Liam vs Conro; the lab challenge round 1

Liam and Conro started their PhD studies in the Hamill lab in October, Liam on a BBSRC DTP and Conro supported by the IACD managed Crossley Barnes endowment. Unsurprisingly, both are working on laminin related projects but asking different questions in different contexts. Additionally , and also unsurprisingly, there is a bit of competition between them so it seemed only appropriate that we would welcome them to the lab with a series of games with the two guys being team captain in every game but with different other lab mates to support them.


First up; a lllama themed game! A mixture of charades, articulate and Pair matching game. Great fun. Conro’s team, despite some amazing acting by JohnJohn (in video he is acting out Nicolas Cage falling off a stage), lost comprehensively. Some might think a key example of how his team was let down was lee struggling to guess otter from a description of the “best animal that holds hands as it floats away” but really it was that Liam had the advantage of having Karen and myself in his team.


Next, a super quick game of beer pong while waiting for a taxi. how this game went is summed up by the video above… Liam , lee and JohnJohn were off their game and conro ultimately won easily. 2 games down , score 1 – 1.


Next, a couple of games of pool. Both captains won one each principally driven by whichever team had lee on it! 2 – 2

And then, the main event; Shuffleboard. On the sandiest table I’ve ever played on. Here you could tell that the presssure was beginning to get to the boys as stones were flying off in all directions. However, as a team game, Liam streaked into an early lead only for conro to pull it back so it was close going into the final ends.


Cometh the hour, cometh the man. Conro took the win and the championship (or at least round 1!) with the shot below… what a way to win. At this point I would mention the staff vs students game but I don’t feel that it is necessary to point out how much better Valentina Karen and I were…

All in all. Awesome fun, I’ve assembled a great team. It’s been awhile since we’ve been out together but I’m really glad this somewhat spontaneous night was arranged. Many thanks to all involved.

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They grow up so fast – JohnJohn’s 1st year talk

Today JohnJohn Knox had his end of 1st year of PhD talk (upgrade seminar). JohnJohnJohn is working on trying to develop a new molecular therapeutic for glaucoma on a project sponsored by UK charity Fight for Sight. He has three supervisors; Colin Willoughby, George Bou Gharios and myself and while Colin is the real driver behind this project (it is his grand plan), George and I contribute our expertise to guidance. and are likely to take a bigger role as he enters the next phase of his project.

JohnJohnJohnJohn did really well in his talk, presenting to a packed seminar room with most of the faculty from IACD in attendance. He did particularly well in dealing with some tricky questions in a really confident and effective way. He got some nice comments and suggestions for future work too so should be off designing new experiments as I write this!

There is some cool stuff coming here so expect more news about JohnJohnJohnJohnJohn’s progress in the near future.

 

JohnJohnjohnjohn

JohnJohn adopting the “intense stare at supervisor” approach to presentation giving

 

If anyone is wondering where they have seen JohnJohn before… he was the face of the sunscreen trial! Famous throughout the land after featuring in most major newspapers and on ITV!

Pratt Figure 1c

 

Sunscreen challenge; article in press

Today the primary research that led to the sunscreen challenge, and all the posts (and TV shows) that you have must seen by now, was published.

The link to the paper at the PLOS one site is here. Have a look, download the paper, make a comment, tweet directly from the site (rather than retweeting this). Will all boost our altmetrics and help the article get some attention. If you prefer a the press release version, check out this link to the University of Liverpool website from when we were promoting this work in relation to the British Association of Dermatologists meeting. camera

Want to see more about our public engagement events related to this work? Check out these posts here, here (filming for ITV), here and here

 

The Sunscreen Challenge turns out for Eye Health Week

This week is Eye Health Week, promoting the importance of eye health and the need for regular sight tests for all. To mark the occasion, a bunch of really interesting stalls showcasing research and raising eye health awareness were on display in the reception of St. Paul’s Eye Unit

One of these stalls was the Hamill Lab’s ‘Sunscreen Challenge’, using our UV modified camera to image the areas people miss on their face when applying sunscreen. The research paper relating to this has just been accepted, so you should see that published soon.

UV setup

Set up camp in the reception area of St. Pauls Eye Unit

The sunscreen study showed that people are pretty bad at applying sunscreen to the area around their eyes. The reason this is so important is that although the region around our eyes is only ~1% of our skin’s make-up, but ~10% of skin cancers are found here. Removing tumours from around the eyes is a difficult task, and can be potentially disfiguring.

