Then and now: Continuing our look at biochemistry in the 80s

In the 1980s a three-part series of videos was published by Portland Press on behalf of the Biochemical Society. ‘The Biochemical Basis of Biology’ video series aimed to present biochemical facts and concepts in a dynamic way to students in further and higher education.

To see how biochemistry knowledge and techniques have changed in the last 30 years, we asked members of the Biochemical Society to review these videos and to write a short text comparing them to where we are today.

Following on from Dr Helen Watson’s review of Cell Structure and Energy Production, today Dr Joanna Wilson (University of Glasgow) looks at the second video Manipulating DNA. Keep an eye out on our blog for a commentary on the final video, DNA and Protein Synthesis, in the coming weeks.

Manipulating DNA

Guest post by Dr Joanna Wilson, University of Glasgow

This video, made in 1994, shows some fundamental techniques in molecular biology, used to manipulate DNA. It is divided into four sections covering [1] restriction digestion (cutting DNA), [2] agarose gel electrophoresis (separating DNA fragments by size), [3] the polymerase chain reaction (PCR, used to amplify tiny quantities of DNA) and [4] cloning DNA (permitting archiving, production and manipulation of specific DNA fragments, as well as expression of genes). Although the video is now over 20 years old, the basic concepts described and many of the techniques used, are central to molecular biology and are still used in labs around the world today.

Some protocol aspects have changed since the making of this video, in particular the methods are now faster and safer, but approaches such as these have led to a revolution in molecular biology, such that, although still used, these techniques now form just one small part of a huge armoury of DNA technology.

So how exactly have the specific techniques shown improved today? Much of the equipment used, such as the powerpacks (for gel ecletrophoresis), the thermocycler (for PCR), the gel camera system, are more efficient, smaller, sleeker, usually computerised and certainly more versatile. For example, gel imaging systems are linked to computers now, for digital image production (instead of taking an analogue photo and having to produce an instamatic print). Thermocyclers have heated lids (no need for oil on top of the PCR sample) to prevent evaporation and maintain precise temperatures and they can be programmed to run multiple temperature parameters at once. Safety in molecular protocols has improved immensely over the past decades. For example, Bunson burners are almost a thing of the past; the method to spread bacteria on an agar plate using an ethanol and flame sterilised spreader – simply replaced now with a disposable plastic spreader (no open flame and alcohol). Although still widely used, several labs have replaced ethidium bromide (a nasty mutagen) to visualise DNA, with safer dyes. One of the biggest changes since 1994 is evident in the method to purify plasmid DNA. In section [4], we see how to make a caesium chloride density gradient to purify the plasmid. I winced when we were shown the use of a sharp needle to collect the DNA, full of mutagenic ethidium bromide, even though this was a method I used to conduct routinely. Just one needle slip would have been very nasty. So what do we use now? We buy a DNA purification kit from a biotechnology company, containing a little column to allow purification of the DNA by its charge (remember it is negative) and in a matter of an hour, we have nice clean DNA, no big ultra-centrifuge for over-night spins, no toxic and mutagenic substances – easy.

What about the molecular revolution? The protocol shown in the first section shows how to cut DNA in a test tube. The use of restriction enzymes is still a corner stone in the lab. But more than this, DNA can now be manipulated in almost every way imaginable.  It can be cut, bits deleted or changed, glued, twisted and flipped, in a test tube and amazingly, even within a living cell. While the principles of PCR, shown in section [3], haven’t changed a jot, the enormity of PCR application was not realised at that time. For example, modern day forensics would be unrecognisable 20 years ago, when PCR was still in its infancy. Now an individual can be identified from a hair or speck of blood using PCR followed by “DNA fingerprinting”. Using PCR, even ancient DNA from Neanderthal man has been analysed and this allows us to work out the evolutionary relationship of Neanderthals with us. PCR and other DNA polymerisation wizardry has also revolutionised DNA sequencing. It took over 10 years to sequence the first human genome, now it takes just a few days and given enough sequencing machines, multiple genomes can be read at once. This exemplifies an area of major advancement in molecular biology. Many of the techniques that can be conducted by one person in a lab, as shown in the video, have advanced to the point where much can be automated and robotic machines conduct the work with very high throughput. The single scientist in the lab is far from redundant, but we can leave a lot of the boring work to machines and biotechnology companies and use kits to speed through our bright ideas.

