Thesis live 1.1 The stem cell niche

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

1.1 Stem cells and regenerative medicine

The concept of the stem cell niche was first proposed theoretically by Schofield exactly 30 years ago in the context of hematopoietic stem cells: “a hypothesis is proposed in which the stem cell is seen in association with other cells which determine its behaviour. It becomes essentially a fixed tissue cell. Its maturation is prevented and, as a result, its continued proliferation as a stem cell is assured. Its progeny, unless they can occupy a similar stem cell ‘niche’, are first generation colony-forming cells, which proliferate and mature to acquire a high probability of differentiation, i.e., they have an age-structure.”

Niches are restricted and specialized tissue microenvironments that integrate local and systemic signals for the regulation and maintenance for resident stem cells. The elements of the stem cell niche include the constraints of the architectural space, cellular components like stromal supporting and descendent/progenitor cells and acellular elements, like soluble and membrane bound molecules, paracrine and endocrine signals from local or distant sources and neural input [Figure by Jonas].

Niches are dynamic entities, could be redistributed and ideally “a candidate niche

Thesis live: 1.2 tissue/stem cell introduction scheme

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

When producing a text, a post my building strategy is not linear, but heavily non-linear (I wouldn’t say it’s circular): I’d like to jump to the part of the story where there is something instantly to write/edit; be it the beginning, middle or end. In case of scientific articles frequently the first part to be build are figures/methods, which forms the bulk, the middle of the story after introduction, before discussion.

1.2. Tissues, organs with different turnover and regenerative potential

In order to discuss the different adult tissues in a unified manner, from a systemic point of view, I use the following tissue/stem cell introduction scheme where data are available: development of particular tissue, number of cell types, bioenergetics (high/intermediate/low energy demand), turnover (high/intermediate/low), regenerative potential (high/intermediate/low), resident stem cells, niche, markers, cell sources from other tissues that can contribute to the particular tissue during normal turnover or chronic/acute injury.

Thesis live: 1.1 Basic concepts: Let’s roll!

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

After the Introduction draft it’s time to actually start to fill in the text and that’s really the hard part. In the text I mix complete sentences, paragraphs (source code, object language) with fragmented metacomments (labeled as /draft, comments are here/) as a GTD technique. Used literature, links come after the text in a reference form like: Rando TA. Stem cells, ageing and the quest for immortality. Nature 2006;441:1080-1086. or Rando TA. (2006) Stem cells, ageing and the quest for immortality. Nature 441:1080-1086. (maybe I should check the official rules here)

Figures, diagrams will be included and I don’t promise to figure out brand new ones (but promise to find good ones), but that’s not a necessary job for thesis writers.

Expect me to start with a low quality (including older texts of mine) material and progress toward something more valuable.That is a trend people usually would like to follow throughout their professional careers.

1.1 Stem cells and regenerative medicine: basic concepts

Looking for the exact definition of stem cell is sometimes the source of endless semantical debates, but at least we do know two generally accepted criteria: stem cells are able to renew themselves and could differentiate into other type of cells. First, they are unspecialized, mitotic cells that renew themselves for any (i.e. long) periods through series of cell divisions, which result in similar unspecialized stem cells. This is the so called and overstated “immortality” characteristics.

Thesis live: Introduction, “contents” draft

From now on I start every “thesis live” post with the standard introduction: In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential

I am not aiming any perfection, my focus is clearly on getting things (the PhD) done here. Anyway, I found the idea of “writing” a complete, lengthy and formal thesis outdated and inefficient (after all, scientists should conduct nice experiments and publish their results in short, inforich and accessible research papers in order to share it ASAP with the research community, not in book-length, otherwise unaccessible PDFs) and so I try to keep myself motivated by

- doing this “thesis live” series as an open science experiment and getting useful feedback from my fellow scientists and readers

- trying to include as many systemic, whole body level material into it that could be relevant for systemic regmed approaches

- reminding myself every day that without a PhD it is hard to move further in science officially (that’s the least motivating factor though as it is official)

After the blah-blah let’s start with the planned introduction points:

1. Introduction:

1.1 Stem cells and regenerative medicine

1.2. Tissues, organs with different turnover and regenerative potential

Gut epithelium,
Blood – hematopoietic system
Epidermis,
Mammary epithelium,
Vascular endothelium,

Warming up to write my thesis on the blog

Not much happened since my announcement on Editing my doctoral thesis on stem cells in a blog: Why not?. I went to the U.S. first and started doing research instead of finishing my PhD education. But now I am back in this “getting a PhD” business as in January I passed the prerequisite comprehensive stem cell and mitochondrial biology exam with a plus.

