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.

Tuesday, 9 November 2010

Problems downloading PDFs of papers using Internet Explorer?

A number of students are having problems download scientific papers from the Internet. The symptoms are you click on the link to download the paper and Internet Explorer (IE) crashes. The following is a potential fix for the problem....

I have reported this problem to ISS on at least three occasions and I am still waiting for reply/fix. The problem is odd in that some students can download PDFs of papers with no crash, whereas others cannot. This makes me think it is a 'profile' problem specific to the user's common desktop account.

During the Informatics Lab a number of the class have encountered the problem, and one student came up with a simple, and ingenious, fix! (I should have thought of it!)

The Fix

Instead of clicking the link (and crashing IE) to open the paper do a right-click to pull up a contextual menu (a menu that hovers on the page), and then use the 'Save Target As...' option.

You will then be asked for a location to save the PDF, save it, and then open using Acrobat.

Tuesday, 26 October 2010

Online maths help (a quiz with feedback)

If you are having problems with doing dilutions and concentrations calculations then you might like to do some practice using our online system, which can be found here on the School teaching website. Or enrol at Maths4Biosciences and take an online course.

The system can help with:

Percentage

Percentage dilutions1

Blog Post Bonus: Download a percentage solution calculations spreadsheet
Molar

Molar calculations

mg/ml

Mg ml

Molar Dilutions

Molar dilutions

Percentage Dilutions

Percentage dilutions

mg/ml Dilutions

Mg ml

Help

The site also comes with additional help:

Help


Feedback

And if you get a question wrong, there is help in the feedback to explain how to do the calculation:

Additional help and feedback

Wednesday, 20 October 2010

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

If you are struggling with 'science maths' then have a look at Maths4Biosciences - there is also a course on Beer-Lambert Law and Spectrophotometry.

Blog Post Bonus: Download a PDF of this blog post for your class notes.
If you would like to test your skills working with the Beer-Lambert Law then you might like to look at the Spectrophotometry tests at: Maths4Biosciences.com.


One question I have been asked a number of 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 actually 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. That is, the Bradford assay is really measuring 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), then 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. That is, 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 give 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) and 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 in the 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 extinction coefficient we wouldn't even have to do a standard curve.

If you are struggling with 'science maths' then have a look at Maths4Biosciences - there is also a course on Beer-Lambert Law and Spectrophotometry.

Blog Post Bonus: Download a PDF of this blog post for your class notes.

Friday, 8 October 2010

Help with printing pdfs.....

Some of the class have been having problems printing pdfs of my lectures if they have more than one slide per page. The following post will walk you through a solution to the problem.

If you are printing pdfs of lecture slides, at say 6 slides per page, on a Windows machine and they keep printing like this (or some variation of this):

Slides in the wrong order

Slides in the wrong order

Whereas you want them like this:

Slides in the correct order

Slides in the correct order

Then there is a problem with the way you have set up printing, that is, you have 'Auto rotate and scale' on (i.e. ticked).

To solve the problem follow these steps:

  1. In the print dialog, make sure that 'Auto rotate and scale' is turned off (i.e. not ticked)

Printer screen

Printer dialog screen

  1. Click on Properties.

Number of pages

Set the number of pages to print per page

  1. Select (click) the 'Finishing' tab, and set the number of pages you want to print per page.
  2. Set page orientation.
  3. Click on OK to close the properties window.
  4. Click on OK in the print dialog window to close it and to print the document.

Wednesday, 6 October 2010

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

If you are struggling with 'science maths' then have a look at Maths4Biosciences - there is also a course on Beer-Lambert Law and Spectrophotometry.

Blog Post Bonus: Download a PDF of this blog post for your class notes.
If you would like to test your skills working with the Beer-Lambert Law then you might like to look at the Spectrophotometry tests at: Maths4Biosciences.com.


A number of the class seem to have had a problem in understanding the relationship between the Beer-Lambert Law and a straight line, and working out the units of the extinction coefficient (ε).