Then and now: A look back at biochemistry in the 80s

In the 1980s a three-part series of videos was published by Portland Press on behalf of the Biochemical Society. ‘The Biochemical Basis of Biology’ video series aimed to present biochemical facts and concepts in a dynamic way to students in further and higher education.

To see how biochemistry knowledge and techniques have changed in the last 30 years, we asked members of the Biochemical Society to review these videos and to write a short text comparing them to where we are today.

Today Dr Helen Watson, from our Education Committee, looks at the first video Cell Structure and Energy Production, produced by E.M Evans and E.J Wood. Keep an eye out on our blog for commentaries on the next video – DNA and Protein Synthesis and Manipulating DNA – in the coming weeks.

Cell Structure and Energy Production

Guest blog by Dr Helen Watson, University of Exeter

This video shows some of the techniques that were used in biochemistry and cell biology to understand cell structure and the function of enzymes in animal and plant cells. As you will see, we have come a long way since this video was made (and not only in haircuts!).

Variations on most of the techniques shown in the video are still used in labs today. In the years since this video was made, big advances in technology have enabled biologists to work with computer controlled equipment rather than doing everything manually. You’ll notice there is no computer attached to the microscope in the video. In modern labs, electron microscopes (and most other microscopes) are attached to computers which enable us to focus images, capture images and build up 3D models of samples so we can better understand the structures inside cells. Techniques such as confocal microscopy and FRET have become common and help us to understand the ultrastructure of cells, including where proteins are located and which proteins interact with each other. The use of fluorescent proteins has been vital in helping us to work out where proteins are localised inside cells and how they move about and interact with each other.

Our knowledge of protein structure has informed our understanding of protein function. We now know the 3D structures of many of the enzymes mentioned in the oxidative phosphorylation pathway. X-ray crystallography and other structural techniques like NMR have told us a huge amount about how enzymes like these function and, in this case, make energy. In the video, oxidative phosphorylation appears as a ‘black box’. Now, thanks in part to structural studies, we know much more about the enzymes and which parts of the reaction they catalyse.

We now know the sequence of the human genome and genomes of many other organisms. Having the technology to quickly manipulate and sequence DNA has enabled biochemistry and cell biology to move at a rapid pace. We can now easily study proteins one at a time by manipulating the gene that codes for them and synthesising the protein in a test tube (in vitro). This has, to some extent, made it unnecessary to fractionate cells and look at organelles, although this is still done in some experiments.

It is interesting to see which techniques have changed and which have remained the same since this video was made. Much of the equipment here is now a lot more advanced. Our microscopes now have computers attached to them to help us focus, record and quantify images. However, lots of the machines and techniques here such as the centrifuges and cell fractionation are still used on a daily basis in biochemistry and cell biology labs today. This video highlights just how fast research and technology in biological sciences moves and what an exciting, dynamic and sometimes unpredictable field it is to work in.

Workshop provides insights on communicating science to the media

VoYS1

Hannah Black (University of Glasgow) recently attended a media workshop run by Sense about Science, a charity the Biochemical Society supports. She writes about her experience in this guest post.

Communication and research impact are key areas that our universities are encouraging academics and students to have an increased awareness of and be more involved in. With this in mind I – along with around 40 other early career researchers from across all the sciences and both academic and industry based – recently had the opportunity to attend a media workshop. Run by the charity VoYS1Sense about Science at the University of Manchester, the workshop was part of the charity’s Voice of Young Science programme. For those yet to encounter the organisation, they encourage early career researchers to become active in science communication, largely through ‘myth-busting and evidence-hunting campaigns’. The aim of the workshop was to help to equip early career scientists with the tools to engage with the media and to stand up for science where we see it being misrepresented.

