Chapter 4 – Effects of daily voluntary wheel running on visceral adipose tissue mitochondrial content in Otsuka Long-Evans Tokushima Fatty rats

Well I have finished Chapter 4 on schedule.  Now it is on to a completely different topic for chapter 5.  The effect of exercise on epigenetic changes in skeletal muscle of mice.  This project was a high impact, high reward, high risk project that the funding agencies loved.  I received an American Heart Fellowship and 5K of research money from the American College of sports medicine to help with research.  The funny thing is, this is an on going project and I will not be done with it by the time I turn my dissertation in.  As long as chapter 4 gets accepted into a journal then I will be fine.  Alright, I have 10 days to finish this chapter.  Time to get to work.

Dissertation Timeline

So I have set an ambitous timeline for finishing up the dissertation.  Just thought I would put it out there.

Chapter 4 – finish rough draft of manuscript and get it to other co-authors by Feb 20th

Chapter 5 – Write up what I have on epigenetics project (will undoubtley not be completed with the data collection, which will likely not be added initially) by March 3rd

Introduction (chapter 1) – Finish by March 14 th, 10 days to write an intro.  Ouch that is going to hurt

Discussion (chapter 6) – Where I learn the art of hand waving in written form, finished by March 28th.  Also apparently the last time in my science career that I really get to speculate.

Edit-Appendixes – Gotta be done by April 9th.

Should be a real enjoyable 8 weeks (minus a day)

T-minus 55 days…and counting

Do you Know an Exercise Molecular Biologist?

Well, most people have heard of an exercise physiologist, but not so many people have heard of an exercise molecular biologist.  Since exercise is undoubtedly an important (maybe the defining) physiological stress it makes sense for a lot of physiologist to attach that moniker to their title and use exercise in their research.  Molecular biology on the other hand, not so much.  Defined by wikapedia as

Molecular biology is the study of biology at a molecular level. The field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein bio-synthesis as well as learning how these interactions are regulated.

While physiologist are looking for interactions between organs in a whole organism, molecular biologist step it down a notch to looking for interactions within single cells.  For molecular biologist the idea of studying exercise is a foreign as the idea of studying protein 3D structure is to an exercise physiologist.  They just don’t overlap…or do they.  It is my belief that exercise, being the quintessential organismal stress, must have genetically conserved and molecular pathways that are activated within each cell.  One major problem to using exercise in molecular biology is the lack of good models.  Apparently its hard to get cells to exercise.

Although it might be hard to get cells to exercise the principles of exercise are applied to the most basic of molecular biology on a regular basis.  With such a small and easily manipulated genome the yeast became the standard organism to study the most basic principles of biology such as protein trafficking, cell signaling, and organelle interactions.  One of the most common ways to manipulate the yeast environment is by switching the energy source in the media around the cell.  That simple switch from glucose to fatty acids is not unlike what occurs with an extended bout of exercise, and the interesting thing is that yeast respond in a similar manner as we do, ramping up the metabolic processes necessary to use fatty acids for energy.

Another example is one that I heard recently by a senior investigator in the Life Science center concerning knockout mouse models and exercise.  It is common practice to knock a gene out of mouse and just look at how the phenotype differs from that of a wild type mouse.  Sometimes dramatic changes occur, and sometimes nothing.  Several mouse models where a gene beilieved to be involved in skeletal or cardiac muscle function have shown no adverse phenotype initially…that is until they exercised the animals.  Sometimes a paper claiming that no phenotype exists is even published before the animal is exercised and the phenotype revealed.  The fact is that exercise invokes a fundemental stress response in the animal, which can bring out the function of a gene previously unknown.  In this case exercise is more than science that is good for you, but good science as well.

Dissertation Time

In months I will be handing in my dissertation to my committee.  Two weeks after that will be my oral defense, and the day after that I close on my house.  So much happening in so little time and yet now I chose to update the blog.  I hope to continue to use this blog as an outlet for the struggles that I will undoubtedly have over the next two months.  So for my dissertation I have the 2nd, and 3rd chapter written, but will need to spend a day or so editing the format so that it works in the dissertation document.  That really leaves the following writing:

Chapter 1 – Introduction – probably 25-30 pages

Chapter 4 – Adipose tissue mitochondria in response to obesity and physical activity (15-20 pages)

Chapter 5 – Epigenetic changes during voluntary running on a high fat diet in mice (15 – 20 pages), although I have a pretty good intro written already

Chapter 6 – Discussion – probably 15-20 pages.  This is really going to be a bitch to try and organize such a wide range of topics into a cohesive intelligent and thought provoking chapter.  A challenge my committee wants me to do.

Appendix(s) – lots of unpublished data going in to the pad the the thickness.  Probably an extra 15-20 pages depending on the depth of discussions, methods, and intros.

So in summary I need to write about 85 – 105 pages (while citing over 200 papers for sure) in 2 months while continuing to do research for the month of February.   At least it is double spaced.

to be continued….