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Physics being physics

Dynamics of self assembly

This is absolutely the first time I have ever felt the need to embed someone else's video in my blog. I run a demo early in the year showing how simple rules and movement can lead to spontaneous assembly of complex structure. My demos with magnets are good and Art Olson's "shaker virus" demo is great. But, this is absolutely AWESOME.

Immune Review

Some guidelines for the immune quiz

Barriers such as skin and mucus, tears etc. form initial barrier

Innate Immunity:

Cell and biochemical defenses against pathogens. These have four main roles:
  1. First responders attack intruders (some specific for particular types of pathogens using recognition receptors).
  2. Cells release pro-inflammatory signal molecules that attract other immune cells to the area (both more innate immunity cells and adaptive cells)
  3. Present antigens for adaptive immunity to surveil
  4. Following adaptation of B-cells and antibody production, some components of innate immunity are targeted more specifically to pathogen by the antibodies

Cells (really just some of them) The figure shows how red blood cell and thrombocytes (for blood-clot formation) derive from the same progenitor cells as the immune system. You don't have to memorize the details. Know B cells T cells (both types) and Macrophages (antigen presenting cells) like in the game.
Macrophage (big mouth). Know this one. Gobble pathogens up, present antigens to adaptive cells in the MHC receptor and release pro-inflammatory signal molecules (other antigen presenting cells include dendritic cells).
Weird-shaped nucleus cells (OK, that's not the official name. They are called "polymorphonuclear cells," which essentially means the same thing). They, along with mast cells, are the main source of the pro-inflammatory signals. They all have slightly different jobs and include the basophil (likes basic stain); neutrophil (neutral pH stain) and Eosinophil (likes acid stain). You wouldn't need to know what each of these do. But, you could get a figure that has them in it.

Mast Cells are probably the worst offender, along with basophils and eosinophils. Probably good to know Mast cells. They are the underlying inducers of allergies and anaphylaxis. Secrete lots of pro-inflammatory signals. Extra information: Eosinophils in particular collect special antibodies made by certain B cells called IgE, which they then use to attack all the multicellular parasites you have, like worms and such. If you don't have worms, they are fond of attacking pollen grains, etc.

Natural-killer (NK) cells. You should know these. Come from the same line as the cells of the adaptive immune system. Activated by macrophage signals, identify infected cells in the body and kill them

Adaptive Immunity

You should know all of this unless noted.
T-cells (thymus) and B-cells (bone-marrow).
B cells are the ones that make antibodies (also known as B-cell receptor prior to class switching).
Both T and B cells undergo "somatic rearrangement" of their DNA to express one and only one T-cell receptor or B-cell receptor. The enzymes that carry out the splicing of the DNA are called "Rag-1" and "Rag-2." (Recombination Activation Gene 1 and 2). This is known as "V(D)J recombination and it generates a different antibody
for each B cell line you have. A very similar thing happens in the T-cells. During maturation of B cells, one V (variable) region, one D region (diversity) and one J region (junctional) are brought together and linked to the Constant region to make the heavy chain of the antibody. The light leaves out the "D" and the C region.
The "antigen-combining site" is at the amino (NH2) terminus of each chain. This is what allows the antibody to bind the antigen.

Cytotoxic T-cells (also called "CD8-positive T cells") identify infected cells and other targets based on specific recognition by their T-cell receptor and secrete chemicals to kill them. They make their receptor through a similar process as the B cell (somatic recombination).

Helper T Cells
These are critical for the full response (and also the target of HIV. They have a T-cell receptor as does the killer. But, they look for B cells that have been stimulated by the same antigen. If they find one, they initiate the highly active response in the B cell in which the receptor evolves into an even more specific antibody. Eventually, the highly activated B cells undergo "class switching," which just means they initiate an alternative RNA splice that gets rid of the membrane-bound creation of the antibody and start secreting it as part of the soluble or "Humoral" response.

The main use of the antibody is then to target components of the innate immunity more specifically toward the pathogen.

I think that's the important stuff. Remember, I sugar wcan show you figures of things I haven't discussed, necessarily. Also, go over the terminology on the online quiz.


