Wednesday, 22 December 2010

The other blog.... Blogging at Scitable

Today I started blogging over at Scitable (Nature Education). The new blog can be found here.

So, why two blogs?

Well, the two blogs have two different functions:

This Blog

The function of this blog is to directly serve my teaching.

I will continue to post material here that is connected with the courses I deliver, and it will also continue to host the 'science' tweets (tweets that link to papers and articles of interest) I post.

The Scitable Blog

The Scitable Blog will be used for posts connected to the use of technology in teaching and learning.

In the Scitable Blog I plan to write about how technology can be used to teach the biosciences, and how students can use technology to help with their studies. The Scitable Blog will contain posts that are (hopefully) of use to both lecturers and students.

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Wednesday, 20 October 2010

Why can't I extrapolate the Bradford Assay graph if the Beer-Lambert Law applies?

If you would like to test your skills in working with the Beer-Lambert Law, you might like to take the Spectrophotometry tests at Maths4Biosciences.

One question I have been asked several times after the feedback on a practical is if the Beer-Lambert Law, A = ε . c . l, gives a straight line, then why can't I extrapolate the data to find the answer for one of my unknown proteins?

The Bradford Assay is an indirect (or colorimetric) method for estimating protein concentrations. The assay is based on a shift in the absorbance of a dye, Coomassie Brilliant Blue G-250, from 465 nm to 595 nm when it binds a protein under acidic conditions. The Bradford assay measures the amount of bound dye and NOT the amount of protein present (although the two are connected until the dye is all used). As the dye is limiting (i.e. you only put in a set amount), you can reach a point when all the dye is bound, and no matter how much more protein you put in, you will not see a change in absorbance. You can increase the protein level to a point where available dye becomes exhausted so the graph would plateau.


Bradford assay graph



Standard Curve for a Bradford Protein Assay

Any value that falls in the yellow area of the graph (i.e. a concentration of more than 15 µg/ml or an absorbance greater than 1.02) cannot be used as the graph is no longer linear and is starting to plateau. Any absorbance that gives a protein concentration below 15 µg/ml can be used as this is in the linear portion of the graph (i.e. blue area), and the Beer-Lambert Law applies as the dye is not limiting.

In the experiment, you are working in the linear portion of the graph above (the blue area), so the line is straight, i.e., it hasn't plateaued. Therefore, we can say that between 0 and x µg/ml (or 15 µg/ml above), we have a certain absorption range, say 0 to y (where y is about 1.01 in the above figure). However, once we get above x µg/ml, or above the maximum absorbance y, we cannot say whether or not the graph has plateaued, so all we can say is the value is greater than x µg/ml. This may seem somewhat limiting (pardon the pun), but the Bradford assay can, in fact, detect protein concentrations over a 10-fold concentration range.

By the way, if we were measuring the protein directly, say at 280 nm, then we could apply the Beer-Lambert Law. In fact, if we knew the extinction coefficient, we wouldn't even have to do a standard curve.

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Wednesday, 6 October 2010

The Beer-Lambert Law, a straight line and the units of the extinction coefficient

If you would like to test your skills working with the Beer-Lambert Law, you might like to look at the Spectrophotometry tests at Maths4Biosciences.

Some students struggle to understand the relationship between the Beer-Lambert Law and a straight line and work out the units of the extinction coefficient (ε).

You may also find the following two videos helpful.




The Beer-Lambert Law states:

A = ε . c . l

Where:

A = absorbance 
ε = extinction coefficient 
c = concentration 
l = path length (i.e. the distance the light travels through the sample)


So, what is the connection between this and a straight line, and what are the units of the extinction coefficient?

The units of the extinction coefficient

In my opinion, the extinction coefficient has some of the craziest units out there.
Absorbance (A) has no units, so the units of the extinction coefficient (ε) are determined by how the concentration (c) and path length (l) are being measured. That is, the units of the extinction coefficient must cancel out the concentration and path length units so that the absorbance can have no units!

