Category Archives: Genetic Engineering & Biotechnology

PCR Song: Class Project & TED Ed Lesson

This song by BioRad is a funny discussion starter on the polymerase chain reaction (PCR) and biotechnology. For a full lesson plan, with editable slides for students and a complete TED Ed lesson (with quiz), visit the full page.

Click to go to the TED-Ed lesson on PCR.

Click to go to the TED-Ed lesson on PCR.

Bad Pharma by Ben Goldacre: quick review & course connections

The Book

There’s a good chance that you’d not be here to read this without the pharmaceutical industry designing and manufacturing the vaccines and medications you’ve used during your life – but how much do we know about where they come from? 

In this thoughtful, well-researched and instructive book, Ben Goldacre* (doctor, evidence-based medicine proponent and author of Bad Science) outlines how Big Pharma works, but also what the issues are and how they can be fixed. He has a TEDMED Talk on the premise of the book (below) and takes care no to write a ‘hatchet-job’ on the industry, but to shine a light on the current state of clinical research and marketing.

I recommend the book to IB Biology and IB Chemistry students and teachers – read a copy before the next teaching cycle begins – as there are many sections of direct relevance to our courses that could be used as lesson ideas or real-world contexts for what we’re learning. It would make a great addition to the reading list for students, especially those intending to pursue medical, biochemistry or pharmaceutical careers.

In each chapter, Goldacre identifies a problem and gives a clear account of why it is a problem, using systematic reviews of academic literature and specific case studies to highlight each point. He makes it clear to the reader why these problems actually are problems, but also offers concrete advice or proposals on how to solve them.

Some highlights for the IB Biology course

Click & Go

Chapter 1 gets stuck in with statistical analysis and why systematic reviews of literature, meta-analyses and careful work with data are so important. It introduces the work of the Cochrane Collaboration and works through a neat illustration of the importance of considering all the data as more studies are carried out. The Cochrane Collaboration’s logo is itself a fascinating story, and you could model this in class with a simple set of investigations in the early stages of the course (see some ideas on the Statistical Analysis page).This video is very useful – from the Testing Treatments page.

The ideas and issues come thick and fast for the rest of the book. 

As you read it, you will see many potential connections to the course, as well as to Theory of Knowledge. Here are just a few ideas that might spark discussion in class:

  • What is the problem with missing trial data and publishing only favourable results? 
    • What does this publication bias do the reliability of the information we use to make decisions?
  • How are drugs designed and tested (this is super interesting, going from in-vitro and animal testing to stage 1, 2 and 3 human trials, and has an obvious link to the IB Animal Experimentation Policy).
    • What are the ethical issues with human testing, in particular the ideal/ representative nature of the patients used and the incentives they receive?
    • What is the impact of outsourcing trials to other countries that might have different ethical codes?
    • What are the ethical issues of randomising and controlling trials with humans, particularly in cases where there is a known drug that helps compared to a new drug?
  • What are the roles of drugs regulators on medicine and are they working?
  • How should trials be designed to give more valid and reliable data (for example, comparing the ‘new’ drug against the current best alternative vs placebo)?
    • How could we use nationwide health records to conduct larger, simpler trials to determine which treatments really are most effective?
  • How do the many branches of pharmaceutical marketing affect decision-making and how can we recognise and mitigate for this?
  • How can we fix it all to keep medical innovation going whilst generating reliable, cost-effective data and drugs?

TED Talk: What doctors don’t know about the drugs they prescribe

*Yeah, I know I’m a bit of a fanboy and have featured him on here a lot, but with this and Bad Science, he has produced a lot of useful content to connect to our classes. 

Anthony Atala: Printing a human kidney [TED Talk]

With links to stem cells, genetic engineering and biotechnology, homeostasis and the kidney, the current science outlined in this TED Talk by Anthony Atala is amazing. It includes a demonstration of a real kidney being printed and a student who has an engineered bladder and now lives a normal life. Wow.

With huge numbers of people waiting for kidney transplants, is this the future of transplant medicine?

Thinking of kidneys, the Guardian has a link to an AP article: Mystery illness kills thousands in South America.

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.

Genetic Engineering & Biotechnology Update

Here is the updated presentation for 4.4 Genetic Engineering and Biotechnology. There are some new slides and clearer explanations, as well as a new visual identity. It should also be downloadable as a pptx file.

For many more resources go to the page for 4.4 Genetic Engineering and Biotechnology.

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)

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.

Some highlights for IB Bio:

How do mutations affect protein folding?

How does gene mutation affect protein folding?

How does gene mutation affect protein folding?

Sickle cell anemia

Cell growth and regulation

DNA

Properties of Water

And loads more here: Biology, Molecular Biology (Chem of life), Physics/Chemistry.

Genetics – Megapost

Get the Essential Biology 04 – Genetics Revision guides here:  Standard LevelHigher Level

Top websites:

Learn.Genetics@Utah awesome resources

Click4Biology Genetics pages: CoreHigher Level

BioEthics Education Project: The Human GenomeGenetic Technology

And as always, click on the shadowed images in the presentations to be taken to source videos and animations.

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Here are all the presentations for the Genetics topics.

Core:

More presentations after the jump…

Read the rest of this entry

Plant and Soil Sciences eLibrary

With all the webspace devoted to genetics and biotechnology at the moment, it’s great to stumble upon a site that is bringing ‘old school’ Science into the new millenium. Though no-one seems to call it botany any more!

The Plant and Soil Science eLibrary hosts a collection of animations on plant science topics and cell biology that are useful, clear and can be easily downloaded. They are all also available in Spanish and many have pdf help notes for students.

The site is designed primarily for people who wish to earn credit for further studies in crop science and contains such units as plant physiology, crop technology and nutrition technology. There’s even some genetics in there.

Click on the image to see their transpiration example.

Genetic Engineering & Biotechnology linklist

This topic is Science at the moment, so let’s keep it as concise as possible. Some people go as far as studying a degree in all this, but that can wait for now!

Here’s the presentation for the IBDP Biology syllabus:

And here’s the revision page from Clcik4Biology

And now by topic:

Polymerase Chain Reaction

Very visual from Dolan DNA Learning Centre

McGraw Hill step-through

Rutgers step-through

and of course, the ever-so-silly PCR Song

Gel Electrophoresis and DNA Profiling (or DNA Fingerprinting)

Easy intro from Court TV

In-depth look from DNAi

DNA Learning Centre’s Electrophoresis animation

Learn.Genetics super-flashy animation

Case study: the case of the pothunters from Learn.Genetics

The Human Genome Project

Official Site How to sequence a genome

Teachers’ resources

Learn.Genetics genome resources

Outcomes: Bioinformatics DNA Microarrays 1 (2)

Outcomes: looking deeper into evolutionary relationships:

Gene Transfer Technology

McGraw Hill animation collection

NewScientist: gene therapy success reverses blindness

Gene Therapy in SCID (severe combined immunodeficiency) from Sumanas

Gene transfer in insulin production from abpi schools

Using the gene gun as a vector from Purdue

Genetic Modification in Crops and Animals

Glowing pigs and fish: Animal Farm TV series

GM food and you (objective, worth watching)

Cloning

Excellent animation from Dolan DNA Learning Centre

Video: Enucleation of an egg cell from Howard Hughes Medical Institute:

Download this Stem Cell cribsheet from SEED Magazine

Therapeutic cloning cures Parkinsons mice

More about cloning from ActionBioscience

If this catches your imagination, dig deeper!

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