E-mail - dark social media? I think not...

Yesterday evening, I had the privilege of engaging in a thought-provoking discussion with Alan Carr on the pervasive use of email in teaching and day-to-day communication.

I won't repeat my views and opinions via email here, but you can read them over at Scitable:

1. My hypothesis: e-mail is evil and deserves to die!
2. Problems with email….. I appear to have touched a nerve...
3. What is wrong with e-mail? Can it be fixed?
4. What is wrong with e-mail? Can it be fixed? - The Programmers
5. What is wrong with e-mail? Can it be fixed? - The Receiver and the dreaded FYI
6. What is wrong with e-mail? Can it be fixed? - The Receiver and meta-data
7. What is wrong with e-mail? Can it be fixed? - The Sender
8. What is wrong with e-mail? Can it be fixed? - My battle to get e-mail working again - some tips and suggestions

Needless to say, I am not a fan of email... (as you may be able to guess from some of the above post titles).

Despite being overseas, I was determined to share my perspective on why email is problematic. Alan, a staunch advocate of email, graciously invited me to his session at SpotOn London 2013. I prepared a compelling video, just in case our Skype connection failed, to underscore the severity of the email issue.

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Observing and genotyping C. elegans

I had a fun day yesterday doing the "C. elegans" practical, which is part of the first-year labs. In the practical, we got to look at live C. elegans and also set up some PCR reactions to genotype some wild-type and mutant C. elegans. It was all fun stuff.

Below is a movie we shot of the worms on the day of the practical and some stills from the microscopes.

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Fun and games with Paramecium

Last week we had our annual first-year 'paramecium practical'. The aims of the session were to familiarise the students with the microscopes and to also introduce unicellular organisms.

In the UK we order the paramecium for the practical from a local supplier. However, in Malaysia, despite 4 months of searching, I was unable to find a supplier. This left me with three options:

1. Don't do the practical
2. Find an alternative supplier
3. Culture my own…

I tried to find an alternative supplier (paramecium are used to feed baby fish), but none of the local pet stores stocked them - although I did get a rather nice bag of water fleas (Daphnia).

A bag of Water Flea - Daphnia

A Water Flea - Daphnia

Finally, I decided to culture them.

After a quick read around the Internet, I found a recipe for culture media and some advice on where to find paramecium.

The general advice for 'hunting' paramecium is to take water from close to the top or the edge of a pond. In the end, I took a sample of water from the surface, plus some material from the bottom of the pond. This was allowed to settle overnight (see photo below).

The culture media consisted of dog biscuits, and 4 or 5 cm² of lettuce leaf, in water.

Dog Biscuits

Lettuce Leaf

Water

Pond Water - a mixture of material from the bottom of the pond, and water from the surface and edge

Two culture bottles and a bottle of bond water

I set up three bottles, two culture media, and a bottle of pond water. These were left overnight.

And the next morning… The pond water had cleared, and the bottles with dog biscuits and lettuce were cloudy (the cloudiness was caused by bacteria growing) - these will be a food source for the paramecium.

One of the 'culture media' bottles was seeded with 20 ml of water from the top of the pond bottle, and the other with 20 ml of water collected near the vegetation at the bottom of the pond bottle.

Next morning - the three bottles…..

An examination of the pond water under a microscope revealed the presence of paramecium, but not that many.

There were also some other ciliates present…

Over the next 12 days, the cultures got progressively more cloudy and exceedingly smelly.

12 days after adding the pond water

Of the two culture bottles, the one seeded with water from the top of the pond bottle produced the best (most and largest) paramecium, and the best place to harvest the paramecium was from the top 5 - 10 mm of the bottle, and in particular the layer of 'scum' that had formed on the top of the water. Paramecium taken from elsewhere in the bottle tended to be smaller.

Movie

The movie below was shot during the practical.

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It is all in the name…. Why am I (not) Dr Nick?

In Malaysia, I am called Dr Nick.... And I couldn't understand why... Today, I found out.

In Malaysia, there are no family names, as in Morris, Smith, Jones etc. Your last name is your father's first name, so if my father's first name was Ian, then I would be Nick Ian. Hence, as I am Dr Nick Morris, this suggests that my father's first name was Morris, and Dr Morris would be my father!

This can get odd for a woman, as they would be Julie Ian, and so would Ms Ian if the European convention was followed.

Thanks to The Simpsons, Dr. Nick has a certain 'feeling' about it. You can read more about Dr. Nick of Simpson's fame on Wikipedia.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Paper published - Adiponectin corrects high fat diet-induced disturbances in muscle metabolomic profile and whole body glucose homeostasis

Great to finally see a paper that I was working on last year out in print….

