the full distance if the powers that be in the admissions office will let me in.

And I think they will.  I mean, I just have this feeling.  I hope it’s not bullshit, but I do think I could do well in graduate school.  I don’t know why I feel this way exactly.  I just really think this is what I’m supposed to do.  Sure, I don’t know everything.  I certainly haven’t maintained that A average.  But I have yet to give up, and science is 90% being too stubborn to quit even when you have no clue what you’re doing- yet.  That’s the beauty of being a scientific researcher.  You don’t have to know everything.  If you did, you wouldn’t have a job anymore.  Research in science is all about not letting what you don’t know stop you.  You learn along the way, and the more you learn, the more you realize there’s a ton you don’t know, and so you do more research.

And “we” don’t know a lot of things yet about Lyme disease and the bacteria responsible for it.  I can do a lot toward a doctoral dissertation studying them little bugs.

So, cross your fingers for me.  Pray I don’t have to blog 5 months from now that I’m a washed out, has been, PhD wannabe.

It would be way cooler if some day you could be telling all your friends you read the blog of the famous Dr. Jones who discovered a way to prevent Lyme Disease and cure chronic Lyme Disease back when she was a strung out, neurotic undergrad.

Heh.  Paging Dr. Jones….

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October 2, 2015

Constellations in my Borrelia

by Janie Jones

So, do any of you ever wonder what I do when I’m in my Lyme Studies lab?

I know, you have been dying to know!

Mostly I count Borrelia burgdorferi, the primary bacteria responsible for Lyme disease in the U.S.  There are other Borrelia species that also cause Lyme disease, but most are not found in my neck of the woods.

In general Borrelia are thin spiral shaped bacteria that swim about independently.  However, they do also form clusters of varying size.  I don’t know why for sure, and I don’t know if anyone else does either.  They might and I just haven’t stumbled on that information yet.

Anyway, I am responsible for a strain that has been genetically engineered to express a green fluorescent protein that makes it glow green.  This has many practical applications, it makes them much easier to see for sure, it also makes it easier to tell if the bacteria is alive as dead bacteria don’t make glowing green protein, they don’t make anything if they are dead.

So every week I gaze into a microscope and check for itsy-bitsy green lines on a field of black.  A healthy bacteria culture has millions or even billions of the little critters all swirling about doing their little bacteria thing.  Often there are so many it looks like the depths of outer space, if the stars, planets, galaxies and nebulae were all fluorescent green anyway.  To see them well it is best to turn off the lights in the lab to reduce the ambient light which can interfere with catching a glimpse of the faint green glow, so it really does often feel like star gazing through binoculars.  The other day it so strongly put me in mind of star gazing that I started looking for shapes in the “constellations” of bacteria.

Lo an behold I found Ursa Major!

Teddy bear Bb edit png

I think I just discovered the evolution of Bear-relia!

April 12, 2015

It has been a grueling week;

by Janie Jones

Janie Jones has officially lost her marbles.

I had so much to do last week that I can’t even tell you how I survived.  Besides, that makes for a boring blog post I’m sure.  What you will probably find more interesting is reading about the signs of my marble losing.

So first, I was trying to cook a pork chop on my single burner hot plate.  It’s temperature control is  dodgy.  Well, it wasn’t getting hot, wasn’t getting hot, wasn’t getting hot, then suddenly it was starting to smoke.  So I pulled it off and set it on the wood cutting board, as I needed to cool it down.  I’ve used a wood cutting board as a trivet before, but apparently this time the hot plate meant business, super heating the pan to I’m-done-messing-around-and-only-sort-of-getting-hot-and-am-now-hot-damn-hot, and the pan scorched the wood.  Smelled like a wood burning shop in the basement for the next two days.

Twice I almost poured orange juice in my tea instead of milk, catching myself just in the nick of time.

I thought I forgot to hand in my physics homework, and ran all the way back to the drop box only to realize I had indeed turned it in already.

