Papers, videos, and transcripts

Hello my Stem Cell Biology people!

First of all, remember to keep checking the google doc of the lecture transcripts.  I always update it ASAP and I've been trying to correct my spelling mistakes and add in a few more explanatory words in case I'm not sure the lecturer was clear on something.

Also I'm experimenting with recording the lectures, b/c for some, they are better audio learners.  Bear with me as I struggle with technology.

Finally, we have one or two papers assigned for every lecture, so I'll post a sum-up of the papers.  I still recommend you read the papers and then read the sum-up, because 1) you need practice if you ever want to be able to digest the condensed jargon of science writing and 2) the more you read the material over and over again the more it sticks in your head.

Here it is from Lecture 1 (Please excuse my casual language.  It is my opinion that to make science available to the general, you must speak "layman"...seriously though.  I am not trying to condescend to anyone, I just want to make sure people can understand, because that's the foundation to building up knowledge later on.)

Also remember that every paper wants to tell you something, but it is always up to you if you choose to follow or take it for its word.  Always ask questions (is this right?  did they do this correctly?  did they consider this?  etc etc)  Whatever I write below is not an expression of something I believe in, but just a paraphrase of what I interpreted the paper was trying to say.  I'm always open to discussion! (hence, comment box)

Spradling, Allan C.  "The living-tissue microscope: the importance of studying stem cells in their natural, undisturbed microenvironment."  J Pathol 2011; 225: 161-162.

We need tools to look at cells in their daily lives without disturbing them.
    Why?  Because we would find out all about normal cell lives, diseased cell lives, new cell to cell and cell to gene and gene to gene pathways that we can't see from frozen or dead cells.

We have the tools to do this:
    Small multicell structures with labels can be seen live, for a long period of time (1-3 hr) and at the level of a single cell.
    approach referenced from Gaisa et al (see citation 4 in this paper) where they used mitochondrial DNA mutations to trace where each cell came from (lineage analysis)

This is super important for stem cell research.
    Why? they are rare and hard to find and hard to identify and basically impossible to label with gene expression tag
    But you can do it with lineage analysis!

How did they do it back in the day without being able to creep on cells in vivo?
    well, they took tissue from active stem cell tissues (like bone marrow or testis), and put them in a host with little to no stem cell activity, and then voila, cells were being made there.
    researchers figured out that there needed to be an area "stem cell niche" to for stem cells to be enriched and function
    BUT they couldn't tell if all the cells they transplanted were actually stem cells or just some of them were…
    some later studies in flies and mice showed that even daughter cells from stem cells that had begun differentiating (progenitor cells we call them now) could reverse and go back to being stem cell if they found a niche-->hmm, it was now supposed that tissues often contain lots of potential stem cells as well as stem cells.

But we still can't pick out and identify specific actual stem cells until we can look at them in vivo without disturbance.  We still don't know where they are in most mammalian tissues.
    But we can fix that!  We need everyone to do lineage tracing in all of the organs!

it used to be that people searched for stem cells on guesses and unfounded assumptions:
    myth: most stem cells are quiet and reproduce only sporadically.
    assumption: it must be cells that are still labeled with BrdU (thymidine analog, gets into DNA) after a long time--because they are quiet--must be stem cells.
    truth**: at least six types of stem cells have been shown to divide continuously

    myth: stem cells spawn huge numbers of daughter cells and these may even be extremely diverse cells (different cell types) once you stick it into tissue culture
    assumption: if we stick cells into tissue and they don't suddenly reproduce a crap ton of cells, they must not be stem cells…
    truth: most stem cells are maintained as stem cells only by their niche.  if they leave or are pushed out, they stop being stem cells and differentiate.
    example: mouse intestinal stem cells need specific cytokines and actual niche cells and other stuff in order to successfully propagate.

(**Keep in mind that I only say "truth" to mean that there is evidence to the contrary, not that this is the as-laid-down-by-the-laws-of-nature-factual-truth.  Remember always to have a healthy dose of skepticism in science.)

    we only figured all that out after the cells were identified by lineage analysis and we could characterize their niche and signals in the niche

    unless we have an exact replica of the niche, stem cell in tissue culture will look nothing like stem cells in vivo.

This is applicable to fields outside stem cell research.
    embryo cells have constant signaling and interaction with their environment during development
    cells in culture also have change in genes/epigenetics, even if their overall karyotype is still the same.
    this is all likely due to the fact that they are stressed in an environment not like what they should be in (different signals, treatments, etc)
    this is why tissue culture instead of just cell culture is better for multicellular biology

lessons learned from stem cell research:
    if we still want to use cell culture but we want to look at things that don't happen just by themselves, we need new tools
    we have to look at the events in vivo or in tissue culture
    when we figure stuff out about the cells of interest and their environment, then we can create a replica cell culture
    then we gotta double-check our model to make sure cells in vitro are behaving just as we had already observed in vivo

you have to follow these steps if you want accurate replication of the crazy complicated system of biology that every cell activity depends on.
    good thing new developments in live imaging and lineage analysis are going to make this easier
    just remember that you don't want to destroy the very biological events/systems that you wanted to study in the first place.

Cell Biology Study Guides

So I realized I must have shared my Cell Bio exam guides elsewhere or in person, b/c it's not on this blog!

