- This is the story of two of them: Squiggy and CeCe.
-
-
-
-
-
-
-
On this week's episode:
-
Squiggy's Identity Crisis!
-
In which our heroes take a ride on HuBMAP's ASCT+B Reporter, learn that "partonomy" has nothing to do with the science of partying, and are reminded why it's always important to read notes from your mother.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
TV narrator: In conclusion, the Human
- Reference Atlas is a
- comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body.
-
-
-
-
-
TV narrator: With the HRA, everyone will be able to find the names and
- locations of all their favorite cells!
-
-
-
-
-
-
-
-
-
-
Squiggy: Hey, CeCe?
-
-
-
-
CeCe: What is it, Squiggy?
-
-
-
-
Squiggy: Have you ever
- wondered about the big questions? You know: Who
- am I? Do I belong? What is my purpose?
-
-
-
-
CeCe: Sure, Squig. I think
- everybody does.
-
-
-
-
-
-
-
-
-
Squiggy: But I have so many
- questions, and I don't know any of the
- answers. This identity crisis has me all bent out of shape!
-
-
-
-
CeCe: Whoa, Squiq! Don't burst
- your membrane!
-
-
-
-
-
-
-
-
-
CeCe: If you'd been paying attention, you would know that we can use the
- Human Reference Atlas to figure out what you are and where you belong!
-
-
-
-
CeCe: And I think I know just the perfect place to start!
-
-
-
-
-
-
-
-
Squiggy: Ahh! Who just turned out all the lights?
-
-
-
-
CeCe: Don't worry Squiggy, it's just a scene transition.
-
-
-
-
Squiggy: Oh, well, I am NOT a fan.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
CeCe: This is the Human Reference Atlas's ASCT+B
- Reporter!
-
-
-
-
-
Squiggy: What does it do?
-
-
-
-
CeCe: Well, it can help us solve your identity crisis!
-
-
-
-
CeCe: You see, the ASCT+B Reporter allows researchers
- to explore anatomical
- structures, cell types, and biomarkers that make up different organs.
-
-
-
-
CeCe: The data tables from which the Reporter gets its
- information are
- authored
- and reviewed by experts in their field.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Squiggy: Do you think I
- have biomarkers that would help scientists identify what kind of cell type I am?
-
-
-
-
CeCe: You bet, Squig!
- Scientists have many ways of detecting the presence of characteristic biomarkers.
-
-
-
-
CeCe: Unfortunately, those
- are way too complicated to get into right now, so let me just look at that tag on your back.
-
-
-
-
-
-
-
-
-
-
Squiggy: Tag? What tag?
-
-
-
-
-
-
-
-
-
CeCe: Right here!
-
-
-
-
-
-
-
-
-
Squiggy: Ooooh!
-
-
-
-
-
-
-
-
-
Squiggy: But how will these help me find out what kind of cell I am?
-
-
-
-
CeCe: I'll show you. Ready to go on another journey, Squiggy?
-
-
-
-
-
-
-
-
Squiggy: Oh, CeCe, please... no more! Don't make me ride this crazy thing again. I haven't recovered from the last trip!
-
-
-
-
CeCe: Alright, alright. Don't pop your nucleus. I've got an idea.
-
-
-
-
CeCe: Maybe we could ask these people out here to help.
-
-
-
-
Squiggy: What people?
-
-
-
-
CeCe: Those nice people out there who have been scrolling along and reading our adventure.
-
-
-
-
-
-
-
-
-
CeCe: How about it readers? Want to help out our friend?
-
-
-
-
Squiggy: Oh, please say "yes!"
-
-
-
-
CeCe: Then head over to the Reporter to find out what kind of cell type our friend is.
-
Remember, Squiggy's biomarkers are Keratin 5/6, Keratin 7, p60.
-
Along with being characterized by those biomarkers, Squiggy is a type of cell that can be found hanging out in the large intestine (among other places throughout the body).
-
Choosing only the large intestine ASCT+B table and starting from there will make your job a lot easier!
-
-
-
- Show hint
- If you're stuck, watch this video tutorial.
-
-
-
- Hey I know! Squiggy's cell type is ...
