Standing up for Science, Pt. 1

On Friday 26th June I attended the VoYS Standing up for science media workshop. It was a fun and informative event chock full of great advice to budding science communicators and scientists wishing to learn/take part in science journalism/media. The following will feature advice from the day that was memorable to me and may not reflect the workshop as a whole. Check out a summary of the day written by SAS themselves for a more balanced perspective.

The first panellist to speak was Dr. Jeremy Pritchard. I’d heard about Jeremy from those who’d studied within UoB’s Biosciences department. I also followed him on Twitter and knew he had a lot to say on teaching and biology (which makes sense as he is a biology lecturer!). I really enjoyed his recap of experiences within the media, especially the televised evolution vs. creationism debate he unknowingly became a part of. More importantly, one particular sentence he spoke early on stuck with me:

“Show responsibility for being a scientist”

For the past few years, I have tried to give back to the community through outreach/engagement volunteering but have never considered it a responsibility. My reasons for volunteering, apart from the fact it is super-fun, do include spreading my enthusiasm and (little) knowledge of science to the interested public. Past this, I try to point out bad science/claims where I can, but find that I don’t encounter this within my circles as most people I interact with on a regular basis are scientists.  I do believe Jeremy is right though. I think we as scientists do have a responsibility to disseminate knowledge and do what we can to promote scientific literacy, especially to those who do not have the education to begin with.

The last point mentioned above was by Jane Symons, a science and health journalist who has written for many tabloid newspapers. She stated that the main readership for The Sun newspaper were those from working class and/or uneducated backgrounds and thus they would be the ones who needed health news the most, especially if it could potentially save lives in the long run. The discussion of this point was interesting, as it made the idea that a health news story that was sensationalist or misrepresented (which most scientists dislike, from what I gather) less black and white. If by sensationalising, the news makes headlines and is read by a chunk of the public who could benefit from it, isn’t that a good thing? Importantly, I’m not endorsing this tactic, but I did find it interesting. The media, which I always regarded as black and white, does have a massive grey area. I also liked Jane’s description of how a typical day in her life works. A lot of it seems to be checking emails and press releases, making sure to read everything just in case she ever misses a great story. It seems very fast-paced and even more stressful when compared to a day in Academia, but may suit some folk.

[On a different note, I liked Jane’s description of a “bollocking box”, a room where you would be taken to be told off in by an editor/superior. I wondered then if there’s a bollocking box in my head and that’s why I criticize myself so much..!]

Dr. David Gregory-Kumar, whom I had first seen at the Birmingham Cafe Scientifique a while back, was charismatic as ever and gave some insights into his job as Science & Environment correspondent for the Beeb WM. I particularly liked the idea of “dicking about” and “noddies” in video’d news reports, where scenery, the reporter/interviewee are filmed looking into the distance or nodding to nobody, possibly from multiple angles, all edited later with voiceover to generate the feeling of a continuous dialogue within the news report.

Great advice from Dave included:

NO COMEDY T-SHIRTS

NO SLAGGING OFF WOMEN” – (Tim Hunt was mentioned a few times in this workshop, mostly in the context of, “please please PLEASE nobody do what he did”)

Jokes aside, (well, almost), Dave went on to talk about how news stories are selected for publishing/videoing- they have to the CFM factor. What is that, you say? “Cor, Fuck Me!”, a sentence uttered by someone upon hearing your science news. If your news can induce this, you’re onto a winner. This probably isn’t how it works all the time, but I would like to think it happens in the majority of cases.

I will write another post soon commenting on the group sessions and some of the lessons learnt from other panellists.

Thanks for reading!

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A Post-doc in need of guidance

The title of this post is somewhat misleading as it is not I that needs the guidance but one of my friends (who I shall refer to as X), who shall remain anonymous. All I can say is they did their PhD in the U.K and are 2/3 through their first post-doc in the U.S – and hated every second of it. Now, I won’t go into any detail as to why this is the case with my unfortunate buddy, but they are looking to come back to work in the U.K. After some discussion, the NHS Scientist Training Programme comes up. X is thinking of applying but does not know anybody who has gone through the process and what it’s like.