 

The Sunscreen Challenge stall had great interest from patients and NHS staff, with many people saying how it had never crossed their minds to take care to protect the area around the eyes. Encouragingly, these people also said that they would definitely be more careful in future to protect the region around their eyes through hats, shade, and improved application, showing that our message was getting through! Success!

It’s also refreshing to get out and speak to the public about our research. There’s an extra level of motivation that comes from knowing that real people will benefit from scientific research carried out in the lab.

Overall it was another great outing for the sunscreen challenge, and who knows where it will next pop up!

Which lab book are you?

Everyone “knows” the importance of lab book keeping. Everyone, but only a few actually realise the implications. If you are a new scientist you “know” the importance, well, simply because you were told as. And you actually try to keep a good lab book so you can have your supervisor off your back or, even more importantly, because you get credits out of it. If you are an experienced scientist, then you probably felt the implications of good lab book keeping, but hey, you are too busy now to put down every single detail, let alone the fact that you already know all your protocols by heart and you remember whenever you make some slight changes. Da Vinci was so good that we can actually build all the “contraptions” he designed half a century ago.

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Figure 1: Da Vinci knew the importance of good note keeping. Do you?

Let’s take a test. Pick your lab book, look through the pages and give it a mark. Quick, don’t overthink it. I can guarantee you that however you marked it, the score should be actually lower. How can I be that sure? Then answer to yourself with a simple yes or no to the following questions.

2Do you have the date in each and every page of your lab book?

Are all the pages numbered?

Do you have a table of contents, or at least left the first few pages purposefully empty?

3Do you start each new experiment on the right page?

If you do a mistake how do you cross it out? (hint: mistakes should be readable)

Do you have blank pages? (Another hint: you shouldn’t, every white space should be crossed out).

And if we want to take it a step further, have you had someone else sign every completed entry? Do you sign over your corrections?

More importantly, can you or someone else of relevant background come back after 6 months, make sense and repeat the experiments while obtaining the same results? (duh!!!)

As the U.S. patent law states

Inventorship is determined by the “first to invent”, not the “first to file”.

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Figure 2: Table of Contents, yes you need one.

In the end, it doesn’t matter how good you are with a lab book. Its nature alone has some fundamental issues that prevent it for being good enough. Dr Nick Morris successfully summarises what is inherently wrong with lab books (even if it’s not your fault). Here is small preview but make sure you check his article to fully understand the rationale behind the next 7 bullet points.

  1. They are not searchable
  2. They may be portable, but they are not ‘shareable’
  3. They are ethically unsound
  4. They are prone to errors
  5. They can’t be backed-up
  6. They can’t be standardised
  7. They are a source of potential contamination

I’ll let you on a secret, I am terrible on keeping a lab book. My handwriting is that of a 6-year old, I am over confident in the way that I wait to see a significant result before I record the changes that led to it and I answer negatively most of the previous questions. It is like trying to read Aristotle and make sense with the first read-through, not going to happen.

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Figure 3: DId you know what we consider today Aristotle’s work is actually his lecture notes? (That’s why is so damn hard to make sense of them)

So? Does that makes us bad scientists? I would like to say NO. We are bad scientists only as long as we do not try to improve upon our deficiencies.

It is the 21st century people, all the information around us is in digital format. We read in digital, we listen in digital, watch in digital. Then why don’t we keep notes in digital as well? Most of the times a today’s lab book is just printed data, protocols and results from a PC (or Mac, really?) and pasted into the lab book. So let’s move. E-books are the solution.

There are so many of them out there, you just have to pick which one you prefer to use. A lot of them are free for users (and some of them for small groups) and each one has its own strengths and weaknesses. You can even find one perfect for CRISPR if you are into gene modification. Most of the time a couple of minutes of previewing are enough to make up your mind. So here is a list for you to try. Go ahead 🙂

  1. SCINOTE

PROS:

  • Very user-friendly and quick to set up
  • Unique experimental workflow
  • Open source license (MPL)
  • Free account with unlimited project users

CONS:

  • Drawing molecules still in development

 

  1. BENCHLING

PROS:

  • Very user friendly and quick to set up
  • Useful DNA tools (CRISPR guide and primer design)
  • Templates for sequence mapping and sharing
  • Free account with 10 GB of storage space

CONS:

  • Free account is tied to a single user
  • Report structure is not flexible

 

  1. RSPACE

PROS:

  • Possible archive management, built-in metrics and analytics
  • Can connect to the eCAT sample tracking system
  • Supports chemical structures
  • Free to use

CONS:

  • No local installation
  • Not open source

 

  1. LABFOLDER

PROS:

  • Sketching
  • Free account for smaller teams and free mobile app
  • Integration with Mendeley