Immunology intro

First: there are reviews for AP Biology that go on after school in the SCPH. The review schedule is here:
link to the review schedule
This won't teach you anything, but may help you identify what you need to cover.

Next: this is from chapter 43. You can do the reading there if you find that helpful. Here is a primer on the cells of the immune system that I recommend to get a good overview. Work though the cells of the immune system. When we get together next, we will spend some time playing a couple of games. You don't have to work on that now.

We will start with this
game. and also play this one: here.

Here is a nice overview slide of the adaptive response:
Adaptive Overview



The question of how we go from a single, fertilized egg to a complex organism is one of the most vexing open questions in Biology. Having said that, a lot has been learned in the last 30 years and some general rules and principles can be laid out.
Early events:
When the egg is first formed, it already has polarity to it. That is to say, one side of the egg is not like the other. This is especially obvious in the fruit-fly, which has an oblong egg. Those horns at the end are breathing tubes.
Fly EggFigure 1
When the egg is made, it is filled with mRNA provided from the mother (maternal mRNA). That mRNA is not evenly distributed throughout the egg. An important example can be seen from this A.P. question.
The first diagram below shows the levels of mRNA from two different genes (biocoid and caudal) at different position along the anterior-posterior axis of a Drosophila egg immediately before fertilization.
BicoidFigure 2

The second diagram shows the levels of the two corresponding proteins translated from the mRNAs along the anterior-posterior axis shortly after fertilization.
Based on the diagrams, which of the following conclusions is best supported by the data?
  1. Bicoid protein inhibits translation of caudal mRNA.
  2. Bicoid protein stabilizes caudal mRNA.
  3. Translation of bicoid mRNA produces caudal protein.
  4. Caudal protein stimulated development of anterior structures.
As we discussed, the egg had mRNA from “caudal” throughout the single, large cell, but from “bicoid” only in the anterior end. As soon as protein translation begins in the fertilized egg, Bicoid protein diffuses away and inhibits the synthesis of Caudal protein. It These maternal RNAs, along with some more, set up the basic anterior-posterior axis. Here is an image I stole that has an additional protein, eve, in the mix. The fluorescent image uses tags for the three proteins so that we can see them in the living embryo (GFP…it’s not just for cats!).
Obviously, this is after many rounds of nuclear division. Based on the image, it appears to be before the cell membranes have formed. This is a
syncytium, lots of nuclei in one huge cell. If you want to learn more about how these maternal effect genes set up the initial polarity, check out the images here.
FlyEmbryoFigure 3
And here is a representation of how two additional genes, Hunchback (yes, that’s it’s name) and Nanos interact. Just as Bicoid blocks Caudal, Nanos blocks Hunchback. Overall, you get a pattern of gene expression you can actually see as stripes on the embryo.
AdditionalGenesFigure 4

Mid-Blastula Transition (MBT)

After formation of the blastula, or “ball of cells,” a critical change happens called the “mid-blastula transition.” At that point, cells have formed and transcription and translation of embryonic genes begins. These gene expression patterns are regulated by where in the anterior/posterior and dorsal/ventral axis the cell finds itself.
These embryonic genes then specify further what cells are going to do in the particular area.
Here is a
link to another site that shows how some of these genes set up.


The next big event is Gastrulation, which involves migration of the cells into three “germ” layers, known as the endoderm, ectoderm and mesoderm. This is stimulated by a morphogen made by specific cells. In humans, it’s called bone-morphogenetic-protein 4 (BMP-4), which is one of the Transforming-Growth-factor superfamily proteins (TGF was just the first one characterized, so the family of related proteins are named for it).
These three germ layers form the basis for all the bilaterian forms, from the simplest worms to us. The regulation of their formation is the same throughout the animal world. They will give rise to structures that correspond to location (ectoderm the more outer structure, endoderm the inner ones and mesoderm the middle ones).
Ectoderm gives rise to skin (in humans), of course, but also brain and other structures. Mesoderm gives rise to most of the muscles, as well as the cells that make blood. The muscles in humans include the “smooth muscle” that contracts in the gut, as well as the skeletal muscle and cardiac muscle. The endoderm gives rise to a lot of the abdominal organs, the epithelium of the gut and epithelial cells that do gas-exchange (alveolar cells) in the lung. That makes sense based on what Connor is learning about lung evolution.
GastrulationHumanFigure 5

I lifted a picture from
this website, which is a pretty good page. Thanks “scienceblogs.com.”