A worked example.

A = ε . c . l

A = absorbance, units - so put in 1 
ε = extinction coefficient, units - unknown 
c = concentration, units - milli-Molar, mM 
l = path length (i.e. the distance the light travels through the sample), units - cm

So...

A = ε . c . l

And, with units:


[1] = ε . [mM] . [cm]
Rearranging...
[1] / ε = [mM] . [cm] 

ε = 1 / ([mM] . [cm]) 

or 

ε = [mM]-1 . [cm]-1


So, the units are mM-1 . cm-1

This can be checked by putting it all back together:


A = ε . c . l 

A = ([mM]-1 . [cm]-1) . [mM] . [cm]

This gives:


A = [mM]/[mM] . [cm]/[cm]

So, the mM and the cm cancel each other out, leaving no units for absorbance A.

A straight line

The Beer-Lambert Law:

A = ε . c . l

Where:

A = absorbance 
ε = extinction coefficient 
c = concentration, units 
l = path length


The equation for a straight line is:

y = mx + c

Where:

m = the gradient 
c = the y-intercept

If you plot concentration against absorbance, then x = concentration and y = absorbance. Plus, from the Beer-Lambert Law, we know that if the concentration is zero, then absorbance must be zero.

A = ε . c . l
A = ε . 0 . l
A = 0 
So...

y = mx + c
absorbance = m . concentration + c

From above, if concentration = 0, then absorbance = 0, hence c must be zero
y = mx + c
absorbance = m . concentration + c*
0 = m . 0 + c 
c = 0

(* note, this c is the y-intercept and not the concentration)

Therefore...
y = mx + c
absorbance = m . concentration + 0
or
y = mx


Comparing:

y = mx
absorbance = m . concentration

With (and rearranging):

A = ε . c . l 

A = (ε . l) . c 

y = m . x
If y = absorbance, and x = concentration, then m (the gradient) must equal extinction coefficient (ε) multiplied by the path length, l, or ε . l. As l is typically 1 cm, the gradient, m, must equal the extinction coefficient (ε).

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Friday, 24 September 2010

Plagiarism: Three tips to help you avoid plagiarism

Here is an interesting question with an interesting answer...

At what age do children see plagiarism as wrong?

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

Over at Plagiarism Today, I read an article about the age at which children start to know plagiarism is wrong—it turns out the answer is around 5 years old.

One point in the article caught my attention:

"Generational Gap: It is interesting that students as young as 5 and 6 see the moral issues of plagiarism in this capacity but, according to research of college students, many seem to lose that moral qualm with plagiarism later on. Could this be a shift in thinking over generations or do many students lose that view over time?"

Plus, a recent (August 1st, 2010) New York Times article (cited in a blog post at Plagiarism Today) pointed out there is a problem with plagiarism at Universities and Colleges and that it is widespread. So, this does raise the question: If children as young as 5 know copying is wrong, how come students in their late teens and early 20s think it is OK? When, where, and why does this shift happen?

From talking to students who have plagiarised and talking to students who are 'sailing close to the wind' (i.e. their work shows some characteristics when scanned with TurnItIn which hint that they may be using 'unsafe' academic practice), three things are commonly mentioned, and if these could be avoided a lot of potential cases of plagiarism would fade away:

1. Time

It sounds odd, but this is often a reason given for copying: I didn't have the time to put it in my own words. I forgot the deadline, panicked, and copied straight from X.

Solution: Watch your time, don't panic and put things in your own words.

2. Citation

This is one of the most common reasons for plagiarising, but I cited (referenced) the paper.

Well, citation (referencing) is not a licence to copy. The function of citation is to say where the information came from so the reader can check the original report/data/experiments and/or expand on their own reading. Think of references as links on a web page - both take you to additional information.

Solution: Don't think that citation is a licence to copy.

3. Best example

This links up with citation - but I couldn't write it any better

Generally, if you find yourself with this problem, that is, you can't think of how else something could be written, then you need to do more reading and understand what you are writing about.