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 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 units of the concentration and path length 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.

Blog Post Bonus: Download a PDF of this blog post for your class notes.
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 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
It can be seen that 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, then the gradient, m, must equal the extinction coefficient (ε).

If you are struggling with 'science maths' then have a look at Maths4Biosciences - there is also a course on Beer-Lambert Law and Spectrophotometry.


Blog Post Bonus: Download a PDF of this blog post for your class notes.

Monday, 27 September 2010

SOLO10 (Science Online 2010) and eBooks - the future?

Just came across a blog post on the eBook session I attended at SOLO10.

As the post says, the session was poorly attended with only about 10 people present. I was surprised at this low turn out, especially when you consider there were around 200+ people present at the conference (the other parallel sessions must have been packed!).

Why was the session poorly attended? And why did I attend it?

Poorly Attended: Well, eBooks are not necessarily exciting! Plus, SOLO10 is 'Science online' and so the delegates may not consider eBooks as 'online'.

Why did I attend: My view is that 'times are a changing' and that eBooks (eTextBooks) are going to be a big thing in the future. Gone will be the days of undergraduates bent double lugging textbooks around in their backpacks (I can dream), and students will have their eTextBook reader of choice loaded up with all the textbooks they need for the course, all weighing less than 750 g.

In the blog post at nature.com blogs Frank Norman has asked some similar questions to the above. And put together an overview of the discussion at the session. I would like to add to that discussion.

Frank has captured the key point of the discussion in his post, and I can see some of my comments (non-attributed) present, and I would like to expand on those:

ebooks are currently overpriced: I believe this is true (well, I said it), and publishers are trying to be greedy and apply their old business model. Just do a search on Amazon for eBooks on Biochemistry or search Amazon for textbook on Biochemistry. Notice anything? Prices are remarkably similar, and yet the traditional textbooks require paper, printing, storage and transport, whereas eBooks are just a series of electrons sent down wires from a hard-drive. I think the cost of eBooks are going to go in the same direction as Apps for smart phones, prices are going to go down, and authors will make money from volume of sales and better 'royalty deals' with the online 'publishers' (Amazon and Apple for example), than with the traditional publishing industry.

roles of Amazon and Apple: Can't recall if I said this, or not, but it was discussed. Apple has gone with the epub format (not a great format in my opinion, it is based on html and css - same as this webpage) on the iPad (and interestingly Apple's Pages word processor can now export to epub), and Amazon has gone with the mobi format for the Kindle (It should be noted that there is Kindle software for the iPad, iPhone, PC, Mac, Blackberry, and Android phones, e.g. Kindle software on iPhone and iPad. In addition, Amazon has a set of tools to convert books from epub to the mobi format (more details)).

value of publishers: This was an interesting point. My argument is that the publishers are 'gate keepers', that is, they control what is published. This was certainly true up until about 15 years ago, and then the world wide web came along and so now almost anyone can publish. However, to publish 'in print' on paper (be it a journal or textbook) you need a publisher. They have the final say. Now, with the advent of devises such as the Kindle and the iPad do we need publishers? Why not publish direct with Apple or Amazon? A publisher present (Cold Spring Harbor Press) in the session argued that publishers add value in connecting the author with their audience. So are publishers going to become 'public relations'?

why do people borrow books?: This was one of my comments. My argument is that the reason people borrow books from libraries is because books are expensive (average biomedical undergraduate text book is £30 - 40). It is interesting if you look at Penguin Books. When Penguin Books was founded in 1935 they produced cheap paperback books for around 6d (that is 2.5p GBP, or about 4 cents US; more details on Penguin history and see How the Paperback Novel Changed Popular Literature). In 1935 a hardback book cost around 8 shillings (that is 40p GBP, or roughly 60 cents US; source). The result was a lot of Penguin paperback books were sold.

