Meet The Humanized Mouse

Meet the humanized mouse. It’s not the talking mouse of movies but an extension of using mice as a model system to study human disease and function. In these mice strains whole swaths of the mouse genome have been replaced with the corresponding sections of the human genome. In these animals where the swap has been made the human genes effectively replace their mouse counterparts, resulting in a human molecular system that operates within the mouse.
Genes however are not enough. For immune system replacements, genetic changes are augmented with organ grafts. Mice strains exist that essentially have a human immune system operating within them. Such strains open an experimental opportunity that would simple not be available otherwise. With such a strain a researcher can gain insights into how a human system would respond because though they are working with mice, those mice contain a reconstituted human system within. Model organisms standing in as a proxy for human subjects must always be evaluated with the knowledge that human responses may differ. That is till true even with these humanized systems, but we are far closer to a human response than before.
  1. Nat Rev Genet. 2011 Dec 16;13(1):14-20. doi: 10.1038/nrg3116. Genomically humanized mice: technologies and promises. Devoy A, Bunton-Stasyshyn RK, Tybulewicz VL, Smith AJ, Fisher EM. Go To PubMed
  2. Nat Rev Immunol. 2007 Feb;7(2):118-30. Humanized mice in translational biomedical research. Shultz LD, Ishikawa F, Greiner DL. Go To PubMed

Is siRNA Therapy Safe?

Often described as the next frontier in gene therapy, siRNA has moved from the realm of the quirky biological oddity to applied therapy very quickly. I have asked the Tox1401 students to describe what they see as potential toxicological problems with this approach.

We used this paper as a description of the possible delivery approaches. The paper is freely (and fully) available from pubmed central.

Read on through the comments to see what they came up with.

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How Complex Is Life?

As the human genome project’s influence grows, one of the concepts that has emerged is complexity. Scientists including biologists have appreciated for some time that genetic networks drive development and biological responses. The cell’s responses to stimuli require and ever changing cast of proteins. The instructions for the protein sequences are encoded within the genome. If we could understand how this large cast of proteins is assembled into smaller pathways and responses we would be considerably further along. The parts list is long and complex, but as the genome project began to uncover the instructions for how the “parts” are made there was a feeling that science may be able to build models that describe function and disease.

The 2010 Nature article describes this aspiration:

The hope was that by cataloguing all the interactions in the p53 network, or in a cell, or between a group of cells, then plugging them into a computational model, biologists would glean insights about how biological systems behaved

And indeed this did (and still does) seem like a reasonable approach. Biological networks have turned out to be as complex as we could have hoped. Systems biology is still moving forward, but the sheer number of possible rules that govern how all of the cellular parts work together and interact suggest that we will be working with this complexity for some time. There is a universe of rules that describe networks; explaining how proteins, ligands, nucleic acids and more interact and result in function.

Towards the end of the article there is an interesting quote from Bert Vogelstein:

“Humans are really good at being able to take a bit of knowledge and use it to great advantage,”

And we are. With some careful science and good detective skills we can take what we do know and put it to good use, combating disease. The fact that biological systems are complex and that this complexity is not simply going to be understood the first time we draw back the curtain is a great finding.

I am asking the Tox1401 students to look into this complexity a bit further. Let’s start with a pathway database like reactome.org. Choose the phase II pathways and select a single protein within that pathway, perhaps the NAT1 arylamine N-acetyltransferase. Provide a description of the protein, and the pathway that it takes part in.

Proteins With Altered Conformations As Agents Of Disease

Prions have been described for some time in the literature, and certainly are known to the public as Mad Cow Disease. You can read more about prions here.

PDB generated prion image

One of the vexing questions about prions is dose, or more simply is there any threshold amount of material contaminated with prion proteins that might be safe? Prions themselves are very tough and stable proteins. Unlike more other infective material that the public is familiar with, there is no safe way to “cook” meat contaminated with prions that will make it safe for consumption.

With this in mind a research group is looking to see if there is such a threshold dose. Using concepts cribbed from toxicology a lab has looked to see if there is a dose low enough at which prion exposure would not lead to disease. You can read the original paper here, but the take home is that there is no safe dose.

When we were looking through the literature on protein folding diseases, a second paper lept into the light, a recent Tau paper, describing the spread of a misfolded tau protein along the intertwined pathways of neuronal cells. This phenomenon is called “tauopathy”; the progressive spread of misfolded tau protein along specific routes through the brain. This pathology is associated with the development of Alzheimer’s disease. One of the unique findings to this work is the decoding of the spread from one spot to another, involving the jumping of the misfolded protein from neuron to neuron.

Though not yet reproduced this finding holds much promise for future Alzheimer’s disease therapeutics as the protein’s march from cell to cell may provide a weak spot in transmission, allowing us to halt the spread of the misfolded protein, and the progression of the disease.

I am asking the Molecular Toxicogenomics students to  write up a post describing how misfolded proteins can be the agents of disease, so if you are interested in the topic, click on through to the comments to get involved in the discussion.