-
-
Sebocyte
-
Epithelial Stem Cell
-
- Squamous
-
-
- Subepithelial membrane
-
-
-
-
-
-
-
-
-
-
-
- External links
-
-
See the ASCT+B tables in all their Excel spreadsheet glory!
-
Want to look at some cool 3D organs? Why, of course you do!
- This is the story of two of them: Squiggy and CeCe.
-
-
-
-
-
-
-
On this week's episode:
-
Something's NOT Registering!
-
In which our heroes explore HuBMAP's Registration User Interface (RUI), rescue
- a stray human tissue sample, and learn that, when it comes to anatomy, "in the ballpark" is not
- an ideal unit of measurement.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
CeCe: Well good morning, Squiggy! You look pretty happy for having just rolled
- out of bed.
-
-
-
-
Squiggy: I'm in a great mood, CeCe! After all, in our last adventure, I discovered my cell type and
- resolved my identity crisis.
-
-
-
-
CeCe: And it looks like you bought yourself a shirt.
-
-
-
-
Squiggy: Oh, wow, CeCe. Thanks for noticing! It's a good thing I wore it
- today because it's getting pretty chilly in here.
-
-
-
-
-
-
-
-
CeCe: Oh, I do
- NOT like seeing that!
-
-
-
-
Squiggy: What is it, CeCe?
-
-
-
-
CeCe: It's a kidney
- tissue sample, Squig, separated from its home organ and all alone.
-
-
-
-
-
-
-
-
Squiggy: Ah, that's no big deal. We can just pick this
- little guy up, and the next kidney we come across, we can just stick him in somewhere!
-
-
-
-
CeCe: No way, Squig!! Don't you know that when you're
- trying to identify a tissue sample, it's all about location, location, location!
-
-
-
-
Squiggy: What do you mean? Just look at that kidney! It
- looks the same all over. Just a big brown blob.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
CeCe: Well, Squig, that "big
- brown blob" contains a great deal of variation.
-
-
-
-
CeCe: Right kidneys are
- different from left kidneys, men's kidneys are different from women's kidneys, and don't get me started
- on how kidneys can vary in shape, size, and location from person to person.
-
-
-
-
CeCe: And don't forget that
- each kidney contains a number of distinct anatomical structures. These smaller structures have different
- roles to play and are made up of different kinds of tissues and cell types.
-
-
-
-
-
CeCe: However, two distinct
- anatomical structures may be only millimeters apart.
-
-
-
-
-
-
-
-
-
Squiggy: So, wait a minute. Are you saying that just guessing where our
- tissue goes may not be a great idea?
-
-
-
-
CeCe: Well, Squig, let's just say that guesstimating is not exactly what researchers
- call "best practice."
-
-
-
-
Squiggy: Well, that sounds impossible. I'm going back to bed.
-
-
-
-
CeCe: It's not hard at all, Squiggy. In fact, there's a tool to make it really easy!
-
-
-
-
-
-
-
-
-
-
-
CeCe: Researchers can register their tissue sample
- data with the Registration User Interface tool in the Human Reference Atlas.
-
-
-
-
CeCe: It takes only about 5 minutes to learn how to
- do it and an average of 2 minutes to register a tissue block.
-
-
-
-
CeCe: All we need to do is select the correct organ.
-
-
-
-
CeCe: Now, let's position this kidney just how we
- want it by using these buttons up here.
-
-
-
-
CeCe: Or we can rotate it with a mouse or keypad.
-
-
-
-
CeCe: Now, we can type in the height, width, and
- depth of our tissue block.
-
-
-
-
Squiggy: What's that?
-
-
-
-
CeCe: That's how our tissue block appears in the 3D
- world of the Registration User Interface!
-
-
-
-
CeCe: Now we can use these sliders here to rotate
- the 3D block and move it into the correct place in the kidney.
-
-
-
-
-
-
-
-
-
-
-
-
CeCe: Now this is the fun part. I'm going to need
- your help, Squiggy!
-
-
-
-
CeCe: We just need to move this tissue block so that
- it's in the same place on this model as it was on the actual organ.
-
-
-
-
-
-
-
-
-
Squiggy: Look at us, CeCe, we're registering tissue!