From this basic body plan, imagine superimposing additional rounds of positional information with similar themes. Morphogens in local area diffuse, interact with receptors and stimulate pathways that include new tissue-specific gene transcription and further development.
How would that look at the genetic and cell biological level?
Well, for one thing, you would see not a novel overall developmental plan (as in, for the human, we do a specific human development), but rather layers of developmental plans. These would require new genetic switches, of course. Gene duplications obviously have occurred, as we see by whole families of genes encoding similar proteins that perform analogous functions in each successive pathway.
As I said, I know only a fraction of what is known and all researchers combined don’t know it all. But, the basic scheme seems reasonable.

How do patterns develop?

In the late 1940’s and early 1950’s, Alan Turing, the computer wiz who broke the Nazi Enigma code, started giving his attention to the problem of how you generate patterns in a developing organism. He came up with detailed mathematical models to explain patterns as overlapping gradients of “morphogens.” He had no idea what these were. We now know that they are gradients of proteins that are signal molecules that then regulate transcription factors, turning on developmental programs. I’ll write more on that later. His original models looked something like this:
Fig. 6
According to his models, a single morphogen diffusing from one spot could set up a gradient that could lead to a pattern of stripes along one axis. Compare the 1-D horizontal pattern above with Fig. 3 above. In reality, Caudal has an interactive relationship (see Fig. 4) with other transcription factors and sets up more complex patterns. How well his mathematical models have held up since the patterns he predicted started being detected in the 1960s and more dramatically in the 1980s.
I’ve often mused how much more we would have learned about morphogenesis early on if Alan Turing had stayed around. Sadly, he was convicted of the “crime” of being homosexual in 1952, was forced to submit to “chemical castration” and a year later killed himself (though some think his death may have been from accidental exposure to cyanide).

More Complex Patterns

The following figure shows how maternal-effect patterns induce changes in early gene expression, which results in more complicated patterns in the early embryo.
ComplexStripes Fig. 7
Some of the interactions are mapped out. However, I cannot tell you exactly how the whole thing works. These are a few of the genes and how they are thought to interact with each other’s function. I just include this to give you the idea.
ComplexRegulationFig. 8

How do they work and why should you care?

As mentioned above, most of these are transcription factors. There are also diffusing signal molecules (growth-factors and similar). They regulate entire developmental programs. In flies, the ones that regulate early embryogenesis control genes that identify what each segment is supposed to be. The latter ones were called “Homeotic genes.” They are the mutants that result in things like legs growing where antenna should be, or an extra set of wings.
It turned out that they all had very similar sequences, encoding very similar proteins. In particular, one section of each gene was very similar. It became known as the “homeobox.” This encodes a short sequence of amino acids that forms three alpha helices separated by unstructured turns (called a “helix-turn-helix” structure). This is the DNA binding domain. The Homeoboxes of each gene differed in the sequence of amino acids that bound the specific sequence, but were otherwise similar.
Fig. 9
This is the antennapedia gene product bound to the DNA it turns “on.”

As for “why do you care?” It turns out that development in you works just about the same as development in flies. The Homeobox genes are found in you, where we call them HOX genes. The Hox genes come in a cluster of genes on one chromosome. There probably was one primordial HOX gene, perhaps controlling the anterior/posterior axis in a simple organism. Over time, this region of the chromosome has undergone many duplications, resulting in many copies of similar genes, each of which is responsible for particular steps in development. The more complex the organism, the more copies of the genes it has and the more developmental stages it goes through. Below is a color-coded alignment of the genes in flies and in humans. We show the same sort of section-specific expression of these regulatory genes. The identity of the genes is known and their arrangement on the chromosome is preserved from the original ancestral copy and is the same in flies and humans.
The pattern of expression from anterior to posterior is also conserved.
PatternExpression2Figure 10