On several occasions I was completely incapable of forming a simple coherent answer to straight forward questions.  It was almost as if they were speaking pig latin.

And I forgot completely to bring my teaching manual to the extra session of Cell Biology Lab I had to supervise.  Way to look like you belong in charge, Janie.

I will spare you any more details as they become less becoming as I recall them.  Suffice to say, I survived somehow.

I actually had a couple bright spots.  I got a 96% on my seminar on Lyme disease vaccine research, and an 84% on my last physics test.  An 84%!  Me.  I couldn’t believe it.

Surviving the week and getting good news meant I wanted to celebrate.  I wanted to take some time off, kick back and chill.  But that wasn’t going to happen.  I had to work the tour guide gig yesterday.  Afterward, though, Leif came to town after one of his shows.  He only stayed for a little while, as he had to get back to the dogginses, who had been left at the farm all day and both of us were totally exhausted, but it was so nice to have a meal together and sit for a half hour and do nothing but drink tea, and talk and be together.  Almost as if I had a life.

College can be really lonely, you know?  You see people and talk to people all day, but you don’t really get that human contact factor.  And spending too much time in society with out having any society is tough.  It wears on your nerves.  I’m sure the solitude is messing with my marbles, too.

Anyway.

It’s a beautiful 60 degrees today.  I want to go walk down by the lake with Leif and the pupkisses.  But they are out at the farm, and I have a microbiology paper to write.  So, the grueling week isn’t quite over yet.  It’s back to the ol’ homework grind.

And as for WordPress, I still haven’t figured out the new system, but I did discover by accident that sometimes you can back-door your way into the classic format.  Which is enabling me to type this post in my comfort zone of normalcy.  We’ll see how long this lasts….

March 30, 2015

Miscellaneous Monday Morning Musings

by Janie Jones

There is only 6 more weeks in this semester.  Halla-good-dog-u-lah.

I’ve been tired before.  I’ve been frustrated before.  I’ve been excited to finish a semester before.  But I tell you all right now, I am having the hardest time ever staying motivated this spring.  I think I’ve finally hit that wall I’ve been seeing approach.  I don’t want to fail, but damn it’s hard to make myself focus.

Sitting at the show Saturday (when I wasn’t forced to engage in inane conversation with Young lady, that is) I kept thinking how I missed those weekends when my time was my own, back in the days of having a real life, when you were tired of the work week and Friday at 5pm meant you were free and could sleep all weekend or read for leisure or go for a walk.  Friday at 5pm now means, if I don’t have to work at my tour guide gig, I have to still get up early to catch up on all the studying I didn’t have time for during the school week.

Gah.

Anyway, there are moments when I really feel like throwing up my arms and walking away from it all.  If I want to go to graduate school, I have to find time to actually apply and sit for entrance exams in the next few months.  Or, I could just stop with my Bachelor’s and hope for the best.  I’d have leisure time again.  Probably no money to enjoy it, but OMG it is soooooo tempting.

And then I get a little carrot.  See it?  It’s right there, dangling just beyond my reach.

Dr. Smythe, the professor who took me on to count Borrelia, replied to my email about my data and the next phase of my project.  He said, and I quote:

“Thanks for the data…. The higher temperature is an interesting issue, one I never considered. Keep up the good work!”

I think of things he doesn’t.  He thinks it’s good work.  Awesome sauce (as those youngsters say).  Considering I felt inept and frustrated the whole time, that casual compliment feels pretty damn good.  Maybe I can do this.

And while we are on the topic of school and things I can do, I’m not struggling nearly so much with using the word moiety.  Dr. Smythe used it during our weekly meeting and I thought to myself, “Aha!  I remember what that means, and now I actually kinda get it!!!”