Solution: Read more papers, understand the subject, and use your own words.

So, three handy little hints (besides the usual and often unhelpful - Don't copy) that may help you avoid plagiarism.

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Original post - What Age Do Children See Plagiarism As Wrong?

Original paper - ‘No fair, copycat!’: what children’s response to plagiarism tells us about their understanding of ideas

New York Times Article - Plagiarism Lines Blur for Students in Digital Age


Thursday, 11 March 2010

What is a Unit of enzyme?

What is a 'Unit' of enzyme.... this always seems to give problems.

1 Unit of enzyme is defined as "an amount of protein that produces 1 µmole of product per minute". The thing that causes the problem is the word "amount".

The "amount" is not a mass; it is, for want of a better word, a 'blob'. You can buy enzymes in 'Units'. You buy a vial that will contain a number of Units of enzyme. You then know that if you dissolve the contents of the vial in a solution, how many µmoles of product per minute will be produced. If you buy 1 Unit of a particular enzyme from two different suppliers you may have vials that contain different weights of powder, but the work that can be done (i.e. the amount of product produced) will be the same.

For example:

Look at these two 'piles' ('blobs') of enzyme:

One unit

Pile 1 of Enzyme

One unit1
Pile 2 of Enzyme

Both 'piles' contain the same number of red balls (i.e. 4), and if 4 red balls are needed to produce 1 µmole of product per minute (i.e. 1 Unit), then both piles can be said to contain 1 Unit of the enzyme, and yet, as you can see, there are many more balls in pile 2... Pile 1 is certainly more pure as there is less contaminant (yellow balls) around.

This is why the 'amount' in "an amount of protein that produces 1 µmole of product per minute" is not a weight; it is an 'amount'; it is a 'pile', a 'blob'.

If you have problems with 'Sciences Maths' then you might like to check out some of the courses over at Maths4Biosciences.

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Monday, 1 February 2010

Plagiarism: Reusing figures from papers and textbooks in your work

One question I get asked is how to correctly reuse figures from textbooks and papers.

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

First, you will gain more marks IF you draw your own figures and do not recycle figures from other sources. However, having said that, it still does not mean you can redraw a figure you have found without stating from where it came, as that would be plagiarism.

Suppose you found the idea figure for your report/essay in a paper....

Original figure no legend

The figure you want to use...

and the paper in question is:

Mol Syst Biol. 2007;3:139. 2007 Oct 16.
PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.
Bodenmiller B, Malmstrom J, Gerrits B, Campbell D, Lam H, Schmidt A, Rinner O, Mueller LN, Shannon PT, Pedrioli PG, Panse C, Lee HK, Schlapbach R, Aebersold R.

If you just used the figure shown above in Figure 1, that would be plagiarism. However, if you used the above figure and stated - 'Taken from the paper of Bodenmiller et al. 2007' - at the end of the figure legend and then gave the complete reference in the bibliography, that would not be considered plagiarism. (One possible problem here may be the figure legend. Some staff members may expect the legend to be rewritten in your own words, even though you have stated the figure source, and some staff members may not. So, to be safe, it is a good idea to re-write the legend.)

Therefore, the final figure will look like this:

Original figure no legend

Fig 1: Text describing the figure in your own words... Taken from the paper of Bodenmiller et al. 2007.

Now, if you changed the figure in some way, you added something to it (see below where a red circle has been added) but were still using the base figure, you would still have to state the source of the original figure. For example:

Adapted figure1

Fig 1: Text describing the figure in your own words... Adapted from the paper of Bodenmiller et al. 2007.

Now, to get the most marks, you should draw the figure yourself and add something relevant to it (don't forget to state where you got the information in the legend, that is, give the reference), but again, you should still state from where you got the original figure.

Own figure

Fig 1: Text describing the figure in your own words... Adapted from the paper of Bodenmiller et al. 2007.

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Thursday, 14 January 2010

Plagiarism: The art of referencing...