Now, if you use the calculator at the National Archive then the 8 shillings is equivalent to £15 (~$22 US) and 6d is around £1 ($1.50 US) in 2010 (this figure is most probably based on the retail price index (RPI)). If you use the calculator at Measuring Worth then 8 shillings is equivalent to £76 (~$120 US) and 6d is around £5 ($7.50 US) based on average earnings (2009 figure)**. This shows that the price of hardbacks has not really changed since 1935, when based on RPI, but has significantly dropped in terms of average earnings. Interestingly the current cost of a paperback has increased based on RPI, but is still in line with average earnings.

So, eBooks may be the 'Penguin' book of today? They will (hopefully) drive down prices and put more books in to the hands of more people.

regular updates: This was another one of mine. Frank argues in his blog post, and also in the session, that authors won't want to do this, possibly due to the "intellectual effort required", and there is no mechanism to recover the cost. Well, in some fields regular updates are required, particularly, for example, in the sciences where published data may rapidly change, or in computing where screen-shots, available systems and databases etc., are constantly changing. An electronic format would allow for rapid and easy updating. And the new version could be released and charged for as a new edition. (After all, every time a new addition of a printed book comes out you don't get a free update (or even a discount) if you bought the last edition.) Plus, if the cost point of the book is right then previous owners may be willing to pay for the new edition, plus new customers get the latest most up-to-date version of the book available.

The bottom line is things are changing. The current publishing industry has lost control of the gates, and they are not adapting to the new way things can be done (and we all know what happens when adaption stops, we get extinction). As Martin Robbins said at in the "Rebooting" (aka the future of) science journalism" at SOLO10 - "there is going to be a bloodbath and we are going to be making black pudding" - and I think this may happen. Guess I might have to put my money where my mouth is.....


** Interestingly biological books cost 0.11 and 0.9 cents US per page (Nature 138, 196-196 (01 August 1936)) in 1935. I wonder what it is now?

Friday, 24 September 2010

Three little hints to help you avoid plagiarism

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

At what age do children see plagiarism as wrong?

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

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 wide spread. 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 that have plagiarised, and talking to students that 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

Sounds odd, but this is often a reason put forward for copying - I didn't have the time to put it in my own words - I forgot the deadline and 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 reason given for plagiarising - but I cited (referenced) the paper

Well, citation (referencing) is not a licence to copy. The function of citation is to say from where the information came, 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 - that is, both take you to additional information.

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

(You may also want to have a look at: Plagiarism: The art of referencing...)

3. Best example

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

Normally if you find yourself with this problem, that is you can't think of how else something could be written, then it means you haven't done enough reading, and you don't really understand what you are writing about.

Solution: Do more reading, find 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.


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

Digest - By what age do children recognise that plagiarism is 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

BGM2055: 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 need 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 '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.

Monday, 1 February 2010

Plagiarism: reusing figures from papers and textbooks in your work

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

First, you will gain more marks IF your draw you own figures and not just recycle the figures from other sources. However, having said that, it still does not mean you can just 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 as shown above in figure 1, then 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 full reference in the bibliography, then that would not be considered plagiarism. (One possible problem here may be the figure legend. Some members of staff may expect the legend to be re-written in your own words, even though you have stated the figure source, and some members of staff may not. So, to be safe it is a good idea to re-write the legend.)

Therefore the final figure will look like:

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, that is, you added something to it (see below where a red circle has been added), but were still using the base figure, then 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, 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.

Thursday, 14 January 2010

Plagiarism: The art of referencing...

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

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. in need to reference the source. So, how do you reference?

There are many different styles of referencing. If you read papers from different journals and you will see a whole range of styles. On the degrees in the School of Biomedical Sciences we tend (unless you have been told otherwise) to use what is called the 'Harvard' style (please note: this may not be true in CMB3000 and CMB3001, please check your module study guides).

No matter what style is being used the approach and idea of referencing is the same. You write some facts/information in your work and you state from where that information came. 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).

And 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 put in the reference in the text and the bibliography, so that will have to be checked.

And 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 on the other-hand 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).