Watson & Crick In 1953

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watson-and-crick-1953In their 1953 “Molecular Structure Of Nucleic Acids” Watson and Crick open with the decidedly unscientific “We wish to suggest…” and in only a short page or so, take us through their thoughts on what shape DNA takes in the natural world. With a tone, that is though decidedly academic, conversational in the way it winds from chemistry to other laboratories take on what structure DNA might take. The paper is notable for what is not present as well. After a careful description or at least inventory of the facts supporting their structure, they proceed to open up a new avenue of discusion; suggesting how the model might relate to the observed biology. In one of the final paragraphs they lead with “It has not escaped our notice…”. They hint that the structure they have described, suggests that there is a very simple solution to another vexing problem remained unsolved in 1953. How does DNA copy itself, and how does it do so quickly?

Here Watson and Crick speculate that they have solved an important piece of this puzzle, and interestingly do so without directly stating what their speculation is! As is to pass off the impoliteness they assure us that these speculations and more data will follow.

They write as if they are having a conversation with you, an old colleague. When in fact they seem to have carefully crafted their thoughts so the reader can follow the unfolding story as if discovering the structure themselves.

For your first assignment I want  you to compose a paragraph or two, describing your scientific response to the idea that DNA is an anti-parallel double helix. Write for a broader audience, not just scientists. Explain why this discovery is important, not from today’s perspective, but how you imagine a scientist in 1953 might respond.

Teaching Anatomy Though Dynamic Activities

I find that getting out of my seat is sometimes the best way to learn. Even as teachers conspire to keep us looking up to them, sometimes the best learning moments come as we watch them struggle just as we students do.

The Carvalho article describes a set of activities that can be deployed to help students understand cardiac function and anatomy. I have asked those who would be most effected by this activity to post their responses to it in the comments section. Read on if you would like to hear what they have to say. I know I do.

So How Did It Go?

For your final post I would like you to trouble shoot this class. You have all worked very hard learning the ins and outs of a new and growing field. If you stay in the sciences you will surely hear more about this field as you continue your careers. I am proud of how hard you have worked and the commitment that you all have put in. Now you are my experts in the class and I would ask for a few minutes of thought and some feedback.

  1. How was the textbook? Would you choose another? What about “Essential Cell Biology“?
  2. What would you change about the class? Why?
  3. What would you keep? Why?
  4. Did you find the papers useful?
  5. Did you find the peer comments useful?
  6. Did you find the writing center sessions useful?
  7. What topics would you like to hear more about?
  8. What topics would you like to hear less about?

Epigenetics Revisted

Epigenetics, as it’s name implies is a collection of genome wide alterations that would change the information that is coming out of the genome, without changing the sequence. These changes are heritable from cell division to cell division, and in some cases from parent to offspring. This idea sounds a bit odd the first time around. We get used to thinking about mutation as one of the few ways that gene information can be changed in a heritable way, but it turns out there are more. Biology is smart, or at least it has had allot of time to figure out how to get things done.

As a field toxicology is concerned with the way that the environment effects living organisims and one area of interest has always been genotoxic compounds. Epigenetics adds a new dimension to this as epigenetic changes cause alter gene expression and if you look for examples there are plenty of mechanical changes in the genome of cancer cells that part of the epigenetic machinery. Toxicologist are very interested in what xenobiotics would be involved in altering epigenetic patterns.

Finally there is one more twist that is worth mentioning. I like all biologist of my time grew up thinking of the world using Darwin‘s evolutionary paradigm. There was another contemporary of Darwin that many of us have heard about that is often used as a counterpoint to stress how other scientists of the time thought of change that occurred across species. The cartoon that I can still remember to this day is Jean-Baptiste Lamarck‘s giraffe stretching to eat the leaves higher and higher in the tree. Ridiculous! But wait, epigentics proposes a model by which the environment might actually be able to influence the genome of an organism and produce heritable changes in gene expression. This may not be what Lamarck was thinking of, but it does sound eerily similar.

The toxicology paper is a good review of epigenetic mechanisms and it has a few “gee-wiz” biology examples.. There are however many practical examples of how epigenetics works, and diseases that may have an epigenetic component. I have asked the Tox 1401 students to head on over to OMIM and search using the term “epigenetic”, to find some examples. Look through the comments to see what they have come up with.

How Much Radiation Can You Take?

Radiation therapy is becoming more and more common and as with many things that we have discussed here, the person to person variation in response to radiation exposure can be large. So what drives this difference in response to radiation dose. An answer is emerging from a series of studies that were undertaken using cells from xeroderma pigmentosum patients. You can read more about xeroderma pigmentosum here, but briefly these patients suffer from a dysfunction in the molecular system that repairs DNA double strand breaks.

In a 2010 Journal of Medical Genetics paper by Abbaszadeh et al. The authors piece together the role that a specific protein, DNA-dependent protein kinase catalytic subunit (DNA-PKcs) plays double strand break repair induced by ionizing radiation. Ultimately specific alleles of the DNA-PK protein are identified that predispose these individuals to an extreme radiation sensitivity.

The authors leave us with an interesting statement:

“Finally, these data show how seemingly ‘mild’ or undiagnosed defects in DNA repair factors, while consistent with viability, can have catastrophic consequences should such an individual require cytotoxic anticancer RT. Simple pretreatment screening protocols such as measuring the induction of repair of nuclear gamma-H2AX foci in patient cells, to identify individuals at risk, would increase the safety of RT for such patients.”

I am asking the Tox1401 students to look into exactly what “pretreatment screening protocols such as measuring the induction of repair of nuclear gamma-H2AX foci in patient cells” is, so if you would like to know more, head on over to the comments section where they will provide a brief description of the procedure.