Category Archives: DNA
How Epigenetics Works
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.
It’s Movember! Grow a mo and raise awareness of cancer.
Serendipitously timed, Grade 11 are looking at cell division as some of the male teachers are growing their mo’s for Movember:
“Men sporting Movember moustaches, known as Mo Bros, become walking, talking billboards for the 30 days of November* and through their actions and words raise awareness by prompting private and public conversation around the often ignored issue of men’s health.”
From the MoVember website.
*Actually, we’re doing Nov 10th – Dec 10th, due to the holiday and being a bit slow on the uptake.
So what’s it got to do with Biology?
Well, tumours – such as prostate and testicular cancer in men; breast, uterine, cervical and ovarian cancer in women; and cancer of everything else in everyone else – are simply the result of uncontrolled cell division. Through apoptosis (programmed cell death) or damage (necrosis), cells are destroyed. These need to be replaced with other cells. As our cells are eukaryotic, they need to go through mitosis to ensure that complete copies of all the chromosomes make it into both daughter cells.
As with other cell processes, this is controlled by genes and, importantly, terminated when the cells have grown appropriately. If there is a mutation or problem with a tumour-suppressor gene, such as TP53, the process of cell division is not stopped and the cells grow out of control. This is a tumour. Alternatively, mutations can affect other genes (oncogenes), which encourage further growth.
Click here for a good 11-minute documentary on cancer development, from CancerQuest.
Tumours can start out benign – growths of cells that are not harmful. If these cells become malignant and invade other cells and damage tissues, this is known as cancer. Damage to other cells and tissues leads to illness and can be fatal if not treated early. As tumours grow, they can recruit blood vessels – called angiogenesis. Now you run the risk of metastasis – cells from the tumour breaking off, flowing through the blood and starting a new aggressive tumour in a different part of the body.
Environmental factors can encourage mutations in key cell-cycle-controlling genes. We all know, for example, that smoking can cause lung cancer, UV radiation can lead to skin cancer and the HPV virus can cause cervical cancer.
So why all the fuss about Movember?
Simply, men’s cancers receive less media attention and men tend to be less willing to talk openly about their health problems (unless, of course, they’re trying to get sympathy with a case of man-flu). As guys tend to put off going to the doctor and generally live a lifestyle that is higher-risk for cancer (high fat, high meat, alcohol, smoking, lack of exercise…), tumours can go unnoticed. Men are less likely to survive a cancer diagnosis than their more health-conscious lady friends.
Through cultivating the moustache, we can start conversations about these issues, raise money for education, prevention, research and treatment and promote anti-cancer behaviours:
- Healthy lifestyle choices and awareness of risk
- Self-checking and regular screening for at-risk groups
- Early diagnosis of and treatment for tumours, should they arise (animation)
So get mo-tivated and join the mo-alition of the willing. Take a mo-ment to think about cell division. And mo-an at the men in your life to make healthy choices. Ladies too can get involved – by becoming Mo-Sistas and also raising awareness. The BIS Team are called the BIS Upper Lips!
In the video above, he talks about how genome mapping can lead to giving an indicator of risk to men. Great technology, based on the Human Genome Project (link to 4.4 Genetic Engineering and Biotechnology).
For the class resources on 2.5 Cell Division, click here. Interestingly, and obviously, hair growth itself is a product of cell division. Something to think about as you grow the mo, yo.
Evolution (Core)
Ecuador Hummingbirds
Start with this reading on Evolution and Darwin: https://www.box.net/shared/6dx95t6ma6 and then watch this video of evolutionary researchers in action in Ecuador.
In the clip below, is Ross using the correct language when he describes the theory and evidence for evolution?
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Here is the class presentation
And the Essential Biology notes can be found here: https://www.box.net/shared/550sxdbx82
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There are many sources of interactives and animations on Evolution on the internet. Here are a few:
PBS Evolution has lots of high-quality activities and videos
BiologyInMotion has a very clear population evolution interactive
The Exploring Evolution weblab has examples of homologous structures and fossil evidence
MMHE has a pesticide resistance tutorial
And there are some good peppered moth simulations here and here
As always, sumanas has a great resource – this time on antibiotic resistance
And John Kyrk has a truly awesome timeline of the evolution of life
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Darwin resources:
Attenborough on Darwin: The Tree Of Life
Dawkins Darwin Lectures from OU/BBC
And of course, all of Darwin’s works are available online from darwin-online.org
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And here’s Dawkins on the evolution of the eye:
Hybrid Hearts: Stem Cell Transplants 2.0
“Can we use stem cells to make a new heart/eye/lung/liver etc?”
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:
Decellularised pig heart: the scaffold (NewScientist)
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?
Useful Sources:
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.
MOLO: The Molecular Logic Project
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.
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Some highlights for IB Bio:
How do mutations affect protein folding?
How does gene mutation affect protein folding?
And loads more here: Biology, Molecular Biology (Chem of life), Physics/Chemistry.
Protein Synthesis: Transcription and Translation (2009)
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.