How do I reference a paper? If I reference a paper, can I copy it? "But that can't be plagiarised, I referenced the paper!!!"

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

These are all common questions and misconceptions about referencing.

Referencing a paper

You have read a paper and wish to report the facts and findings in your report/essay, etc., but you need to reference the source. So, how do you reference?

There are many different styles of referencing. If you read papers from different journals, you will see a whole range of styles, such as the Harvard and Vancouver styles, to name but two.

No matter what style is used, the approach and idea of referencing are the same. You write some facts/information in your work and state where that information came from. For example, you have read a paper on an amine oxidase found in adipocytes and in your essay, you wish to talk about the protein. So, the full reference of the paper you read would be:

Morris NJ, Ducret A, Aebersold R, Ross SA, Keller SR, and Lienhard GE. (1997) Membrane amine oxidase cloning and identification as a major protein in the adipocyte plasma membrane. J Biol Chem. 272(14):9388-92. - link

In your essay, you state that:

The first membrane-bound amine oxidase was discovered in 1997 and was found in adipocyte plasma membranes (Morris et al., 1997).

In your bibliography (references at the end of your work), you would write:

Morris NJ, Ducret A, Aebersold R, Ross SA, Keller SR, and Lienhard GE. (1997) Membrane amine oxidase cloning and identification as a major protein in the adipocyte plasma membrane. J Biol Chem. 272(14):9388-92

(By the way, please note that et al. should normally be in italics or underlined. Also, please note the full stop after the al. in et al.)

Now, depending on the referencing style you are using, there may be some rules governing how many authors you include in the references in the text and the bibliography, so that will have to be checked.

Finally, with 'names referencing,' there can be the problem of the same name publishing two papers in the same year. So, for example, imagine there were these two papers.

Morris NJ (2010) Everything you wanted to know about plagiarism. J. Plag. 123(10):992-999 

and

Morris NJ (2010) How to plagiarise and not get caught. J. Cheats 1(13):10-15

The way you would cite them in your text would be as (Morris, 2010a) and (Morris, 2010b), and in the bibliography as:

Morris NJ (2010a) Everything you wanted to know about plagiarism. J. Plag. 123(10):992-999
Morris NJ (2010b) How to plagiarise and not get caught. J. Cheats 1(13):10-15

If you were using a numbering style of referencing, it may look like this:

The first membrane-bound amine oxidase was discovered in 1997 and was found in adipocyte plasma membranes (12).

In your bibliography (references at the end of your work), you would write:

12. Morris NJ, Ducret A, Aebersold R, Ross SA, Keller SR, and Lienhard GE. (1997) Membrane amine oxidase cloning and identification as a major protein in the adipocyte plasma membrane. J Biol Chem. 272(14):9388-92

If I reference a paper, can I copy it?

No. Referencing does not mean you can copy the text from a paper. All referencing does is state where you got the data, idea, or hypothesis so that other scientists can check the facts, look up the method etc. Putting a reference in your text as a link on a webpage allows the reader to find additional information.

Referencing does 'protect' against ideas plagiarism because referencing the source states who originally had the idea and where it was published.

"But that can't be plagiarised, I referenced the paper!!!"

This is the most common comment I receive from students when discussing plagiarised work.

Just because you reference a paper does not mean you can copy from it.

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Plagiarism: What is plagiarism and how can I avoid it?

Plagiarism, a serious academic offense, is defined as the act of copying another person's work and presenting it as your own. The consequences of plagiarism can be severe, ranging from academic penalties to damage to one's professional reputation.

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

Plagiarism can be split into four main types:

  1. ‘Text’ - copying text from a book, paper, document etc.
  2. ‘Diagrams’ - copying a diagram
  3. ‘Idea’ - passing off another person's idea as your own
  4. ‘Auto’ - copying from yourself!

