In the first of two podcasts, BMC Medicine Senior Editor Ursula d’Souza, spoke to chair of the DSM-5 taskforce, David Kupfer, on the main challenges faced by DSM-5 and its potential impact on global mental health classifications and diagnosis.

David Kupfer, professor of psychiatry, University of Pittsburgh, USA.

“We wanted this fifth edition to help clinicians more precisely diagnose mental disorders. DSM-5 does that by representing the best available science and clinical experience. This new manual is truly a guidebook that will help clinicians better serve their patients”
David Kupfer, University of Pittsburgh

David Kupfer is both professor of psychiatry and professor of neuroscience and clinical and translational science at the University of Pittsburgh, USA. Having qualified in medicine at Yale University, USA, Kupfer continued to his clinical and research training at Yale New Haven Hospital and the National Institute of Mental Health. He also served as chair of the Department of Psychiatry at the University of Pittsburgh School of Medicine, and director of research at Western Psychiatric Institute and Clinic, USA. Kupfer’s primary research interests focus on long-term treatment strategies for recurrent mood disorders, the pathogenesis of depression, and the relationship between biomarkers and depression.

Taking a view from across the pond, Eric Taylor, emeritus professor of child and adolescent psychiatry at the Institute of Psychiatry, King’s College London, UK, reviews the changes in DSM-5 with regards to ADHD, and considers whether this will affect clinical practice and what the future holds for the diagnosis of this disorder.

Eric Taylor, emeritus professor of child and adolescent psychiatry, King’s College London, UK.

“[ADHD] is not part of disruptive disorders now, it’s part of neurodevelopmental disorders, which I think is a step forward. […] The changes in DSM-5 have also made it a bit easier to diagnose ADHD in adults”
Eric Taylor, King’s College London

In addition to his position at King’s College London, Eric Taylor is an honorary consultant at the Maudsley Hospital, London, UK. Taylor has chaired the UK’s NICE (National Institute for Health and Care Excellence) guidelines development group for ADHD. He is also a trustee of the National Academy of Parenting Practitioners, non-executive director of the South London and Maudsley NHS Foundation Trust, fellow of the Academy of Medical Sciences and honorary fellow of the Royal College of Psychiatrists.

A number of limitations are introduced when these dynamics in biological interactions are not accounted for. A false time window during an experiment, for example, can lead to missed activation events of important signalling components; equilibrium is not accounted for in signal transduction cascades that are assumed to be unidirectional; and experimental studies miss the full complexity of a regulatory network while focusing only on sub-modules of the network, such as individual feedback or activation loops.

“Biologists are used to interpolating their data without knowledge of the dynamic behaviours of the system between the points measured. Furthermore, the complexity of regulatory networks does not allow intuitive estimations on the dynamics of the entire network.”
Fred Schaper, Otto-von-Guericke University Magdeburg

Fred Schaper, from the Otto-von-Guericke University Magdeburg, Germany, combines laboratory experiments and mathematical modelling in a systems biology approach to investigate how signal transduction is induced by interleukin-6 type cytokines. As someone who believes in the need, challenge and benefit of taking a systemic and dynamic view on signalling pathways and networks, Schaper was well qualified to be Guest Editor, alongside Stephen Feller from the University of Oxford, UK, for the Systems Biology and Medicine review series published in Cell Communication and Signaling this summer.

Emphasising that good models are still models and not a copy of the real system, Schaper highlights a number of benefits to taking a systems biology approach. Among these is saving time and money through modelling a system’s behaviour to promote an optimal experimental design. Models can be used to reject or refine a hypothesis, and to help identify new connecting components of a regulatory design, but an experiment will always be needed to confirm a hypothesis.

The Systems Biology and Medicine review series provides a comprehensive overview of current models and known networks in signal transduction, including reviews on apoptosis, dopamine metabolism and probabilistic Boolean networks.

Highlights include Steffen Klamt and Regina Samaga from the Max Planck Institute for Dynamics of Complex Technical Systems, Germany discussing the usability of logical modelling, such as interaction graphs, logical networks and logic-based ordinary differential equations. This review will enjoy great popularity among scientists involved in systems theory, but also addresses biologists open to a structured systems view on biological networks. Thomas Sauter from the University of Luxembourg and colleagues extend this view for the more advanced reader by presenting biomedical applications of probabilistic Boolean networks.

The biological systems used as examples in these two reviews, EGF signalling and apoptosis, are discussed in more detail in the accompanying articles of Boris Kholodenko and colleagues and Inna Lavrick and Kolja Schleich, respectively. These articles clearly demonstrate the benefit of a systems view on complex biological processes.

With this review series on Systems Biology and Medicine the benefits of systems biology in biological research is clarified, with the aim of encouraging the development of a systems view on complex biological regulatory networks, in light of the reasoning that pure intuitive understanding is not sufficient, and may even be misleading.

The complete list of series articles:

Systems Biology and Medicine

What is the ultimate goal of this area of research?

The end goal is to develop a cell-based cartilage replacement therapy that can delay or prevent the need for joint replacement surgery. Joint replacements are very effective treatments for osteoarthritis, however these replacements typically last in the order of 15 to 20 years, and revisions can be complicated and carry additional risks. Therefore, tissue engineered cartilage replacement strategies would be an ideal strategy to delay or avoid joint replacement surgery altogether, particularly for younger and more active patients who will outlive currently available artificial joints.

