Monday, 26 November 2012

Seeing Cells

Science images are becoming commonplace on social networks. But how are these beautiful, artistic images made and what use are they in research?

Human cells stained and probed for DNA, actin and protein.
I (Heather Doran) took this image -  please don't reuse it. 

I've taken quite a few images throughout my PhD. So many my university computer struggles under the weight of them. I've been taking microscopic images of cells to understand how the cell cytoskeleton allows them to move. And it has been one of the most interesting and favourite parts of my PhD project.

There are a number of ways of creating these images. The images all represent one or two components of the cell. Cells need to be fixed (in a fixative, like methanol or paraformaldehyde, to preserve them and the proteins and structures inside the cell). Different fixatives can be used depending on what it is you are looking for and how you are looking for it. Fixatives stop all movement, any reactions happening in the cell(s) and preserve and protect from degradation.

Once fixed, you can 'probe' the cells for what you want to look at..

I stain the DNA with various stains (below is a DAPI) stain. DAPI binds to A-T rich areas of DNA and becomes fluorescent. This is useful as all the cells I look at contain a nucleus containing DNA, the DAPI staining is strong and allows me to find, and focus on the cells under the microscope.

I also stain the cells for actin (actin is a vital part of the cell cytoskeleton - what helps the cell keep its shape) with something called phalloidin, which is actually a toxin that binds to the actin. If you attach a fluorescent tag to the phalloidin molecule, you can see the actin in the cell. 

Look for particular proteins using a primary antibody directed against particular proteins of interest. Antibodies detect a specific epitope on the antigen (which in this case would be the protein of interest). Then you can use a secondary antibody, that detects the primary antibody, but the secondary antibody has a fluorescent tag attached... and you can see if the protein is there, and where it is in the cell.

There are other ways of looking at proteins, the primary antibody can have a fluorescent tag itself, or you can genetically modify the cell so it expresses a protein that has a fluorescent tag attached. 

For the physics of fluorescent microscopy and confocal microscopy (which allows you to take a slice of a cell) see this fabulous explanation here.

All the images featured were taken by me. Please don't reuse them without permission. Thanks! 

Friday, 23 November 2012

Is the sherry that makes you merry going to make you heavy?

Alcohol and weight gain are two things associated with the season of merriment also known as Christmas. Most people pile on a few pounds over the festive period but is it really down to the sherry?

Falalalala la la la la
A recent story highlighted  the hidden calories in booze and warns of high calorie intake from alcohol in the US population.  It makes a good point, people forget that drink contain calories and therefore may unintentionally be consuming more than they realise, leading to an increase in dress size. The NHS choices website from the UK also have a section about booze, weight and hidden calories. 

If you didn't know, alcohol is made from sugar and starch and is extremely calorific. On the scale of calorie content to volume it comes second only to fat itself. There are around 500 calories in a bottle of wine, which if you are female is one quarter of your recommended daily calorie intake. You can use this handy drinks calculator (which includes different brands and mixers) to work out the calories you are taking in when drinking. 

But don't put your glass of port down just yet... the link between alcohol, calories and weight gain isn't 100% clear.

However, (put that glass of port back on the table) that doesn't mean that there isn't an association because if there is a direct association then it would be extremely difficult to demonstrate...

Weight gain can be caused by any number of different reasons. As you as a human probably realise. A new job, age, genetics, illness, medication, holidays, time of the year (and month) can all cause fluctuations in weight. Over a number of years and lifetime weight can vary enormously too. On top of all this many studies that monitor weight and try to look for associations often rely on participant recording of weight, height, amount of exercise,  food intake and alcohol consumption. This is important and problematic because people lie, especially about their height, weight, exercise, food intake and alcohol consumption. See a previous blog post about a study about how people lie about the amount of chocolate they consume.

No-one drinks pure ethanol either, and that adds a further complication. Alcohol is extremely calorific but drinking it with mixers that are fat and calorie heavy (like milk and sugary drinks) obviously increases the calorie intake. If you are part of a study and you mix up your drinks a lot, how can you (and it makes it difficult for studies) record your intake accurately.  And how can studies separate out an infinite number of drink combinations to decide if it's the alcohol or the chocolate milkshake that you drank with it that is causing your waistline to bulge?

Alcohol and calorific mixers would suggest that drinking more would lead to an increase in weight. It isn't all doom, gloom and hidden calories though, going back to the systematic review (pick that glass of port back up again).. some rather interesting findings were made.

Across all the different types of trials analysed, the results were inconclusive. BUT, big news for those that like the vino, when studies analysed the type of drink consumed a negative association between wine and weight gain was found (people that drink wine are skinnier).. This doesn't mean wine makes you skinner.. it could all be explained by the particular diet choices, and the lifestyle of wine drinkers. However, some studies (on rats, not humans) have shown that red wine can reduce fat  (associated with the red wine, not the alcohol) through a compound called resveratrol that is found in red wine, and is the source of many 'red wine is good for you' stories (note, studies are done on rats, or in dishes, not on humans) I found one study on resveratrol in humans. It wasn't reported very well and I debunked it here

Unfortunately drinking spirits was positively associated with weight gain. So if you like your whisky you are more likely to be a wee bit chubbier (but that might not necessarily be due to your tipple of choice).

A study of 37,000 US citizens (non smokers), investigated the amount and frequency of drinking alcohol determined that the people that drank alcohol the least (but did drink frequently) had lower BMI values than those that drink more, but less frequently. This study corrected for activity levels, suggetsing that something

Interestingly a US study found a positive correlation between slight to MODERATE alcohol intake and activity levels - which translates to mean that people that have a moderate alcohol intake are more active. This correlation continued even at high levels of alcohol intake. 

It has also been found that, alcoholics exercise less, but also have a lower body weight. Which contradicts the above study. But alcoholics might eat less as they can replace food intake with drink, and drinking excess alcohol can lead to liver disease, and other complications which can prevent the body from breaking down other nutrients causing malnutrition...

There are endless limitations, problems and variables associated with all of these studies. Which, like I said at the beginning, makes it difficult to understand the real relationship between alcohol and weight gain.

However, if you know that after a glass or two of wine, or a pint or two of beer you start reaching for the leftover turkey or cooking up a storm of fatty treats despite sticking to large helpings of sprouts and carrots during the daylight hours..... then sadly you probably know that a few nights getting merry might cause you to tip the scales in the wrong direction.

Alcohol has been proven to increase risk of other health problems so be wary of the amounts you drink. See here for more information and advice.


Sayon-Orea C, Martinez-Gonzalez MA, Bes-Rastrollo M. Alcohol consumption and body weight: a systematic review. Nutr Rev 2011; 8: 419–431. | Article |

Monteiro RSoares RGuerreiro SPestana DConceicao CAzevedo IRed wine increases adipose tissue aromatase expressin and regulates body weight and adipocyte sizeNutrition. 2009;25:699705.


S. Liangpunsakul, D. W. Crabb, and R. Qi, “Relationship among alcohol intake, body fat, and physical activity: a population-based study,” Annals of Epidemiology, vol. 20, no. 9, pp. 670–675, 2010. View at Publisher · View at Google Scholar · View at Scopus

Thursday, 8 November 2012

Monday, 5 November 2012

Online Tools for Academics at Conferences

I am presenting a session at the #PhDjourney conference about social media and the PhD on Wednesday. I will post my slides and information after the talk, but as I was preparing I thought I would put together a list of useful online tools for keeping up with what is going on (and remembering what has happened) at conferences.

Please add any suggestions and thoughts.

Facebook - conferences usually have a facebook page, which can be useful before the conference to connect with people and learn more about what will be happening at the conference (and useful for keeping up to date, when full programmes are announced). Find the page by searching facebook for the conference, or looking for a facebook link on the conference website. Facebook is of limited use during the conference as you will only be able to see official updates from the organisers and/or posts from people you know at the conference. A facebook can be a good way of sharing blogs and other posts after the conference.

Twitter - hashtags e.g. #phdjourney can be used to follow any discussions that are happening at the conference, about the conference and by conference organisers. The conference itself should have a twitter account that you can follow for updates (like facebook). Individual sessions may have their own hashtags which can be followed as the sessions are happening. This way, if you know the hashtag you will never need to miss a conference session again! You can interact with the tweeters and even get delegates that are tweeting at the session to ask questions on your behalf at the session if you tweet in time. This method relies on people tweeting from the session in a way that allows you to follow and understand the talk and discussion. Twitter can be used at the conference to make new contacts, and conferences can be a great way of meeting people you already tweet. Create lists of people who are tweeting from the conference and follow all their activity through the list. You can also block a hashtag, which is handy if you have a lot of people tweeting from a conference at once.

Storify - Storify can be used to collate tweets (by searching by the hashtag) and other social media posts about conference topics and sessions into one readable online document. Really easy to use. The document can then be shared on twitter, or embedded into blogs. Storify can handily notify all the people who have tweeted about the session too (if you include tweets from them in your storify). If you do want to storify, I find it easiest to storify a session as you go, otherwise you might find it difficult to find all of the content. There are some tools that allow you to search on twitter see here.

Topsy - Topsy collates information about a search topic from twitter and the web. So you can search for a conference name/hashtag and get all the web posts and tweets that relate to your search term. Great for looking at online content and tweets. Click 'experts' on the left hand side and get a list of tweeters who have a number of mentions.. follow them on twitter and you are likely to pick up a lot of content related to the conference/topic.

- Slideshare - Share slides online...!

For keeping in contact with people you meet at the conference I find following them on twitter and adding them on linkedin is the best solution. I haven't managed to get round to finding any handy tools that beat writing a bit of information including their twitter @ on the back of their business card for remembering who I have met where, and who they are!

If you are sharing things from a conference talk or session, try and ask the speaker before sharing anything. If they are sharing new results, they might not want them splashed all over the internet...

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