This is where you come in! Have you been through the programme? Would you mind answering some questions X prepared? If the answer to both of these questions is yes, awesome! Please answer in the comments below. If you don’t want to answer but would like to help in some way, shape or form, please feel free to contact me via twitter or the comments.

If you know someone who has been through the programme, please forward this post to them, it would help out a lot!

And now without further ado, the questions:

1) What is the starting salary and what does it increase to and level off at?

2) Does the salary cap depend on the area of specialty?

3) Are you guaranteed a job after you finish the programme or do you have to look for a job with the NSH and apply+go through interviews again?
4) How different is the day-to-day or week-to-week work Vs. post-doc, is it more translational with immediate impact?
5) What do they look for in a candidate, relevant experience or translational skills or both? i.e would a protein biochemist/structural biologist be appropriate?
6) What’s the work/life balance like? Regular hours i.e 8 a day with odd weekend shifts now and then?
Thanks for reading. It’s shameful that this is my first blog post for over 3 months. This will likely change once I’ve written and submitted my thesis so hold tight for now and expect some bloggy goodness come start of April.

Virocopia

Viruses have been an interest since first learning about their existence. My academic interest also became sci-fi interest when Resident Evil and the so-called ‘T-virus” associated with the franchise emerged. Though our RE knowledge is feeble at the best of times, it didn’t stop my friends and I from having awesome discussions during break times; we would (as most kids our age undoubtedly would) attempt to hypothesise a likely mechanism that would cause an organism to die, only to reanimate moments later as an icky, brain-eating zombie. “What if” questions such as, “What if the T-virus mutated and no longer left you mindless and out of control whilst infected” stirred our imaginations. What if it gave you powers instead, like in the comic books? What if scientists could cure diseases using viruses? What if natural viruses weren’t all that bad? Most of these questions are being addressed at the moment by scientists (I’m still waiting on that Super Soldier Serum from Captain America), gene therapy being the flavour of the month when it comes to utilizing viruses to treat diseases, particularly those with a genetic origin.

Unfortunately, viruses still get a bad wrap in the realms of the public eye. Bird/swine/seasonal flu, norovirus (or winter vomiting bug), cold viruses and HIV make infrequent appearances in the media, as well as emerging outbreaks of MERS and other hyped epidemics viral in origin. That isn’t to say they shouldn’t get media attention at all; at times it is useful to engage and educate the public in spotting the signs of illness and what to do in the event of suspected viral infection. But in general, viruses are often dismissed as plagues of humanity and nothing more. Few come to understand the importance of viruses in the ecosystem, and appreciate their diversity and role in Life’s history.

Earlier last month, a Virology buddy bought me a copy of Virus Hunt by Dorothy Crawford, which I finished just over a week ago. This was a like for like birthday gift, as I had bought them a copy of Virolution by Frank Ryan previously, which I had finished in July. Both were great reads and are thoroughly recommended to anybody fascinated by viruses. The books may not be the best ‘introductory’ peepholes into virology, but keep you enthralled while they take you on a journey into the evolutionary history of HIV (Virus Hunt), and the way certain viruses may have had a hand in shaping the evolution of Homo sapiens (Virolution). 

Front cover of Virus Hunt

Front cover of Virus Hunt

One of the things I loved about Virus Hunt was the way it tied in historical events with the rise of the HIV pandemic; you really come to appreciate how difficult it is for particular viruses to cross the species barrier (this can range from near-impossible to almost-certain in probability) AND maintain an infection within a population. Too harmful, and your host will die before they get a chance to pass it on. Sometimes however, as is the case with HIV, opportunity favours those who are prepared to take it…and it just so happened that the area HIV sprung up in was undergoing some major changes (in population, way of life, you name it..), which ultimately allowed World domination.

Virolution was great in that it covered a myriad of topics, all relating back to viruses, allowing the reader to immerse themselves in a viral pool of knowledge. Chapter 1 had me hooked, and this is why:

Not only is this creature beautiful, it is also has a fascinating life history. Organisms like this make me wish I did Zoology instead. Anyway, read Virolution if you get a chance, you won’t be disappointed!