Liu,Y., Turdi,S., Park,T., Morris,N.J., Deshaies,Y., Xu,A. & Sweeney,G. Adiponectin corrects high fat diet-induced disturbances in muscle metabolomic profile and whole body glucose homeostasis (2013) Diabetes 62 743-752

Pubmed Link: http://www.ncbi.nlm.nih.gov/pubmed/23238294

There is also a very nice commentary (subscription required) at: http://diabetes.diabetesjournals.org/content/62/3/701.full

The others did all the hard work; I just applied my geeky computing skills to crunch and analyse all the lovely data that was produced. Happy days!

Glycogen Synthase Kinase 3 (GSK3) and Glycogen Synthase (GS) - the phosphorylation equilibrium

This one causes students problems every year - the relationship between Glycogen Synthase Kinase 3 (GSK3) and Glycogen Synthase (GS), and their phosphorylation states and activity.

If you look at insulin signalling overall:

You will see that activated protein kinase B (activated by phosphorylation) phosphorylates and inactivates GSK3. This means that GSK3 can no longer phosphorylate its substrate, GS.

Now, GS, when phosphorylated, is inactive. Hence, as GSK3 is no longer active (as it is phosphorylated) it cannot phosphorylate GS and inactivate it, therefore GS remains un-phosphorylated and therefore active so it can make glycogen.

The key to understanding this is that phosphorylated (inactive) and un-phosphorylated (active) forms of GS are in a state of equilibrium and that the kinase, GSK3, drives the equilibrium to the right (inactive) in the figure below, whereas the phosphatase (which removes the phosphate) drives the equilibrium to the left (active). Therefore, if you inhibit the action of the kinase (GSK3) the net result is more un-phosphorylated GS, hence more glycogen is made, which is just what we want…

One key thing to keep in mind is that the phosphorylation of a protein can cause it to become active or inactive. It all depends on the protein.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Additional Resources

• 📗 - Biochemistry (Stryer) (affiliate link)
• 📗 - Principles of Biochemistry (Lehninger) (affiliate link)

Calculating Percentage Solutions

For some reason, percentage solution calculations cause students some problems. However, hopefully, once you have read this blog post, you should have a good understanding of percentage solutions and how to do the calculations.

If you want to practice your 'science maths', then have a look at Maths4Biosciences

What are percentage solutions?

A percentage solution is an amount or volume of something per 100 ml or 100 g of a solution. It is as simple as that. It is a percentage.

Why are they used?

Percentage solutions are a convenient and easy way to record solution concentrations. One advantage is that you don’t need to know anything about the compound in terms of molecular weight; all you need is the percentage of the required solution.

Why are there three types of percentage solutions?

This is slightly difficult to explain. However, there are three types of percentage solutions:

• Percentage weight by volume (w/v)
• Percentage volume by volume (v/v)
• Percentage weight by weight (w/w)

The percentage weight by volume (w/v) is the number of grams of compound per 100 ml of solution. This type of percentage solution is used when describing the amount of powder in a solution. For example, 5 g of powder made up to a final volume of 100 ml would be a 5% (w/v) solution. Likewise, 2.5 g of powder made up to 50 ml would also be a 5% (w/v) solution, as you would have 5 g in 100 ml.

The percentage volume by volume (v/v) is the number of ml of some liquid per 100 ml of the solution. This type of percentage solution is usually used to describe a solution made by mixing two liquids. For example, 5 ml of a liquid made up to a final volume of 100 ml would be a 5% (v/v) solution. Likewise, 2.5 ml of a liquid made up to 50 ml would also be a 5% (v/v) solution, as you would have 5 ml in 100 ml.

Finally, the percentage weight by weight (w/w). This one is more difficult to understand, but the principles, as explained above, are still valid. A percentage weight by weight (w/w) solution can be the weight of a powder or a liquid made up in a solution to the final weight of the solution. So, for example, 5 g of a powder (or a liquid) made up in a solution with a final weight of 100 g would be a 5% (w/w) solution. Likewise, 2.5 g of a liquid or powder made up to give a solution that weighed 50 g would also be a 5% (w/w) solution, as you would have 5 g of the powder or liquid in 100 g of a solution.

 

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Additional Resources

•  📗 - Maths and Chemistry Refresher for Life and Biomedical Scientists - Google Play Book Store
•  📗 - Catchup Maths and Stats - (affiliate link)
•  📗 - Catchup Chemistry - (affiliate link)
•  🌎 - You can practice your lab calculations at: https://maths4biosciences.drnickmorris.com/