Here’s one last thought.  My seminar grade isn’t posted yet, but I think it went well.  Now that it’s over I do have a question I can’t quite shake.  You see, in the U.S., mice are the primary natural reservoir for Borrelia, the bacteria which cause Lyme disease.  If it wasn’t for the tick feeding on mice carrying Borrelia, the tick would not pick up and be able to pass it on to humans and other animals.  But if Borrelia naturally live in mice, where did the mice get the Borrelia?  In my seminar I made a little joke out of it saying it was kind of like asking which came first, the chicken or the egg.  But really, seriously, how did Borrelia get in mice in the first place?

Oh-ho-ho.  Possibly a doctoral thesis theme?

Perhaps I’m hallucinating that there’s an entire carrot farm just up the hill….

March 25, 2015

My fortune says: Today you will hold the attention of your peers

by Janie Jones

I give my Lyme disease seminar in one hour.

I’m not so much nervous about giving the speech as I am about staying within the 30-35 minute time frame. I get docked points if I go over or under. So far practicing my speech at home I’m generally running right at 35-36 minutes.

Interesting side note:

My February issue of Better Homes and Gardens magazine (yes, I’m a little behind) says that the Fortune cookie was invented by the Japanese, not the Chinese.

I wish my fortune said wealth and contentment will befall you soon.

March 7, 2015

Random fact and a mini science lecture

by Janie Jones

Two hours.

That’s how long it takes to count 5,500,000 Borrelia burgdorferi, which are the microscopic bacteria that cause Lyme disease.

Being microscopic, you need to view them under a magnification of at least 400 times and even still they look like wispy, kinky fine hairs.  For the super curious, they are only about 0.2-0.3 micrometers in diameter and can be up to 20 micrometers long.

They look sort of like this:

borrelia edit

I don’t know the magnification of this image I stole from Google images, but they look bigger in this photo than they do on the scope I use in the lab, so I’m guessing this is in excess of 400 x magnification.

Now, if you’ve never worked with microscopic stuff before, you might wonder how do you count 5 and a half million of some uber-tiny critter?

Well, you don’t actually count them one by one.  That would be crazy and nigh impossible.  You use science math.  And, a special slide called a Petroff-Hausser Counting Chamber.  It was actually made for counting sperm, but works for any super tiny microscopic thing.  It looks vaguely like this this photo I also stole from Google images:

petroff hauser

You place 5 microliters of your sample (sometimes you even dilute that, because a lot of microscopic critters can be suspended in even just 5 microliters), on the slide.  It has microscopic grid lines on it.  Then you count all the Borrelia in the grid.  Using science math you can then calculate how many of these guys you would have in a milliliter.  It actually is pretty easy.

What took so long is that I had to count nine different samples.  Which means not only did I have to count the little buggers nine different times, but I had to prepare 9 dilutions, and clean the slide between each sample.

I’ll be doing this a lot.  Maybe I’ll get faster.

Or maybe I’ll go cross-eyed.

February 10, 2015

Tuesday Titters: If you’re not the homework service, I’m not answering the door

by Janie Jones

Knock, knock!


Who’s there?


Canoe.


Canoe who?


Canoe help me with my homework?

 

For some reason my seminar instructor is ramming us through the preparation process.  I have to have my outline for my Lyme disease seminar ready tomorrow.  It is homework I actually enjoy, but for pity’s sake, this is an educational process not a freakin’ race.  Seriously.  Research into a thorough review of studies investigating new Lyme vaccination methods is not gained overnight, especially when I have three other classes all vying for homework time.

I’m thinking of the title:

Lyme vaccines are worth our time

or

If Fido can be vaccinated against Lyme disease, why can’t his best friend?

It is so much fun being a part of the Lyme research group at the medical school.  I actually was able to answer the question when the boss asked, “Are any of you familiar with DNA barcoding?”  In fact, I had just read a very lengthy research paper on it.  So I was able to answer intelligibly enough to earn a “That’s exactly right, Janie.”

I’m still glowing.  It is awesome to finally feel you are where you belong.  Now if only I didn’t have to spend 30 hours a week buried in homework.