CONS:

  • Not very intuitive
  • Unflattering structured design
  • Free version is limited up to 3 team members

 

  1. LABARCHIVES

PROS:

  • Pubmed references entry editor
  • Interface with GraphPad Prism

CONS:

  • Graphical User Interface needs to be improved
  • Quite complicated, extra training necessary
  • Very low amount of  storage space in free package makes it unsuitable for most users
  • Not Open Source

 

  1. DOCOLLAB

PROS:

  • Easy to use with useful tips
  • Free account

CONS:

  • Not possible to write comments
  • Not compatible with mobile devices
  • Local installation is not possible

 

  1. LABGURU

PROS:

  • Advanced tagging system for easy search
  • Track recording from batch number to concentration

CONS:

  • Not very intuitive
  • Project view too complex
  • No free license available
  • Expensive monthly subscription

 

  1. HIVEBENCH

PROS:

  • Plate designer
  • Free account with 10 GB of storage space

CONS:

  • Creating protocols is very rigid
  • No possibility to create tables
  • Free account is tied to ten users
  • Works only on iOS

 

  1. MBOOK 

PROS:

  • Supports all operating systems and browsers
  • Can be used in different fields of science

CONS:

  • No free account
  • No local installation
  • Not very intuitive interface

Happy note keeping 🙂

 

Thanos Papadimitropoulos, BSc, MSc | Eye and Vision Science | Institute of Ageing and Chronic Disease
University of Liverpool | Room 108.8 | The William Duncan Building |6 West Derby Street | Liverpool | L69 3BX

And so it begins…

Hi!  I’m Conro Sugden (aka Conor), and I’ll start my PhD in the Hamill Lab in October investigating  the mechanisms through which age and disease associated alveolar epithelial matrix changes drive development and progression of pulmonary fibrosis. This isn’t my first time being a part of the Hamill Lab; Dr. Hamill was my supervisor for 2 x 12 week projects during my MRes.

I studied my undergraduate degree in Biochemistry here in Liverpool, taking the chance to complete a sandwich placement at the University of Navarra in Pamplona, Spain (see below). Here I got my first taste of what it was like to be a research student, where I was part of a group developing novel plasmids to analyse Leishmania parasites.

Three Firsts

Three firsts: (Left to right) The first picture I took in Pamplona; My first conference poster; The first image I captured of Leishmania major parasites expressing our pXG-mCherry plasmid (kinetoplasts appear blue after staining with DAPI).

Following my undergraduate degree, I completed an MRes in Clinical Sciences, completing 3 x 12-week projects (2 of these projects, here and here, were supervised by Dr. Hamill!) in the Institute of Ageing and Chronic Disease, and this is where I fell in love with matrix biology. My work in the Hamill Lab so far has involved (with the help of Lee Troughton) using minigene constructs to investigate intron retention with alternative polyadenylation (IRPA) in the LAMA3, and then following up this research testing ways we can manipulate this ratio. The data from these projects has been exciting and encouraging, and I’m glad that I get to carry on being a part of this.

During my time in the Hamill Lab I’ve attended my first Burns night, an awesome ‘Assembly, Dynamics and Organisation of Filaments and Cellular Responses’ workshop at Durham University, and I’ve helped with the ‘Sunscreen Challenge’ at Meet the Scientists and other outreach events.

Time in the Hamill Lab

From my time in the Hamill Lab so far: (Left to right) Project 2 presentation; project 3 poster; Sunscreen Challenge preparation.

I’m in the process of becoming a STEM ambassador, and I’m planning to bring the ‘Sunscreen Challenge’ to my old high school so that I can talk to the students about what it means to be a research student. Alongside my PhD research I’ll continue with the outreach activities, and I’ve also enrolled onto a Spanish language course (can’t let myself forget everything I learned when I was over there – I will be fluent one day!). Recently I wrote for The Biochemist blog about the link between inflammation and fibrosis, you can find that here.

Going forward, I couldn’t be happier to begin my PhD in the Hamill Lab. The atmosphere is great, as are the lab members. The research currently being carried out is extremely exciting, and I can’t wait to get stuck in and make my contribution to the field.

Thanks for reading,

Conro 

 

You can see a lot by looking – TIRF

Time for a new series. “You can see a lot by looking” basicaly cool images from our research + a little explanation. Microscopy in its various forms has always been one of my favourite things to do, especially when trying out new modalities that open up opportunities to ask new/deeper questions, so I figured we might as well show off some of our pretty images.

