Guest blog: Peroxisomes explored in Germany meeting

Will Stanley (Research Associate, Northern Institute for Cancer Research, Newcastle University, UK), a Biochemical Society General Travel Grant recipient, shares his experience at a peroxisome meeting in Germany. Find out more about General Travel Grants on our website.

I’ve been to the 4th Open European Peroxisome Meeting (OEPM) in Neuss, near Düsseldorf in the Ruhr region of Germany. So have about 150 other people. It may come as a surprise to some that Europe has such a thriving community dedicated to researching a small and deceptively insignificant organelle.

However, the humble peroxisome has some major parts to play in human health, with a number of severe diseases ensuing from malfunction, emerging roles in cellular senescence and novel avenues in drug targeting to specialized peroxisomes in microbial pathogens*.

OEPM has something of a tradition of giving the stage to PhD students to present their work in an international setting with an audience ranging from novitiates to experts and emeritus peroxisome enthusiasts. Most talks cover recently published or soon to be published work, which gives every OEPM a vibrant, cutting-edge agenda.

It’s intriguing to see how trends change over the years and how one “star” protein or point mutant can jump out as a hot topic and be touched upon by a number of talks. One thing that particularly struck me (as a structural biologist) this time was the change in trends of structural techniques being applied to peroxisomal components – while previous OEPMs have showcased crystal structures of important peroxisomal proteins, it’s now become necessary to look at mechanistic details things that will not readily crystallise, for example large flexible and disordered domains are yielding some very promising NMR structure/function data and multi-protein complexes from the peroxisomal membrane are being tackled by cross-linking mass spectrometry and electron microscopy, leading to some quite unexpected results.

During the three days of the conference, 35 talks were given and 62 posters presented. People came along from 14 countries – mostly in Europe but also as far afield as China, South Korea and Canada. The conference organisers kept us all neatly tucked away in the conference centre and made sure to feed us well and provide plenty to drink in the evening – especially at the magnificent conference barbecue (Germans know a lot about good barbecuing).

Thus, plenty of socialising went on, with inevitably dubious jokes about peroxisomes occasionally escaping. The whole affair was pretty anarchic and the novitiate and emeritus delegates all muddled in together, which makes for an excellent scientific community spirit beyond the duration of the conference. And, as usual for OEPM, there was a free exchange of ideas. I found this especially helpful as I had gone along with a new research avenue in mind. I was delighted to find that nobody at the conference seemed to think I was crazy to be entertaining such notions and it looks like I’ve even managed to coax a couple of people into some new collaborative work.

I would like to warmly thank the Biochemical Society for the General Travel Grant which made this possible. OEPM happens every two years and has previously taken place in Leuven (BE), Lunteren (NL) and Dijon (FR). The 4th OEPM in Neuss (DE) was splendidly organised by Prof. Ralf Erdmann and his very enthusiastic team from the Ruhr Universität, Bochum (DE). The 5th OEPM will take place in Vienna (AT) in 2016 with Johannes Berger (Medical University of Vienna) leading the organisation.


*If you’re interested in finding out more about these mysterious little peroxisomes, an excellent recent review takes a look at them from a historical perspective: Vamecq, M. Cherkaoui-Malki, P. Andreolotti & N. Latruffe (2014). The human peroxisome in health and disease: The story of an oddity becoming a vital organelle. Biochimie 98: 4 – 15.

Then and now: the final part of our biochemistry in the 80s series

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 Gerhard May, from our Education Committee, looks at the final video DNA and Protein Synthesis, produced by E.M Evans and E.J Wood. You can see posts about the previous two videos here.

DNA and Protein Synthesis

Guest post by Dr Gerhard May

This video made in 1987 and titled ‘DNA and Protein Synthesis’, is split into three sections. These sections are loosely connected to each other and can easily be viewed in isolation, however, parts 1 and 3 provide historical perspectives supporting the molecular concepts described in part 2.

Part 2 of the video, entitled ‘Mechanism of protein synthesis’, gets to the heart of the matter and describes what Francis Crick had originally termed ‘The Central Dogma’. It clearly describes the basic structure of DNA and how the 4 nucleotides are used in triplets to encode the sequence of amino acids in a protein. It nicely illustrates how DNA is transcribed into messenger RNA and how this is translated (with the help of ribosomal and transfer RNAs) into protein. Although the animation is a little dated and the narration a bit slow, this information remains central to biochemistry, molecular biology and genetics and all biology students will need to understand this process. What it doesn’t describe, because this was not known about at the time, are the multiple other types of non-coding RNAs that regulate gene expression; in particular, the very small RNAs (called microRNAs, only about 22 nucleotides long), that act to inhibit the production of protein.

The first part of the video shows an experiment to demonstrate that protein is made from amino acids, by components present in the cytoplasm of a cell. Thirty years ago, this could only be accomplished in the laboratory by radio-labelling amino acids and ‘following’ the radioactivity. Therefore, much of the video comprehensibly explains the nature of radioisotopes and how they can be detected. While radioisotopes are still used to some extent in biology labs today, for most applications they have been supplanted by safer, better and more versatile methods to label biomolecules. For example, proteins can be detected directly using fluorescent labels or using antibodies to specific proteins. The labelled antibodies can then be visualised by fluorescent, chemiluminescent or even infra-red methods. DNA sequencing methods have massively advanced since the making of this video, when sequencing 400 nucleotides required a full day and a big acrylamide gel, using radioactive nucleotides (as shown). Now 2nd ‘next generation’ sequencing methods permits the parallel sequencing of thousands of molecules, using optical methods of detection (including fluorescent or luminescent labelled nucleotides) or non-optical methods, for example detection of hydrogen ion release. This area continues to progress at a pace, and 3rd generation methods, including labelling nucleotides with heavy elements (such as halogens) and detection by atomic force microscopy is just one approach of many under development.

The third section of the video describes a classical experiment to show that DNA, and not protein, carries the heritable information of a cell, a fact that we all take for granted now. In the early 1950s, before the structure of DNA was known, it wasn’t clear how heritable information was passed on and it was not easy to find out. To understand how the 1952 Hershey and Chase experiment was conducted, some knowledge about viruses that infect bacteria (bacteriophages) is required, which the video provides. Again, radioisotopes are used to label and track the bacteriophage DNA. The Hershey-Chase experiment is still mentioned in passing during undergraduate degree programmes in the biomolecular sciences. It is an excellent example of the use of radioactivity in molecular biology, and is of particular historic interest for anyone who wants to learn more about ‘how on earth did they find this out’. Watching this video will not only teach you some basic concepts in molecular biology, but also demonstrate some aspects of the techniques that were used to unravel those concepts.

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.