I can’t mention viruses and leave out one of my favourite things about them: what they look like! Viruses come in all shapes and sizes, some being tiny, like the porcine circovirus type 1, rolling onto the scene with a capsid (protein shell of a virus) diameter of only 17 nanometres, and some being huge, like the pandoravirus (what a gnarly name), reported to be around 1 micron (1000 nanometres).

Rather than taking on the same bucky-ball type structure, viruses have evolved capsids of varying shapes. Take tobacco etch virus for example. Or the T4 Bacteriophage. And yes, the latter is a virus. Not a miniature spider, an actual, bacteria-hunting virus. How do they end up having these shapes? As it happens, viruses are made up of proteins and contain a genome, just like other organisms.

One particular structure found within the bacteriophage particle is the connector region which, surprise surprise, connects the head and tail portions of the bacteriophage together. A research group based in Toronto, Canada published a paper outlining the crystallographic structure of one of the connector region of ‘bacteriophage HK97‘, HK being short for Hong-Kong, where the virus was first isolated.

Connector complex of HK97  (PDB ID:  3JVO)

Connector complex of HK97 (PDB ID: 3JVO)

IT LOOKS LIKE A STARGATE! THIS IS WHY VIRUSES ARE AWESOME!

Ahem, anyway, another group published a structure of the entire HK97 capsid, piecing together the molecular architecture of HK97 bit by bit. This time, the focus of the study was gp5, a protein capable of assembling hexamers and pentamers (60 of the former form the faces, and 11 of the latter form the vertices). Along with a dodecahedron of the portal protein gp3, an intact capsid can form.

Left: Multimer of Hk97 capsid protein gp5. Right: Intact mature empty capsid of HK97

Left: Multimer of Hk97 capsid protein gp5. Right: Electron microscopy reconstruction of intact mature empty capsid of HK97 (PDB ID: 1OHG)

Viral capsid proteins are an interesting area of research in that most have the ability to form large complexes from a small number of the same proteins. The core HIV capsid coat is made of a single protein dubbed p24, which, like the gp5 protein of HK97 mentioned above, also has the ability to form pentamers as well as hexamers. When these larger complexes themselves form even larger complexes, we get a funny shaped capsid that looks like this:

HIV Capsid (Source: pubs.acs.org/cen/_img/87/i25/8725NOTWp8.gif)

HIV Capsid (Source: pubs.acs.org/cen/_img/87/i25/8725NOTWp8.gif)

Up until recently I thought HIV capsids were spherical or icosahedral in nature, but as it happens I was confusing the capsid for the ‘envelope’ of the virus. The envelope is made up of the host cell’s cell membrane, and gives most viruses the characteristic spherical shape you see in electron micrographs. However, a study published earlier this month dives into the structure and dynamics of the capsid protein that constitutes the HIV capsid and how exactly it is able to simultaneously form complexes of different sizes, and how then these complexes come together. It is quite an elegant study, using SAXS and residual dipolar coupling data collected by NMR, as well as ‘a novel computational framework’.

Hopefully I’ve given you a tiny glimpse into the Viral world, this post is by no means comprehensive and represents the reading and observations I have made over the past few months, all untidily squashed together to form what you’re reading now.

Viruses, their life cycles, genomes, proteins and interactions with the ecosystem they inhabit are a fascinating area of study, whose ingenuity and simplicity never ceases to amaze. The more we learn about these life-forms the more we learn about ourselves and, with a bit of lateral thinking, the more we understand about our own origins.

Thanks for taking the time out to read this, if you’re curious about the hidden lives of viral organisms, do check out This Week in Virology, also known as TWIV, hosted by Vincent Racaniello and friends. It is chock full of great dialogue and information, and is a pleasure to listen to. If you have any comments, constructive criticisms suggestions or questions, there is a home for them in the comments section below. Happy Virusing!

Going Loopy

My imagination is nothing to marvel at, but sometimes I’ll look at something and it will remind me of something entirely different. In this case, I was writing up my thesis at home and happened to glance at a charger cable on the desk, immediately it conjured up the thought of a loop region of a protein. Nothing too abstract, as in both cases the cable and protein loop are indeed loops, just on entirely different scales:

For those of you wondering, it's an old blackberry charger.