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Core (for everyone):
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Additional Higher Level:
Click4Biology page: Transcription – Translation
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Further resources:
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)
WH Freeman
RNA Splicing tutorial (HL only)
Bio3400
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
DNA Replication (Core and AHL)
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:
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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.
More animations from North Harris College and from LearnersTV.
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Revision materials:
Click4Biology pages: Core & HL
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Here is the top-rated video on the subject on YouTube:
Parthenogenesis – Virgin Births in Nature
Happy (belated) Christmas!
How do you really reproduce without sexual reproduction? Asexual reproduction, of course. Simple, really… but not for the females of some species.
There are loads of links in this post, so click on them to learn more.
Parthenogenesis
Some plants, insects, shark and lizard species are known to reproduce by parthenogenesis – embryo development is carried out without fertilisation by a male -so called ‘virgin creations.’
Parthenogenesis can take a range of pathways :
- The egg can be fertilised by a polar body (a ‘leftover’ of egg production), making the chromosome number diploid and triggering embryo development. Here is a simple explanatory animation from amateurmicrography.net.
- Chromosomes in the egg can self-replicate, making up the diploid number and the embryo develops from there.
Other methods include suppression of male genotypes (technically still sexual reproduction?), or eggs cells dividing by meiosis.
The resulting offspring are going to be all the same gender. In some species, the XY system determines gender and parthenogenesis produces all females. In other, the ZW system dictates that they will all be male.
Parthenogenesis is a reproductive strategy that sacrifices the genetic variation (a driving force of evolution) of sexual reproduction for the simple ability to reproduce. Small invertebrates, such as aphids, can use it to produce large numbers of females very quickly.
Komodo Dragons
Larger organisms, such as Komodo dragons (Indonesia link!), have been known to use parthenogenesis in the absence of males, producing an all-male clutch of eggs. It is thought that this might allow them to set up new populations on isolated islands, using just a single female. Here’s a quick video of a Komodo dragon parthenogen hatching:
Some interesting Komodo readers here from Richard Dawkins and Not Exactly Rocket Science.
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Parthenogenesis in sharks
Parthenogenesis has also been observed in captive sharks – the female had no access to males, yet gave birth to live young (though only one, where the normal litter would be larger). Genetic tests confirmed parthenogenesis, rather than the alternative hypothesis of superfecundation (storing sperm for a long period of time). Read the full paper here, and another on hammerheads here. BBC audio explanation here.
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So can it work in us?
Let’s let House MD explain:
In short, no. Not naturally.
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Generally, we use mitosis to replace and repair damaged cells and tissues and for growth and development – filling in the gaps with copied cells. Along the way, our cells differentiate to their function and we end up with a body full of specialised cells – each cell’s structure and biochemistry reflect its function.
We don’t use mitosis for reproduction, as it narrows genetic variation – one of the driving forces of evolution. Instead, when sperm and eggs are produced, meiosis is used – producing daughter cells with half a set of chromosomes. During meiosis, crossing over occurs, giving some recombinants – or ‘mixed up’ chromosomes – leading to some varation. The greatest variation comes from the process of sexual reproduction itself – the gametes – sperm and egg – meet in fertilisation, combining their chromosomes to make a new blastocyst, which becomes an embryo, then a fetus and out pops a baby.
All the offspring of organisms that reproduce sexually carry two copies of each chromosome – one from each parent – and each chromosome carries different alleles – ‘versions’ of each gene. This leads to a great deal of variation and this genetic diversity keeps the the population going.
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What about uses in technology?
Funny you should ask that…
Induced parthenogenesis is being pursued as a method for obtaining embryonic stem cells. Read this New Scientist article to learn more.
The disgraced Korean scientist Hwang Woo-Suk, who shot to infamy after faking stem cell results, was actually and inadvertently pivotal in the use of parthenogenesis as a method to produce human embryonic stem cell lines:
Normally these parthenogenic embryos die after a few days, yet researchers are able to harvest them for stem cells for research. Ethically, these are considered engineered eggs, rather than human embryos. How do you feel about that?
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Questions to think about:
1. How does parthenogenesis differ from binary fission in bacteria, or vegetative reproduction in some plants?
2. How do the XY and ZW gender systems work?
3. How does sexual reproduction lead to genetic variation?
4. What are the costs of parthenogenesis in terms of evolution or resistance to disease?
5. How would the genetic fingerprint of a parthenogen differ from its parent?
6. How would researchers use genetic fingerprinting to determine whether the offspring were parthenogens or were the product of sexual reproduction?
7. What are the ethical considerations of using parthenogenic human ambryonic stem cells?
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References:
Chapman et al. Parthenogenesis in a large-bodied requiem shark, the blacktip <i>Carcharhinus limbatus</i>. Journal of Fish Biology, 2008; 73 (6): 1473 DOI: 10.1111/j.1095-8649.2008.02018.x
Chapman et al. Virgin birth in a hammerhead sharkBiol Lett. 2007 August 22; 3(4): 425–427. Published online 2007 May 22. doi: 10.1098/rsbl.2007.0189.
i-Biology 