-
-
-
-
CeCe: Now this is kind of cool. Watch as we move into the space of the 3D model, we'll
- see an example of what's known as "collision detection."
-
-
-
-
Squiggy: Collision!! Ahhh!!! CeCe, I knew your crazy adventures would be
- the end of me! Oh, goodbye cruel world!
-
-
-
-
Squiggy: Oh. Well, that was not very dramatic.
-
-
-
-
CeCe: Nope, Squiggy. You supplied ALL the drama we needed.
-
-
-
-
CeCe: You see, what our block is "colliding" with are anatomical structures. The RUI is
- just letting us know what our tissue sample is bumping up against as we move it through the organ. This
- helps for both placement and identification.
-
-
-
-
-
-
-
-
-
-
Squiggy: Well, I see what's been registered already, but it
- looks like more information is needed.
-
-
-
-
CeCe: That's right, Squig. The Human Reference Atlas
- is always looking for more data.
-
-
-
-
CeCe: The more tissue that's registered, and the
- more other researchers can benefit from your correctly identified data, the more complete our picture of
- the human body becomes.
-
-
-
-
CeCe: And that's a very good thing for understanding
- our body in health and disease!
-
-
-
-
-
-
-
-
-
CeCe: So click on this link to the Registration User
- Interface and register your tissue data today!
-
-
-
-
Squiggy: And don't forget to spay and neuter your pets!
-
-
-
-
CeCe: Wrong public service announcement, Squiggy.
-
-
-
-
Squiggy: But it's still a good idea.
-
-
-
-
CeCe: Yeah, I suppose.
-
-
-
-
-
-
-
-
-
- External links
-
-
If you prefer your demos conducted by a real human being, not a couple of animated cells, check
- out this video on the Registration
- User Interface.
-
Avoid the embarrassment of using the RUI with your procedures all unstandardized. These RUI standard operating
- procedures will help you do things the right way!
-
-
HuBMAP lets us visualize healthy cells in the human body in ways the naked eye can't do on its
+ own. With a
+ mountain of data available to us, we can better understand the different roles these cells play in
+ keeping
+ everything running smoothly.
+
+
Using data expertise we can break down each organ into anatomical structures, functional tissue units
+ (FTU),
+ and cell types. The purpose of the three classes is to locate where in the body the cells are by
+ identifying
+ the organ, its smallest tissue unit that performs a unique physiologic function multiple times, and the
+ cell
+ types within that unit. From these perspectives, we can freely view the healthy human at multiple
+ scales.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
While some parts of the human body can be easily recognized, like the kidneys in the graphic above, many
+ of us have no idea what the tissues and cells that make up a kidney look like.
+
The human reference atlas currently
+ allows us to examine in some detail some of these cells. For instance: the renal corpuscle in the
+ kidney.
+
+
+
+
+
+
The Renal Corpuscle
+
+
In simple terms, the renal corpuscle is located in the kidney and works to filter out toxins through
+ urine
+ and reabsorb necessary nutrients back into your body.
+
+
+
+
Within this FTU, there are several cell types
+ that
+ depend on each other for it to function. The renal corpuscle is made up of even smaller parts like
+ podocytes. Which, in turn, contain NPHS1 genes.
+
+
+
+
+
+
+
+
+
+
The Large Intestine
+
As it did for the renal corpuscle, HuBMAP also gives us the ability to map the crypt Lieberkuhn Glad in the
+ large intestine in detail. There are several cell types that work together to allow this FTU to renew the
+ lining of the intestine and produce mucus.
+
+
+
+
+
+
+
What you've just seen is a glimpse into the possibilities HuBMAP can create. Imagine how our
+ understanding of human cells would accelerate if we did this for the entire body. From the crazy scales
+ it can go to, to the in-depth analysis of each cell, the human reference atlas can heavily influence the
+ advancement of human health and prospective research while serving as a convenient reference tool.
+
On that note, we invite you to check out Andreas Bueckle's VR Organ Gallery that will soon be available
+ on the app store. The program is designed to be user-friendly in order to observe cells in 3D.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/index.html b/index.html
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@@ -47,10 +47,10 @@
3. Learn about the Number of Cells in the Human Body
-->