The resemblance is uncanny! For those of you wondering, it’s an old blackberry charger. Mundane, I know. (Protein PDB ID: 4DGP)

The protein I’ve chosen to compare the cable to is part of a larger multi-domain protein and is called an SH2 domain. I will probably cover this in more detail another day, but for now I can say that loop regions are important in proteins both structurally (connecting other bits of secondary structure together) and functionally (may contain amino acid residues important in binding other biomolecules and/or catalytic function, amongst other things).

Some research groups study the nature of protein loops, such as their dynamics – loop regions are often disordered, which means they flop around in solution and are able to sample a larger area of space than say, their more ordered cousins, the alpha helix and beta strand. Solution NMR can tease out the dynamics of amino acids in a protein (click here for more info). There are specific experiments one can do to obtain information on protein dynamics (measuring t1 and t2 relaxation times and relaxation dispersion experiments, more info here). Another, arguably lower resolution method than the ones mentioned above is to look at the individual models generated during structural calculations that used NMR data. Simply put, many models are generated (>1000) and are then compared and clustered so that an ensemble of structures are chosen that best represent the data you gave to the program. When NMR structures are submitted to the Protein DataBank, it is normal to submit the 20 best models. Superimposing these models on top of one another visually demonstrates how flexible a protein can be:

Spinach acyl carrier protein; superimposition of 20 NMR structures (PDB ID: 2AZA)

Spinach acyl carrier protein; superimposition of 20 NMR structures (PDB ID: 2AVA)

As you can see the helical regions of the protein are superimposing well (aside from the C-terminal helix; red), whilst the two loop regions in the foreground (green and orange) are not superimposing well at all, indicating dynamic nature. It is worth noting that loop regions can be ordered too (as can be seen from the above structural ensemble, the loops in light blue and yellow superimpose well).

X-ray crystallography can give an insight into protein dynamics too, through study of the temperature factor (also known as B-factor) of regions of the protein. In general, one can assume that the higher the B-factor value, the more uncertain you are of the exact position of the atoms that make up the amino acid residues- this information can be tied back to protein dynamics, though it is by no means definitive (i.e MORE RESEARCH IS NEEDED!)

Temperature values depicted on GCN4 leucine zipper helices. Blue: low, green-yellow: mid, orange-red: high. (PDB ID: 1ZIK )

Temperature values depicted on GCN4 leucine zipper helices. Blue: low, green-yellow: mid, orange-red: high. (PDB ID: 1ZIK )

I have personally never performed any dynamics experiments myself but find the research area interesting, as it can give a deeper insight into the behaviour of proteins and lead to a greater understanding of how they do the things they do.

Thanks for reading, if you have any comments or feedback do let me know in the comments section below or feel free to message me personally.

Have a good week and stay dynamic!

P,S There are a number of reviews out there on protein dynamics, particularly this one, though it may be pay-walled.

Sprayed Walls and Tiny Proteins

(I apologise in advance for not staying on topic long enough to discuss matters in more detail. This is largely due to my fleeting attention span at the time of writing and looming deadlines IRL. I hope you still like this relatively short post!)

This piece of graffiti I photographed whilst taking a stroll down Regent’s Canal reminded me of the secondary structure of proteins:

We may have a structural biology-literate artist on our hands...

We may have a structural biology-literate artist on our hands…

No magic eye images here thankfully, just an alpha-helix and two unstructured loops either side of it that have cyclized. I’m sure there are real-life examples of simple, short peptides like this. “What is the smallest structured protein?”, I hear you ask? Why that is a very good question….a question I will probably cover in more detail at a later date.

As a quick teaser (yeah right), here is the TRP-Cage miniprotein:

Kinda looks like a blue tapeworm splashing a dookie

Kinda looks like a blue tapeworm splashing a dookie, don’t you think?