Text Plagiarism: This is the easiest to understand and the most common form of plagiarism. Basically, it is the copying of text from some source (a paper, textbook, fellow student, internet) into your own work and then passing it off as your own. It should be noted that adding a reference (i.e. stating from where you copied the text) is no 'protection' and doesn't mean you can copy. If you find yourself reaching for the copy and paste keys on the computer, then there is a good chance it will be plagiarism.

Diagram Plagiarism: This is where you copy a diagram or figure from a textbook or paper and pass it off as your own (this can also be viewed as 'idea' plagiarism as someone has thought long and hard about constructing (and drawing) the figure). You can 'protect' against diagram plagiarism by simply stating from where you got the figure (see later post for more details).

Idea Plagiarism: This, in my opinion, is the worst form of plagiarism, as you would be attempting to pass off the hard work and intellectual property of a fellow scientist as your own. You can write about the ideas and thoughts of other scientists, but YOU MUST STATE FROM WHERE YOU GOT THE IDEA. Basically, this is one of the reasons why we reference sources of information; you are stating who had the original idea and how they came by it. Effectively, by referencing, you are acknowledging the hard work of the other scientists.

Auto-Plagiarism: This form of plagiarism is the one most people have difficulty understanding. After all, how can you plagiarise yourself? You 'own' the work and the intellectual property! Well, basically, auto-plagiarism would occur if you handed in the same piece of work for two different assignments and got two lots of marks for it. Put another way, it is like making one burger at McDonald's and selling it twice.

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Wednesday, 13 January 2010

Single letter amino acid codes

The amino acids have single and three-letter codes, and these are worth learning for your degree.

Remembering the single-letter amino acid codes is a breeze. In most cases, it's just the first letter of the amino acid's name.

AAlaAlanine
CCysCysteine
GGlyGlycine
HHisHistidine
IIleIsoleucine
LLeuLeucine
MMetMethionine
PProProline
SSerSerine
TThrThreonine
VValValine

However, in 9 cases it is not the first letter:

DAspAspartate
EGluGlutamate
FPhePhenylalanine
KLysLysine
NAsnAsparagine
QGlnGlutamine
RArgArginine
WTrpTryptophan
YTyrTyrosine

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PKA, PDE, HSL, cAMP, phosphorylation and perilipin

One of the questions I had during a feedback session was on PKA, hormone-sensitive lipase (HSL), phosphorylation and perilipin, and how this all relates to the breakdown of triglycerides.

PKA phosphorylates HSL and perilipin. However, for PKA to do that it has to be active, that is, cAMP needs to be available to activate the kinase (see figure 1).

If the PDE is active it hydrolyses cAMP, this will reduce cAMP levels, and this will reduce the level of active PKA. Net result, less HSL phosphorylated, less perilipin phosphorylated, therefore less triglyceride broken down. That is, HSL has to be phosphorylated to be active and to remove the perilipin from blocking HSL access to the fat droplet in the adipocytes it also has to be phosphorylated.

Hsl2

Figure 1: Regulation of lipolysis. Activation of a G-protein coupled receptor (GPCR) by a hormone (A) (e.g. glucagon) or catecholamine (e.g. epinephrine) causes an exchange of GTP for GDP on the α subunit of a heterotrimeric Gs protein. The active GTP bound α subunit activates adenylyl cyclase (AC), which converts ATP to cAMP. cAMP activates protein kinase A (PKA), which in turn phosphorylates, and therefore activates, hormone-sensitive lipase (HSL), and phosphorylates perilipin and removes its 'block' on the fat droplet. Net result: increased lipolysis and hence the production of fatty acids and glycerol. The activation of the insulin receptor (IR) by insulin (I), via insulin receptor substrate (IRS) and a number of other proteins, results in the phosphorylation of protein kinase B (PKB), which in turn phosphorylates and activates phosphodiesterase 3B (PDE3B). The active PDE3B hydrolyses cAMP to AMP, and therefore effectively lowers intracellular cAMP levels, therefore reducing PKA activity. As phosphatases (P) are removing phosphates from HSL and perilipin there will be a decrease in phosphorylated HSL and perilipin as PKA is not replacing the phosphates. The net result is less HSL and perilipin is phosphorylated, so lipolysis is reduced.