For me, the workshop was a great experience. I learned lots and considered issues with communicating science I had not thought about before. One of the main things I took from the day was to prepare well before sharing your findings with the public. It was pointed out that it can be daunting sitting in front of a microphone or speaking in public (an environment that is alien to those of use used to being in a lab), so make notes and know what point you want to get across, whilst avoiding slipping into using jargon. Through a group discussion with journalists it also became apparent that the media and scientists face very different pressures when putting together a story – mainly time and target audience. Whilst research papers include vast amounts of detail and very carefully considered conclusions, media stories need to be snappy and often numerous pieces are prepared per-day, by any one journalist. It is therefore important for us to think about what we want our ‘top line’ or take home message to be when approaching the media with a story.

VoYs2I came away from the day with confidence; believing I was much more prepared to approach the media. It was great to get the chance to discuss different approaches to public engagement and find out what others thought was good and bad about how science is reported. Admittedly, whenever I have conversations about science reporting it is often to grumble about where I’ve seen it done badly. However, the feeling of the day was very positive. We all agreed that cooperation is the key. Journalists (for the most part) aren’t trying to give science a bad name and we have a common goal – to tell interesting and cutting edge scientific stories. After all, the majority of our work is funded by public money and so we arguably have a duty to give back and explain the research that we do. That is not to say all reporting is done well and we were advised to contact journalists when we spot misrepresentations so they can be cleared up.

It was also great to be around so many early career scientists who are actively aiming to improve their communication skills. I have wanted to play a more active role in communicating science but have felt a little overwhelmed and not known where to start. From this workshop I’ve learned it’s not just me, most of us have the same concerns and through networks like Voice of Young Science we can get support and communicate science creatively and effectively – you don’t have to go it alone.

Taking Science To The Public Is Addictive

Alastair Stewart:

Great tips on organizing a public engagement event from one of our Scientific Outreach Grant recipients. If you’re interested in running your own event, we may be able to provide up to £1000. The current funding round closes on 29 April 2015. http://www.biochemistry.org/Grants/ScientificOutreachGrants.aspx

Originally posted on professoralisonjsinclair:

“Discussing science with the public – what would I say or do?” – is a wary but quite understandable reaction from many academics. These personal encounters are critical to spreading the messages that science is important, science is fun and that science research is still needed. The key challenge that academics face is to overcome our natural hesitancy and have a go.

My first encounter was to take some experiments into a local primary school, very hard work but fun. Two years ago I volunteered myself again, this time for a public engagement activity at the Brighton Science Festival. I formed a team of ten researchers from the University of Sussex Biochemistry and Molecular Biology Group and we led the audience in a piece of performance art, re-enacting the packaging of DNA. Afterwards everyone was eager for more, so with an expanded team we devised some experiments to take to…

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Science and the General Election – the science community needs you!

General-Election-2015With only a matter of weeks to go until the General Election, and with the dissolution of Parliament looming on Monday, the UK is about to enter into full-blown election fever.

Understandably, science is never likely to be a ‘doorstep’ matter when it comes to election campaigning. However, a lot of the issues that are – health, wellbeing and the economy to name but a few – are reliant on a productive scientific research base.

It is important that Prospective Parliamentary Candidates (PPCs) are aware of this and are encouraged (or reminded!) to support science and the scientific community as part of their pre-election campaigns. It is vital that they are aware that science can improve lives, underpin livelihoods and jobs, and drive economic growth.

Our current world-leading science base rests on the foundation of historic continuous investment. However, the science budget has been ring-fenced since 2010 which, in real terms, means that it has been gradually eroding due to inflation. It’s arguable how much longer the UK science community can remain world-leading without further investment to enable it to thrive.

There is a strong economic case for increased investment in science. Research has shown that for every £1 spent by the Government on research and development (R&D), private sector R&D output rises by 20p per year in perpetuity, by raising the level of the UK knowledge base (CaSE, 2014). Furthermore if Government made a one-off increase in public spending on R&D of £450m (5% of its £9bn total R&D spend), market sector output would rise by £90m per year, every year (Haskel et al. 2014).