This protein is composed of 20 amino acids and was truncated and mutated from a larger (39 amino acids) protein, Exendin-4, orginally isolated from the oral secretions of the Gila Monster. The authors solved the structures of both exendin-4 and the TRP-Cage miniprotein by solution-state NMR. The two share remarkable structural homology, as can be seen when they are superimposed:

TRP-Cage in cyan, exendin-4 in light pink

TRP-Cage in cyan, exendin-4 in light pink

You can find the original papers describing these two proteins here and here.

It was during an external seminar back in my undergrad days that I first heard  about designing proteins from scratch (de novo protein design) and the field of protein engineering. The field is part of the larger, more well known field of synthetic biology (loads of resources on the subject can be found here), but has found use in attempting to answer more basic research questions such as those in protein folding.

The idea of taking a protein out of nature, fiddling around with it, fusing it to another protein, mutating a few regions to alter binding ability or enzyme specificity is one that continues to fascinate me. We are now reaching the point in our collective understanding where we know enough about a given system or molecules to begin dismantling discrete portions and putting them back together in new ways to produce something with a curiously awesome function. The potential benefits and solutions such a discipline could bring to today’s problems is near limitless. I will most definitely expand on this in a later post.

Thanks for reading, and if by chance you know of any other small, folded proteins that can be mentioned in my eventual, longer post, please let me know in the comments section! You can also give your own input, including constructive criticism, in the comments section, and maybe get a discussion going.

Until next time, happy protein designing!

Who are you MSSD CNNCTN?

I live about 18 minutes away from my lab, within the grid system of Uni. of Birmingham’s unofficial student village, Selly Oak. I first moved here back in 2009 and apart from a brief (okay, 1 year and 3 months) stay in Five Ways (the name still makes me smile) it’s been this neighbourhood that I have called home.

Most of the time, walking to work involves switching to auto-pilot and listening to a podcast (I highly recommend The Pod Delusion and Little Atoms) but once in a while I will spot the graffiti a guerilla artist has left behind for the World to marvel over. I actually like graffiti, it doesn’t look unsightly; it adds to the urban landscape, a terrain I have spent my life immersed in. Okay, the quality isn’t consistent, but then again beauty is in the eye of the beholder, so it’s gotta be beautiful to someone, right?

One particular piece that caught my eye was a white label, with something written in permanent marker on it:

image

This was found a few doors down from number 40 Tiverton Road.  I liked the message and even empathised with it. Here I saw someone trying to let someone specific know how much they mean(t) to them, in their own cryptic manner, without giving away many clues to present their identity. That said, the artist (or would author be a better word? Yeh let’s go with author) even signed with an alias/pen-name/pseudonym: MSSD CNNCTN.

Another one turned up, this time on the way home from Sainsburys:

image

And another one on the side of a recycling bin near Bargain Booze (opposite Selly Oak Station).

A quick google search of this line came up with As I lay Dying’s Confined . The lyrics may be somewhat telling, or maybe not.

…..Aaaaand another one spotted on the front of the now abandoned Gun Barrels pub on Bristol Road…

image

A plumber? His princess? Finally something a little more specific! For a while I pondered over this, looking at it too literally. Maybe the author met a guy in this pub and they got talking about ‘the one that got away’ or something like that. Then it hit me. Goddamn MARIO!

The last one I saw deviated from the white label format, toward what I would call humorous graffiti, intended to be light-hearted:

image

It’s very probable that there are more examples of MSSD CNNCTN’s work elsewhere in Selly Oak, but I haven’t seen it. However, there is a Flickr photostream of their work, with stickers turning up in Redditch and Liverpool…

If anyone spots art that could be attributed to their work, please let us know in the comments below! Tweet your sightings along with a log of where and when you found it.

MSSD CNNCTN, if you happen to read this, thanks for making Selly Oak a little more interesting, I find myself more aware of my surroundings, purely in the hopes of finding one of your stickers. I would like to meet you at some point (and no, I’m not a copper).

Should the world end tonight, I just want you to know….

*[edit 27.07.13 12.40] My friend RoughHawkBit identified that MSSD CNNCTN could be ‘Missed Connection’ without the vowels in. Reading the wikipedia article on the practice, it fits pretty well with observations.