How similar is regulation of developmental genes in humans and flies? I've mentioned before a gene in flies known as "eyeless." It encodes a transcription factor, now known as Pax6, which is required to stimulate the development of the fly eye. Below is a figure showing how eye development is affected in various organisms with one or more mutant (non-functional) copy of Pax6

We know how to link genes up to specific promoters and put them into Flies. What would happen if you, for example, made the gene for Pax6 turn on in the leg of a fly? As you might expect, the fly develops eyes on its legs.
The figure below is even more striking, however, because the gene expressed in the leg of the fly is the human version of Pax6. That is, the human transcription factor turns on development of the fly eye. Cool, isn't it.

More Karyotype etc

Here is a link to a site at Stanford that helps you understand pedigree. If the link downloads a file instead of opening a page, you have to do the following: right-click or control-click the link and select "copy link." Then paste it into an address line and change the ending from "swf" to "html." Then it should work.
There is a short quiz you can take. I won’t see the results.
and here is the Karyotype activity
Below is a blog I wrote on the topics. You can use it as a reference if it helps.


(as usual, images from wikipedia).
Karyotyping is a technique for looking at all the chromosomes in a cell. Briefly, a pro-metaphase cell is is stained with a dye that binds chromosomes. There the traditional dye, giemsa, stains the chromosomes in a banding pattern that is different for each one. So, the banding pattern of chromosome 1 is different from that of chromosome 2, etc. These days, there are specific color-coded probes that make it easier. The cell is then photographed and the picture is enlarged. Then, traditionally by literally cutting up the picture, but now digitally, the chromosomes are cut out and aligned so that we can see that the individual has 2 copies (one from mom and one from dad) of each of the 22
autosomes. The largest is chromosome 1 and the smallest is chromosome 22.
Then look at the last pair: The really tiny one, smaller even than chromosome 22, is the “Y” chromosome (so this is a male). The larger one next to it is the X.
Look how much cooler it is with the modern technique:

As you can see, this individual is a female.
Using techniques such as this, we can look for large changes to the DNA, rearrangements of the chromosomes we call “inversions,” “deletions” (both self explanatory), translocations (where a piece of one chromosome is spliced to another), extra or missing copies of one chromosome (“trisomy” or “monosomy”) or, even whole extra sets of chromosomes.
Some common disease states result from this. Trisomy 21 causes Downs syndrome.
This can occur when the sister chromosomes of 21 do not separate at meiosis I (this is called “nondisjunction”). That results in a 2 gametes getting no chromosome 21 and 2 others getting 2 copies of it. If one of that latter group fuses with a normal gamete, the resulting zygote has 3 copies.
Check out this karyotype:
Do you see what’s wrong? This person has Kleinfelter’s syndrome, where he has 2 X chromosome and a Y.

Pedigree Analysis:

Here is the pedigree example given in the Campbell Book.
Females are circles, males are squares. People with the trait being followed usually are filled in with a color, people without the trait are not. This trait, the appearance of the “widow’s peak,” is a dominant allele on one of the Autosomes (not sex linked). How can I tell? Remember that the recessive allele can be covered up by a dominant allele. So, two people with the trait, if it is dominant, can produce a child without it. Notice that this happens in the mating in the second generation. Two “widow’s peak” people had a non widow’s peak child. You never see enough children to invoke statistical predictions in a generation. You should see only ¼ homozygous recessive in the 3rd generation…but there are only two kids. Even if there were 4, the numbers are not good enough to make predictions.
I know it is not on the X because an affected mother in generation 1 married an unaffected man and had an affected daughter. That would be impossible for a recessive allele on the X (the daughter would have to have 2 copies, one from each parent. But Dad cannot have it since he does not show the trait). I know it is not on the Y because it appears in women.

Here is the pedigree for hemophilia (a severe bleeding disease) in the royal families of Europe. The mutation seems to have occurred in Queen Victoria.
  1. Is this trait sex-linked?
  2. How do you know?
  3. How do we know that Irene (number “3”) is a carrier?
  4. Is it possible that Queen Elizabeth is a carrier?
  5. Could the disease show up in any of the children Prince William and Kate Middleton might have?