And in your bibliography (references at the end of your work) you would write:

  1. 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

For more details have a look at:

http://www.ncl.ac.uk/students/wdc/learning/conduct/references/
http://www.ncl.ac.uk/students/wdc/learning/conduct/citations/

If I reference a paper can I copy from it?

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

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

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

This is a possibly the most comment I receive from students when discussing plagiarised work. Just because you reference a paper does not mean you can copy from it.

If you have any questions about plagiarism and/or referencing please feel free to email me: n.j.morris@ncl.ac.uk.

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

At a really simple level plagiarism can be defined as copying, that is, you take the work of another person and pass it off as your own.

Plagiarism can be split in to four main types:

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

Text Plagiarism: This is the most easy to understand, and the most common form of plagiarism. Basically it is the copying of text from some source (a paper, text book, 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 text book or paper and pass it off as your own (this can also be viewed as 'idea' plagiarism as some one 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. Or put another way, it is like making one burger in McDonald's and selling it twice.

If you have any questions about plagiarism please feel free to email me: n.j.morris@ncl.ac.uk.

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.

The single letter amino acid codes are fairly easy to remember. In eleven cases it is just the first letter.

AAlaAlanine
CCysCysteine
GGlyGlycine
HHisHistidine
IIleIsoleucine
LLeuLeucine
MMetMethionine
PProProline
SSerSerine
TThrThreonine
VValValine

And in 9 cases it not:

DAspAspartate
EGluGlutamate
FPhePhenylalanine
KLysLysine
NAsnAsparagine
QGlnGlutamine
RArgArginine
WTrpTryptophan
YTyrTyrosine

For those of you who wish to test their knowledge of the single letter amino acid codes I have put together a little test (it gives random questions so you can try it as many times as you like), which can be found on the teaching website https://teaching.ncl.ac.uk/bms

CMB2002: PKA, PDE, HSL, cAMP, phosphorylation and perilipin

One of the questions I had during the CMB2002 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 perlipin. 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 catecolamine (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 cylcase (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 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 catecolamine, or with insulin, or a combination of insulin and catecolamine you may see the type of result shown in figure 2. Basically, in the absences of insulin or a catecolamine cAMP levels are at a basal level. Upon the addition of a catecolamine 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 catecolamine the levels of cAMP may be higher than basal, but not as high as catecolamine only as PDE3B is active (see figure 2).

C amp

Figure 2: Hypothetical levels of cAMP upon ligand challenge. Stimulation of adipocytes with a catecolamine 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 catecolamine and insulin dampens the response of the catecolamine 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 on to 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.

Friday, 8 January 2010

Plagiarism: Making notes from papers during your projects

During your projects 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....

When you are making notes from a paper for your own personal use there is no problem in copying from the paper, to your note book, 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 have forgotten 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, 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.

If you have any questions on plagiarism please feel free to email me: n.j.morris@ncl.ac.uk.

CMB3000/CMB3001: Projects and Plagiarism

Over the next few weeks I will be putting out a series of posts on how to avoid plagiarism in your projects.

At Newcastle you have a number of pieces of work scanned for plagiarism during your degree. The aim of this scanning is not to catch you plagiarising, but to make sure you know how not to plagiarise. That is, in conjunction with the lecture on plagiarism, the scanning helps you know that you do not plagiarise, and that your 'academic practice' is good.

My aim through this process is to make sure everyone understands plagiarism, and the academic consequences of plagiarism, before they embark on their biggest piece of academic work, the project. The last thing I want to see is plagiarism occurring during the projects.

If you have any questions on plagiarism please feel free to email me: n.j.morris@ncl.ac.uk.

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 to the order around because it's in a timeline of events."

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 Calvert in a paper in 2010 reported:

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

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

And you wrote:

"The discovery of X in London by Smith in 1920, and the subsequent discoveries of Y by Jones in 1933 and Z by Brown 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 Calvert as your own. The correct way to report this would be:

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

That is, the inclusion of the reference of Calvert '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 plagiarism.