Mr. Gunn’s dissertation on blog: Investigating the role of MSCs in repair of bone

Mr Gunn’s thesis is in a far more advanced stage, and even nerdier than mine. 

Choosing a proper title for the thesis: The physiologic role of stem cells…

In my last “live” thesis post I said that the first steps of building a thesis are: figuring out a unifying concept behind all my experimental work and finding a proper thesis title.

During my PhD work I’ve done various stem cell transplantations (local and systemic) into brain, heart, muscle tissues using different stem cell sources, just like freshly isolated bone marrow derived cells (hematopoietic, mesenchymal stem cells), murine embryonic stem cells, cultured hematopoietic stem cells. And I was heavily involved in the mechanisms by which exogenous stem cells can contribute to host tissues and the way these exogenous cells and lesion models can motilize the built in endogenuous stem and progenitor cell populations. So for me the unifying concept behind is a kind of systemic approach, that is to collect many stem cell data from various tissues, organs, compare them to each other and derive some unifying principles from them that could be adapted to other tissue environments too. And I really would like to introduce some systemic point of view into stem cell biology and regenerative medicine.

Next is finding a proper title for the thesis which embraces the systemic concept, simple but scientific enough to be approved by the academic people. Also it must be broad enough and not too restricted.

My first, rough idea was: Stem cells‘ regenerative mechanisms in tissues with different regenerative potential (turnover)

The “live”, thesis building blogxperiment: progress through little steps

I am really grateful for the echoes in the scientific blogosphere on my live onblogging doctoral thesis trial. (I especially liked PZ Pharyngula Myers’ thesis story which inspired me to put some pictures and texts into Comic Life.)

What is crucial here: this way I can perfectly match my professional daily job with my blogging activities and amplify it.

I am ignorant about the details yet but I would really like to use the WordPress content management environment as a true working surface for preparing the thesis.

Also I would like to share the background story of editing a thesis with a lot of how-toos.

All the progress here will be done through little steps and the thesis project by no means will turn Pimm a one-channel, thesis-only adventure.

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Let us assume you met all the local and global requirements in order to start to write your thesis: enough experimental work, published articles and ongoing manuscripts.

Moreover, you want a little more than just compiling your published articles and existing material together. You aim for quality.

What are the initial steps that come into your mind?

Well, for me the first steps are: figuring out a unifying concept behind all my experimental work and finding a proper thesis title.

Editing my doctoral thesis on stem cells in a blog: Why not?

OK folks, after reading the official rules about how to get and manage a doctoral thesis, and after speaking with my supervisor asking for his permission, I’ve decided to edit my ongoing doctoral thesis in Pimm. Or at least the introduction of it, which is intended to be no other than a review-like summary of some current results in the stem cell biology of different tissues, organs. What will remain hidden in the first round (but can follow later): the data-heavy yet unpublished results and the discussion, conclusion session. Objectives, Materials & Methods: we shall see it. Sounds like there are complete parts of the thesis, but that’s dead wrong, at this time my doctoral thesis is in an embryonic form. Also no idea on how challenging, meaningful this project, a sub-series in Pimm, will be. What I know is that continuous experimentation with genres and frames is the essence of free blogging!
After all, what do I risk here? If someday I’d like to write a review out of the published introduction, can this cause a publishing problem? According to Maxine Clarke, Publishing Executive Editor of Nature (i.e. peer review and publishing policy expert) the status of a thesis is: “No, a doctoral thesis does not count as “previously published” and yes, you can submit work that was part of your thesis, with an appropriate citation.”

I also asked Maxine by mail and she was kind enough to enlighten me: There is no problem with you publishing your thesis in this way, so far as consideration for publication of any part of it for a Nature journal is concerned (or any NPG journal). We encourage communication between scientists via discussion of work and unpublished drafts in the form of theses, meetings, preprint servers, online scientific forums (between scientists) etc.