Category Archives: DNA
Neil deGrasse Tyson presents this short PBS NOVA overview of how epigenetics determines the differences between gene expressions in identical twins, how epigenetic variations build up over time and how it affects us. A relatively new, but very interesting field of medicine and genetics, this is a good introduction.
Epigenetics is not directly mentioned in our syllabus, but does help us to connect the ideas of nature vs nurture, genetic variation and inheritance. To what extent does the nurture of our cellular environment (lifestyle) affect the genetic nature of who we are?
For some more really good resources on epigenetics, visit the brilliant Learn.Genetics site from Utah.
Thanks to Ed Yong for posting this on his weekly links roundup.
This is the predictable and perennial question that comes up from at least one student when we are looking at stem cells, genetic engineering, cell differentiation and transplanting. Until now, the answer has (perhaps in an oversimplified way) been ‘no’.
We can use stem cell transplants to treat lymphoma. Recently a young woman had a trachea transplant based on stem cell technology. Skin grafts from a patient’s own cultured cells are also possible, as are stem cell-based bladders. However, these are all rather simple technologies.
To treat lymphoma, bone marrow cells are replaced, and are all the same. The trachea transplant was a pre-existing trachea simply coated in the patient’s stem cells to prevent immune rejection. Skin transplants are basically sheets of epidermis that cover a wound, yet do not have the intricate functions of original skin: temperature regulation, secretion, senses. The bladder is a bag.
The challenge with using stem cells to transplant a more complex organ, such as a heart, is that it is not a simple sheet made of one type of cell. It is complex 3D structure, with a range of cells performing specific tasks within the organ. These cells have differentiated to perform their functions: cardiomyocytes (beating cells), vascular endothelial cells (smooth internal surfaces) and smooth muscle cells (blood vessel walls).
How can we get the stem cells to become the right type of cell, in the right position?
The answer to this question could be the key to opening up new doors in the search for viable transplantable organs in medicine, and bears much in common with the trachea case. It also marks a return to form for the NewScientist YouTube channel, who have this short clip of the new hearts in action:
A full article to accompany the footage is here.
In a nutshell:
1. Find a suitable transplant organ, such as a pig’s heart.
2. Strip of all cells and DNA, using a detergent. Only the collagen ‘scaffold’ remains, as in the image of the decellularised heart to the right.
3. Coat the scaffold with the recipient’s stem cells.
4. Ensure that the blood supply is adequate and will provide the right signals for differentiation.
What is amazing in this case is how the cells ‘knew’ what specialised cells to become. The leader of the research group, Dr. Doris Taylor, puts it down to the mechanical stimulus of the pressure of the blood in the vessels and chambers and chemical signals from growth factors and peptides that remained on the stripped heart structure.
They even went as far as replacing a healthy rat’s heart with one of these new hybrid hearts. The rat survived for the trial, but she says they need to focus on producing more muscular hearts in order to ensure long-term survival of transplant recipients.
Food for thought:
Read the whole article and some of the links within it. Discuss these questions:
1. What are the potential uses for this kind of transplant technology?
2. What are the current limitations of this method and how might they be overcome?
3. What are the ethical issues related to using hybrid (pig-human) organs in medical transplants? How would you feel if you were the patient?
4. Who are the various stakeholders in this technology and what are their viewpoints?
Dr Doris Taylor’s research page from the University of Minnesota
NewScientist Article: Hybrid hearts could solve transplant problem
BioAlive stem cells links and resources
Can stem cells repair a damaged heart? from the NIH
Research reveals how stem cells build a heart, from Harvard news.
The Molecular Logic Project aims “to improve the ability of all students to understand fundamental biological phenomena in terms of the interactions of atoms and molecules”. They achieve this with an extensive database of online java-based simluations and models for students to use. The animations are simple, and there are a lot of activities to choose from. To make it work, you’ll need to install their software.
Some highlights for IB Bio:
This is a re-post for the class of 2009 to revise and the 2010 group to catch on the first time… As always, click on the shadowed images for a link to an animation, or visit the links posted below.
Core (for everyone):
Additional Higher Level:
There are many decent Flash animations and the like on the internet, but the majority cannot be embedded. Below this YouTube video, there are some direct links to resources, some of which can be easily saved.
Learn.Genetics @ Utah
Transcribe and Translate (good, basic, interactive)
How do fireflies glow? (puts it in context)
University of Nebraska:
Protein Synthesis overview (Good enough for SL)
Transcription Details (fits DP Bio HL very well)
Translation Details (fits DP Bio HL very well)
John Kyrk: (visit the parent site at www.johnkyrk.com – excellent)
Transcription (fits DP Bio HL very well)
Translation (fits DP Bio HL very well)
St. Olaf College
Transcription (clear and simple)
Translation (clear and simple)
EDIT: Two more animations (from mrhardy’s wikispace, original source unknown)
RNA Splicing tutorial (HL only)
Translation with a genetic code dictionary (shows position in the ribosome)
Some more in-depth animations (newly added):
Translation from Wiley Interscience
Translation from LSU Medschool
Translation from The Chinese University in Hong Kong
Protein targeting from Rockefeller University
This topic is well-resourced on the internet – almost too well! Standard level students need to know the bare basics, which equates to the process of replication of the leading strand for the HL students. Here is the presentation, with some good links to follow:
DNA Replication animations:
St. Olaf’s nice and clear animation.
Another clear one from Wiley.
Nicely illustrated one from Harvard.
John Kyrk’s complicated molecular animation.
The Meselsohn Stahl experiment from Sumanas.
Here is the top-rated video on the subject on YouTube: