2017 Sée Lab Nuffield Students

In the summer of 2017, two year 12 students from the North West of England visited the Centre for Cell Imaging on their Nuffield research placements.

Their placement involved testing a semi-high-throughput screening method for anti-cancer drugs using cell-migration as their readout. They worked with a Glioblastoma cancer cell line during their time in the facility and shared the following comments about their experiences:

 

Charlie Fogg:

“I believe that this summer placement at the University of Liverpool was the greatest experience of my life, and I will always remember it as the reason I firmly decided that this was the career in which I needed to pursue. I believe that this summer was an eye-opening experience into the real world of science, specifically cell microscopy, and it gave me countless new ideas and theories which I will take away with me into the future, and hopefully begin to research into myself one day. The placement inspired me to want to carry on pursuing science for the rest of my life and fed my ambition to achieve in a new world which I now see with many more possibilities than I had originally perceived.”

Fahda Albaba:

“This summer was not the same of all my previous summer, it was amazing and interesting because I spent it in department which I’d like before to be on, I learnt a lot of useful things: using high demand microscope, experiment skills as well as the importance of organisation, planning  and time management for each project. This placement gives me the chance to recognise the enjoyable feeling of practical and research world. Also this project allows me to deal comfortably with analysed imaging software which I am never deal with before, these wonderful software will make me think more deeply about the experiment, is not the same of the past (just follow the instructions).”

 

U87 cells stably expressing a red nuclear marker. Timestamps are HH:MM

Quantum dots for Immunofluorescence

Guest post by Dave Mason; reblogged from rapha-z-lab

In modern cell biology and light microscopy, immunofluorescence is a workhorse experiment. The same way antibodies can recognise foreign pathogens in an animal, so the specificity of antibodies can be used to label specific targets within the cell. When antibodies are bound to a fluorophore of your choice, and in combination with light microscopy, this makes for a versatile platform for research and diagnostics.

Most small-dye based fluorophores that are used in combination with antibodies suffer from a limitation; hit them with enough light and you irreversibly damage the fluorochrome, rendering the dye ‘invisible’ or photobleached. This property is the basis of several biophysical techniques such as Fluorescence Recovery After Photobleaching (FRAP) but for routine imaging it is largely an unwanted property.

Over 20 years ago, a new class of fluorescent conjugate was introduced in the form of Quantum Dots (QDots); semiconductor nanocrystals that promised increased brightness, a broad excitation and narrow emission band (good when using multi-channel imaging) and most importantly: no photobleaching. They were hailed as a game changer: “When the methods are worked out, they’ll be used instantly” (ref). With the expectation that they would “…soon be a standard biological tool” (ref).

So what happened? Check the published literature or walk into any imaging lab today and you’ll find antibodies conjugated to all manner of small dyes from FITC and rhodamine to Cyanine and Alexa dyes. Rarely will you find QDot-conjugated antibodies used despite them being commercially available. Why would people shun a technology that seemingly provides so many advantages?

Based on some strange observations, when trying to use QDot-conjugated antibodies, Jen Francis, investigated this phenomenon more closely, systematically labelling different cellular targets with Quantum dots and traditional small molecule dyes.

Figure 3 from doi:10.3762/bjnano.8.125 shows Tubulin simultaneously labelled with small fluorescent dye (A) and QDots (B). Overlay shows Qdot in green and A488 in Magenta. See paper for more details. 

The work published in the Beilstein Journal of Nanotechnology (doi: 10.3762/bjnano.8.125) demonstrates a surprising finding. Some targets in the cell such as tubulin (the ‘gold standard’ for QDot labelling) label just as well with the QDot as with the dye (see above). Others however, including nuclear and some focal adhesion targets would only label with the organic dye.

The important question of course is: why the difference in labelling when using Quantum Dots or dyes? This is discussed in more detail in the paper but one explanation the evidence supports is that it is the size of the QDots that hinder their ability to access targets in the nucleus or large protein complexes. This explanation further highlights how little we really know about the 3D structure of protein complexes in the cell and the effect of fixation and permeabilisation upon them. Why for example, can tubulin be labelled with QDots but F-actin cannot, despite them both being abundant filamentous cytosolic structures? At this point we can’t say.

So why is this study important? Publication bias (the preferential publication of ‘positive’ results) has largely hidden the complications of using QDots for immunofluorescence. We and others have spent time and money, trying to optimise and troubleshoot experiments that upon closer study, have no chance of working. We therefore hope that by undertaking and publishing this study, other researchers can be better informed and understand when (or whether) it might be appropriate to use Quantum Dots before embarking on a project.

This paper was published in the Beilstein Journal of Nanotechnology, an Open Access, peer-reviewed journal funded entirely by the Beilstein-Institut.

 

Thoughts on #LiveTweeting

As a part of the Centre for Cell Imaging and a member of the Microscopy and BioImage Analysis community, I occasionally get away to conferences like the recent NEUBIAS training school and symposium in Portugal.

Since having joined Twitter last year (@dn_mason), this is the second conference that I’ve been to, and as a result, was the second time I tried (with reasonable success) to Live Tweet at the conference.

Live What Now?

Going right back to basics, Twitter is a platform for broadcasting small messages (of ~140 characters). Some describe it as micro-blogging. To many, the brevity of each tweet is both it’s greatest strength and also one of the most frustrating features.

Live tweeting, is basically the act of providing a running commentary of a seminar, event or even a whole conference. All of the tweets associated with such an event can be tied together using a text-tag called a #hashtag (which starts with a hash like that last one).

You can always go back through the twitter website (or app) and see all of the tweets associated with a hashtag. For example, check out all the #NEUBIAS tweets.

OK, I get it, but why bother?

I find myself being asked this question quite a bit. So here are my three main reasons for live tweeting (in no particular order):

1. OPEN NOTEBOOKS: Like most people these days, I have way too much paperwork. Between manuscripts, notes and admin, the last thing I need is more paper on my desk. By live tweeting, I can keep track of who presented what, and when (and, what I or the audience thought of that in the question periods/breaks). Once you get the hang of it, you can check and record links to papers and websites on the fly so you know that you’ve not made a mistake in writing down the the URL (especially important if your handwriting is less than clear). Everything is time-stamped and fully searchable so it’s easy to find that note you took six months ago (can you say the same about your regular notebooks?).
2. ACCESSIBILITY: Plain and simple, live tweeting, gives people who aren’t at the event access to some of the ideas, thoughts and opinions that are expressed there (see endnote #1). Perhaps you’re off at another conference but want to stay abreast of the latest research, or maybe your budget doesn’t stretch to a trans-atlantic flight. Furthermore, this taps into the idea of open science. By sharing your ‘notes’ via Twitter, everyone gets interactive access to them and the community can start a conversation around them.
3. NETWORKING: This might be a slightly broader point, but a lot of scientists use Twitter. By becoming part of the twitter ecosystem surrounding an event, you will probably find it easier to get yourself and your work known. You’re also becoming a bigger part of the community and getting involved with discussions to which you would otherwise be oblivious.

Tips for Tweeters

I am by no means a twitter expert (a twexpert?) least of all regarding live tweeting, but below are a few tips that might help you to get started:

1) Ditch the default website

At least 3% of your screen here is taken up by beard.

The twitter homepage (above) may look nice but it’s really inefficient on space. Once you move to Tweetdeck, you will never look back. Tweetdeck is a very customisable app built into twitter. Compare the image above with the one below. Left to right, I have my home feed (tweets from people I follow), my notifications (people talking directly to me or interacting with my tweets) and the #NEUBIAS hashtag, all on one page.

You can add as many columns as you want, so you can follow individual people, hashtags or direct messages, tailoring exactly what you see in each column (likes, retweets, follows &c)

2) Tabbed browsing

It’s fairly obvious that Twitter is a web application (see endnote #2). So you probably already have a web browser open. Learn how to use and manage tabbed browsing, so you can quickly search for websites (IE the speaker’s homepage), papers (PubMed or your equivalent repository), or relevant links that you might want to come back to later. Learn shortcuts to quickly switch between and close tabs.

3) Links and Hashtag

Does the speaker use twitter? If it’s not on their title slide, a quick search is a good way to find out:

Assuming you don’t have a ridiculously common name…

If they do, include it in your tweet. It lets them know that people are discussing their work and opens up another avenue for discussion (once they’re off the stage).

Where is @dn_mason 's amazing #NEUBIAS twitter feed?!?! Oh… he's on stage… guess thats the only way to silence his feed… 😉 pic.twitter.com/hZEkJluXfy

— Florian Jug (@florianjug) February 17, 2017

This also helps with the visibility and networking mentioned above. Same idea goes for hashtags. If the event has a tag, use it in every tweet. Also, try to hashtag topics that will expose your tweet to others who might find the content interesting. #Don’t #over #do #it #though.

4) Harness the power of images

A tweet with an attached image is more visible and easier for you and others to find later when scrolling down a timeline. I try to add images at least once per logical break, even if they’re screen grabs from a website or company logos.

Get to know how to screengrab, crop, save and upload an image quickly on your platform. Most browsers can open PDFs directly so you don’t need to download and open in an external application to screen grab an interesting figure or notable schematic from a paper. Make sure you include a link (a DOI or URL) so people can put the image in context.

5) Get to know the tweeps!

As I said before, a lot of scientists use Twitter. Try to figure out who are the people tweeting at a conference and make sure to follow them to see what they’re talking about. You may find extra insight or perhaps an interesting discussion point in which you can get involved (on or off-line).

The last word…

Live tweeting is not for everyone, but hopefully I’ve given you some reasons why you might at least want to follow a conference hashtag, even if you don’t contribute. Like any community however, the more people that get involved, the more everyone benefits.

 

ENDNOTES

#1: There is a really interesting discussion around this point, which extends to recording and/or streaming a conference. The argument goes that if people can “be at a conference” from their computer why would they ever pay the flight/hotel/conference fee to go to a conference in person? To me, this argument is patently ridiculous. Attending (most) conferences is about being part of a community, and this is a 2-way interaction. Some of the most interesting discussions happen over drinks or at meals, not necessarily during the talks and question periods. I’m fully for recording and streaming talks at conferences, and I seriously doubt that this would impact attendance.

#2: Many people use Twitter on their smart phones. The one and only time I do this is if I want to take a photo and tweet it directly. Otherwise, it’s just too slow and lacking in the editing / lookup tools (eg. good tabbed browsing) and screen real-estate to make the most of tweetdeck. If you can, always use a laptop or maybe (if you’re really good with it) a tablet.

11 Nuffield students visited IIB this summer

This past summer, the Institute of Integrative Biology has once welcomed Nuffield students, just, many more than last year. Thank you to Jane Hurst, Michael Gerth, Philipp Antczak, Violaine See, Luning Liu, Dave Mason and Raphael Levy for providing these placements.

Welcome Chloe Rodgers and Jamie Patient to work in Liu Lab as Nuffield Placement students 2016. #nuffieldiib pic.twitter.com/ZMo7jDYZEf

— LiuLNLab (@luningliu) July 20, 2016

 

Looking fwd to hosting @NuffieldFound students at the @CCI_liv.

Can we use #cell & #nucleus shape to assess health? pic.twitter.com/CqG8J0QaQh

— Dave Mason (@dn_mason) August 8, 2016

 

Nuffield students Bibin @CarmelCollege and Jess @LiverpoolBCS acquired hundreds of images of cells @CCI_liv today! https://t.co/UFkTHUlo6R

— (((Raphael Levy))) (@raphavisses) August 19, 2016

Work Experience Placement in the CCI

Dania Al-Baden, a year 12 student from Notre Dame Catholic College spent a week in the Centre for Cell Imaging:

My placement was for 1 week in December in the Centre for Cell Imaging at the University of Liverpool. I was able to work with some students who were using the microscopes for their projects and learned how microscopy helps them conduct their research which was very enlightening. Working in the lab has also taught me some key skills such as pipetting very small volumes as well as how important it is to avoid contamination in cell culture.

The staff in the CCI was amazing, friendly and helpful. I worked with Joanna, Joan, Marco and Dave who have all inspired me to carry on my studies with science. I enjoyed my time immensely in the CCI and I would love to come back as well as recommending it to other students who have an interest in this field.