#1 in the series is from today; Lee and I used the new Total Internal Reflection Fluorescence (TIRF) microscope at the University of Liverpool’s Centre for cell imaging. This was the first time we have used this microscope and these are just a couple of a set of really nice images, acquired thanks to the expert help of Dave Mason (@dn_mason).


Why is it cool? Well, TIRF is pretty awesome. Basically, whereas normal microscopy involves illuminating the sample directly and then collecting either the transmitted light or the reflected light depending what you are looking for, TIRF involves illuminating the sample at a shallow angle and collecting the light that is internally reflected  (the same principle that fibre optics work by). The practical upshot of this is that when you image at the critical angle, you effectively limit the illumination to near the cell substrate boundary, the bottom ~75nm (1/750,000 of a mm!). You can see the difference this makes in the images below; left = TIRF, right = conventional imaging. Without the TIRF it is much harder to see the fine organisation of the protein at the bottom of the cell.

How are we using it? Well in the magenta and green image, we have imaged live corneal epithelial cells where we have induced expression of the LaNt alpha31 protein with a green fluorescent tag and laminin beta3 with a mCherry tag (shown in magenta) and while the whole cell expresses these proteins, we have limited what we are looking at to just the point where the cell is touching the glass. So here, where we see codistribution of signal i.e white, it’s showing the LaNt and the laminin are close together at the bottom of the cell. The green only signal, e.g. on the left middle, is where there is lant but limited laminin or vice versa for the magenta. In the image below, I have split one of our other images into its component parts (left=LaNt, right=laminin), in this cell there is a much closer match up in the patterns of the two proteins. Proximity alone doesn’t mean interaction but these data add to the other pieces of the story that we are building about how these two proteins influence each other. FYI the scale bar in the image below is 10 micrometers, 1/100th of a mm, you are looking at just a small part of one cell)

TIRFcr
This ‘scope itself pretty amazing, not only can you do TIRF but also Atomic force microscopy at the same time. Looking forward to the next set of experiments…

Sunscreen challenge filming for ITV

Yesterday the TV cameras were in IACD filming a programme about summer sun for which our little piece about sunscreen will form a part. Here are some pics of Austin McCormick, eyelid cancer specialist and co author of the forthcoming paper, being filmed for his contribution. As my wife said, “Austin has the better face for TV!” Watch out for the show sometime in August.

Kareem trying to convince Austin that he knows what he is talking about!

Austin in action

Discussing the images

Thankfully (for the story) the kids did miss their eye area and especially the medial canthus

Austin on the monitor

Dr Iorio! 

They grow up so fast – PhD viva edition!

On Thursday my first PhD student Valentina Iorio defended her thesis at her viva voce examination. An incredibly proud day for her and for her supervisor (I,e. Me!)

 It was a thoroughly unusual day; due to a clash in commitments of her external examiner, Vale, myself and the internal examiner Dr Simon Tew traveled up to the university of Dundee on thurs morning. In essence, a reverse viva then took place with the “external” examiner Prof Irwin McLean hosting us in his dept. Valentina gave a seminar to Irwin’s lab and that plus her thesis clearly impressed as the rest of the exam felt like a foregone conclusion and more of a discussion of what to do next rather than a defence of what she did. 

In a circle of life type thing, Prof McLean was my PhD supervisor and so Valentina is not only my first sci “child” but also Irwin’s first “grandchild”. Valentina was also the first person to join my lab and has been instrumental in all that we have done. She read all my first grants and taught everyone who followed how to do things. In the last few months since leaving the lab to write up and go on her honeymoon it’s been really apparent how much she is missed!

I’ve posted a bunch of other things about Valentina’s work here here here and here so for now it’s just time to say congratulations Dr Iorio!

Valentina en route to viva!!!

Hello readers!

It’s Valentina here, the first PhD student to have joined the Hamill’s lab. I am writing my first article on a very special day…on my way to Dundee to defend my thesis! It’s been a really cool adventure, full of incredible discoveries. 

When I have started, the only available data on LaNts were related to the skin; after three years and many exciting experiments we now know the effects of LaNt a31 in the cornea…which may seem only a little organ of the body, but how amazing is it to be able to see the world?! We have loads of beautiful videos of live laminin’s deposition from corneal epithelial cells and we have established a LaNt a31 overexpression animal model, the first one ever! 

Working in this lab has been fantastic and hopefully today I will be able to transmit my excitement to the examiners 🙂 If my work could open at least one more door to future projects and ideas, then I’ll be doubly proud. 

Going on, the Hamill lab, laminins and LaNts are waiting to be completely undercovered 🙂  much more to follow on this exciting topic…

Soon to be (hopefully) Dr. Vale