So here they are!  Cell Bio exam 1 guide and exam 2 guide.  There's already a post for exam 3 somewhere on this blog.

exam 1: https://docs.google.com/file/d/0B99-sSwVe231OWM2YjA3OGItOTU3Ni00MGFiLWEzYzEtMzViNTczMTljYmY5/edit?usp=sharing&authkey=CLKk8NQB

exam 2: https://docs.google.com/file/d/0B99-sSwVe231NTI4Mzk1MWMtMGQwYi00M2JlLWFkM2YtMGRkYTM4NDNhYTFl/edit?usp=sharing&authkey=COCampkH

Again, let me know if the links don't work!  (via comment or something)

Stem Cells

For the purpose of the class I'm taking, I'll be making three kinds of posts:

1) script -> the class at our university does not have podcasting, so I will be transcribing a misspelling-prone version of near-verbatim of the lectures.  Please find it here: https://docs.google.com/document/d/1iFMdbzr9tr0M8PuvGmHvYGXVrPMIAV78OSxW2cGsQxM/edit?usp=sharing
I have little time to spellcheck or grammar check, so please comment if you find something confusing that I can clarify!

2) study guide -> this will be prepared prior to every exam.  hopefully it helps!

3) list of papers -> a significant portion of this class involves reading primary documentation, so I will be listing citations of the papers we read (and that will contain info that I will probably include in my study guides).

Ready for stem cells!

Thank you!

Hello!  I've been missing for a while (read as "not taking science classes").  This semester I will be back with Stem Cell Biology.

I've just discovered that this blog has rocketed in pageviews over the course of the past several months.  I'm not sure what happened, but at least half of my total pageviews have come from Belgium.  Not sure who's reading up on science, but I certainly hope it helps!  It's very encouraging to know people are looking at what I post, since the purpose of this is to try and share science in a more understandable and explained way than the condensed jargon-dense speech of textbooks.

Cheers!

Development Biology Exam 3 (Final but not comprehensive)

http://dl.dropbox.com/u/22080433/3777_001.pdf
http://dl.dropbox.com/u/22080433/3778_001.pdf
http://dl.dropbox.com/u/22080433/4148_001.pdf
http://dl.dropbox.com/u/22080433/4467_001.pdf

And don't forget to check out fly battle vids:
http://www.youtube.com/watch?v=ia57rw7PE_8
http://www.youtube.com/watch?v=4pDU-cqvKJc

and fly sex vids:
http://www.youtube.com/watch?v=zXXqQ2zJVMA

*5/13/12 edit: Thanks to Nadav who pointed out this nuance: stem cells can renew indefinitely, and progenitor cells can also self-renew, but only for a few more rounds.

*5/14/12 edit: More for future sake, it's not unoplakin but uroplakin in 4/13/12 lecture (which makes so much more sense i.e. ureter and all that) AND for 4/18/12 lecture, I wrote in for bone marrow transplantation that one needs mice clones, but actually that's not necessary.  Using naked mice means they don't have an immune system to reject transplants anyway.  The reason that's difficult in humans is you can't irradiate a human to ablate leukocytes (I mean you could, but who'd let you?)

Dev Bio Exam 2 Notes

Part 1
http://dl.dropbox.com/u/22080433/3214_001.pdf
Part 2
http://dl.dropbox.com/u/22080433/3215_001-1.pdf

Notes from 3/16/12 (when I was sick, so these are neat notes courtesy of Angela Hsieh)
http://dl.dropbox.com/u/22080433/3218_001.pdf

Part 3
http://dl.dropbox.com/u/22080433/3216_001.pdf
Part 4
http://dl.dropbox.com/u/22080433/3219_001.pdf

The scanner and I had a few more spats, so if you can't read anything, leave a comment or email/fbook me and I'll translate :D

****4/8/12 UPDATE
Edit to notes from 3/9/12:  nodal is expressed in LPM not "central plate mesoderm."

Edit to last diagram from 4/6/12: the yellow boxes or "sclerotome" split and rejoin, not the blue ovals of the myotome.

Edit to description of trunk NCCs from 3/14/12: trunk NCC migration in the dorsolateral direction is inhibited by both slit and ephrin.  At first glance, ephrin as a repulsor may seem counterintuitive since ephrin is a cell-cell adhesion molecule.  But as it turns out, ephrin to ephrin receptor binding can result in both adhesion and repulsion, depending on relative levels of expression of both molecules (the details of which are beyond of the scope of lecture).

Many thanks to Nadav Nahumi for pointing out these errors.  If anyone else spots some, please notify me.

In preparation for DevBio exam 1 in two days!!! Our professor talks really fast (despite being interesting at the same time) so I provide these transcribed notes in case you are missing something.  And you now have something to follow with the podcasts.  :D

Because I was squabbling with the scanner, I had to scan it in 4 parts.  The first part being the first page.....yeah..  Enjoy!

DevBio Exam 1 teaser (a.k.a. page 1): http://dl.dropbox.com/u/22080433/devbioexam1pg1.pdf
DevBio Exam 1 section 2: http://dl.dropbox.com/u/22080433/devbioexam1section2.pdf
DevBio Exam 1 section 3: http://dl.dropbox.com/u/22080433/devbioexam1section3.pdf
DevBio Exam 1 section 4: http://dl.dropbox.com/u/22080433/devbioexam1section4.pdf

Note: there are a few Q's on the side panels--you can ignore some of those.  I pestered our professor with those, and they are mostly out of scope of the lecture he said.