If you were to examine the intracellular cAMP levels of adipocytes that been stimulated with a catecholamine, or with insulin, or a combination of insulin and catecholamine you may see the type of result shown in figure 2. Basically, in the absences of insulin or a catecholamine cAMP levels are at a basal level. Upon the addition of a catecholamine levels are raised 2 fold. If insulin alone is used then levels of cAMP are reduced below that of basal, and in the presence of insulin and catecholamine, the levels of cAMP may be higher than basal, but not as high as catecholamine only as PDE3B is active (see figure 2).

C amp

Figure 2: Hypothetical levels of cAMP upon ligand challenge. Stimulation of adipocytes with a catecholamine causes an increase in intracellular levels of cAMP. Stimulation of adipocytes with insulin causes cAMP levels to fall below basal levels as PDE3B is activated. The stimulation of the cells with catecholamine and insulin dampens the response of the catecholamine as PDE3B is activated by insulin.

What you have to remember is these systems are dynamic and in a state of equilibrium. cAMP is being made (adenylyl cyclase) and destroyed (PDEs). Kinases will be putting phosphates onto proteins, and phosphatases will be removing them. All that is happening is this equilibrium is being changed and pushed in one direction or the other, active or inactive, phosphorylated or not phosphorylated.

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Friday, 8 January 2010

Plagiarism: Making notes from papers during your research

When writing essays, you will read many papers and make lots of notes. During this process, you have to be careful, as there is the danger that you can accidentally copy material from a paper to your notes and then from your notes to your final write-up and, therefore, plagiarise.

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

When you are making notes from a paper for your own personal use there is no problem in copying from the paper to your notebook, word-for-word. At least that way, you know you have the information correct...

However, when you return to your notes some days or weeks later, you may forget you have copied word-for-word from the paper and think your notes are all your own work and, hence, can be used directly in your write-up. The result is that you plagiarise.

When you make your notes mark the notes that are 'word-for-word' in a way so that you know they are copied, so you don't inadvertently use them in your final write-up. Put the notes in inverted commas or underline them. Do something to make them stand out and help you remember that they are copied and, therefore, can't be used directly in your final work.

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Wednesday, 6 January 2010

Plagiarism: timelines and historical events from text books

Question: "Is it plagiarism to read a section in a book and rewrite it in your own words? It's hard to change the order around because it's in a timeline of events."

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

Answer:

This is a tough one...

Yes, it is plagiarism if you are copying word for word.

It could also be plagiarism if the timeline was a specific argument (i.e. it could be 'idea' plagiarism), as opposed to a historical report of events.

For example (assuming your own words):

11:05 John went to the pub
11:10 John ordered a pint
11:15 John sat down

would not be (in my opinion) plagiarism as you are reporting a series of events.

But, if Smith, in a paper in 2010, reported:

"1920 X was discovered by Brown in London
1933 Y was discovered by Jones in Paris
1977 Z was discovered by Green in Tokyo

This led to the discovery of A by Morris in 2010"

And you wrote:

"The discovery of X in London by Brown in 1920, and the subsequent discoveries of Y by Jones in 1933 and Z by Green in 1977, led to Morris discovering A in 2010."

Then, although that wouldn't be 'text' plagiarism, it would be 'idea' plagiarism as you are passing off the hard work and reading of Smith as your own. The correct way to report this would be:

"The discovery of X in London by Brown in 1920, and the subsequent discoveries of Y by Jones in 1933 and Z by Green in 1977, led to Morris discovering A in 2010 (Smith, 2010)."

That is, including Smith's reference 'protects' against an accusation of 'idea' plagiarism, and putting the 'findings' in your own words 'protects' against 'text' plagiarism.

Alternatively, if you have made the connection between the events yourself (i.e. you have done all the hard work of finding the original papers and making the connections), then it would not be plagiarism.

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