At the last spending review, capital investment was removed from the science budget leaving resource spending behind in the ring-fence. Resource funding is funding for scientific research and for people; capital investment is for infrastructure and equipment. The Government have subsequently made several flashy announcements of dedicated capital funds for projects such as the Turing Institute in London or the Sir Henry Royce Institute in Manchester. (Cue media-friendly shots of George Osbourne or Vince Cable in a high-vis vest and hard hat.)

While increased funds for science are obviously a good thing, there are two issues which must be considered with such announcements. Firstly, decoupling capital from resource spending means that there may not be the skilled personnel to operate big scientific infrastructure. It is vital that physical infrastructure is matched with the appropriate skills infrastructure. Secondly, such Government announcements flaunt what is commonly referred to as the Haldane Principal. This states that decisions on scientific spending should be made within the scientific community rather than within the corridors of Whitehall. The Research Councils embody this principal and operate at arms-length from the Department of Business Innovation and Skills (BIS).

A number of learned societies and organisations have created materials to help ‘make the case for science’ in the run up to the election. The Society of Biology has a useful webpage that details key statistics to back-up the points detailed above. The Campaign for Science and Engineering have created 2015 General Election, a page outlining the ten actions they propose the next Government take to champion science and engineering, we support this call for action. They are also posting a series of blogs from PPCs in the run up to the election in which candidates detail why science and engineering is important to the UK and how they would support this as an MP.

The UK National Academies have set out key priorities and actions for the next Government to make the UK the location of choice for world class research, development and innovation in their publication Building a stronger future.

It is vital that securing a positive future for UK research and innovation is a key goal for all PPCs in this year’s general election. A way you can try to ensure this is to write to your own PPCs and highlight to them the importance of science. MPs and PPCs are often consumed by issues within their own constituencies so it’s importance to highlight how science has an impact in their community – you’d be surprised how big this can be! Aiming correspondence at the constituency level can be a real driver to encourage your MP to take action.

I recently wrote to my representative Sadiq Khan, MP for Tooting, to encourage him to include science in his pre-election campaign. Below is the letter I wrote – I encourage you to use this as a framework or a template for an e-mail (or letter) of your own. To find out who your current MP is, visit the ‘find my MP’ Parliament webpage.

If you write and receive a response please forward it to the Policy Team at the Biochemical Society at policy@biochemistry.org.

Dear Sadiq,

Please allow me to introduce myself, I’m Cat Ball and I’m Science Policy Adviser at the Biochemical Society and the Society of Biology. However I am e-mailing you in a personal capacity as a resident of Tooting Bec and one of your constituents.

With the dissolution of Parliament and the election on the horizon, I wanted to highlight to you the importance of the science community in the UK and to urge you to support it in your election campaign. There is an active cohort of world-class researchers resident at St George’s Hospital and as such, science has a crucial role in your constituency.

Since 2010, the science budget, despite having been protected from the worst of the austerity measures, will nevertheless have depreciated in real terms by up to 20%. In fact, it has now dropped below 0.5% of GDP for the first time in 20 years. If we don’t act now, it could take generations to recover.

In parallel, near-sighted policies on immigration, and inaction on the precariousness of the scientific career structure, threaten the day-to-day business of science, and those who depend on it.

Supporting the science community is the right decision for a number of reasons:

1. Science drives investment and growth

For every £1 spent by the Government on research and development (R&D), private sector R&D output rises by 20p per year in perpetuity, by raising the level of the UK knowledge base (CaSE, 2014).

UK research is cited in 10.9% of all patent applications worldwide (Elsevier for BIS, 2013). If Government made a one-off increase in public spending on R&D of £450m (5% of its £9bn total R&D spend), market sector output would rise by £90m per year, every year (Haskel et al. 2014).
 
2. Science improves lives

One eighth of the world’s most popular prescription medicines were developed in the UK (ABPI, 2014).

A change in natural habitats that causes a 1% reduction in sedentary behaviour would provide a total benefit of almost £2bn across a range of health conditions (Mourato et al. 2010).

3. Science creates jobs

The health and life sciences industry alone employs 176,000 people and has a £51bn turnover (BIS Growth Dashboard, 2015).

I urge you to support the science community and the science budget as part of your election campaign.

Best wishes,

Cat