How would findings from this field of research  impact on  health, and the economic costs of osteoarthritis and other cartilage diseases?

Osteoarthritis (OA) is one of the leading causes of morbidity in the US and abroad due to the pain and loss of mobility associated with the disease. It affects around 630 million people worldwide and is most commonly associated with aging. As people are living longer, there is a growing opportunity to both improve quality of life for millions of people as well as to significantly reduce health care costs by improving osteoarthritis treatments and outcomes. There are also a number of other significant risk factors for OA aside from aging, including obesity, joint trauma (Anterior cruciate ligament (ACL) and meniscal tears), and overuse.

Specifically in the context of the worldwide obesity epidemic, the burden of OA is only expected to increase. In addition, OA and cartilage focal defects that occur in the younger patient population (30s, 40s and 50s) often occurs following joint injury, such as ACL or meniscal tears. It is this younger patient population that would likely benefit the most from cartilage tissue engineering, where it could have the potential to both improve outcomes and allow patients to return to work and other daily activities.

What specific factors need to be considered to produce an effective and stable cartilage tissue replacement from mesenchymal stem cells?

Chondrogenic differentiation of mesenchymal stem cells (MSCs) is a complex process that is still not fully understood. However, generally speaking, we know that stem cell differentiation is influenced by both chemical signals, such as growth factors and cytokines, as well as physical factors, such as the stiffness of the cells physical environment and mechanical stimulation. Chondrogenically differentiated stem cells need to elaborate an extracellular matrix that in combination with any scaffold or other support will perform the mechanical function of the cartilage it is meant to replace. The ideal timing and cocktail of growth factors needed to sufficiently differentiate stem cells into chondrocyte-like cells capable of producing this functional tissue is still be investigated. Furthermore, it is important that the implanted cells stay differentiated once implanted, and do not return to a de-differentiated state or continue through a hypertrophic pathway, which chondrogenically differentiated MSCs typically do during events such as fracture healing. The purpose of this review is to put into context all of the latest findings on how mechanical factors may be able to participate in enhancing and maintaining this differentiated cellular state.

You mention that some researchers are working on models that mimic the forces imposed on joints in vivo. What are the challenges of developing such a model and do you think a realistic model is achievable?

Creating an in vitro environment that precisely recreates all of the biophysical factors that exist in the joint is highly challenging due to the multitude and complexity of these many factors. Engineering a device that could impart all of these forces in controlled manner would be a technical challenge to build and program. However, the latest work in the field has shown that when multiple stimuli are integrated, such as shear plus compression, you can elicit a more chondrogenic response then with either alone. It remains to be seen if adding even more factors to a bioreactor like this, such as osmotic or hydrostatic pressurization or fluid flow, could drive an even stronger chondrogenic phenotype.

You mention a number of potential avenues for further research. Which do you think are the mostly likely  to provide the most important or useful insights?

We are very interested in understanding at a mechanistic level mechanotransduction pathways that participate in both chondrogenic differentiation as well as extracellular matrix production. This would allow for both more predicable approaches to tissue engineering, as well as potentially identify novel pathways involved in cartilage mechanoregulation that could then be tested as pharmacologic targets. In the more general area of chondrogenically differentiated stem cells, induced pluriopotent stem cells appear to be an important and emerging enabling technology for this type of research, giving researchers a virtually unlimited supply of chondrogenically-capable cells. This will hopefully lead to, among other things, improved in vitro tissue and disease modeling, which we could use for further understanding cartilage mechanotransduction, as well as high throughput therapeutic drug screening, and even potentially a large pool of autologous pluripotent stem cells for tissue regeneration.

How far away in terms of years do you think this field is from achieving cell-based cartilage replacement therapy?

Autologous chondrocyte implantation, where chondrocytes are removed from a non-weight bearing location, expanded, and placed back into a focal defect, is currently approved and performed in a number of countries. However, the efficacy of these types of treatments still needs to be evaluated. In terms of stem-cell based therapies for articular cartilage replacement, it would not be surprising to see a stem-cell based therapeutic intended for the treatment of OA being submitted to regulators in the next five to ten years. However, it is important to remember that there are further steps in most countries, including animal models, safety, and efficacy, that need to be passed before regulatory approval and clinical adoption.

Dale Sanders, Director of the John Innes Centre, UK.

Leading plant scientist Dale Sanders, Director of the John Innes Centre, UK told Biome his views on what GM has to offer. Sanders obtained his PhD in plant biophysics from Cambridge University, UK before heading to Yale University, USA to study how plants absorb mineral ions. He has maintained this interest to this day in his current laboratory within the metabolic biology department at the John Innes Centre – an international centre for research into plant science and microbiology, where amongst other investigations work is being carried out into genetically modifying crops.

Will a rapidly growing global population affect the way we need to produce food in the future?

Yes, it will affect it in several ways. First of all we will need to produce more, obviously. And we will need to produce it sustainably – in other words, without adding to the already large carbon footprint. Moreover, we will need to produce it more intensively. Almost all of the arable land available for food production is currently in production, so we need to think about ways of sustainable intensification, which will enable greater productivity with lower environmental impact.

What are genetically modified (GM) crops, and how do they differ to crops generated by domestication?

In fact they’re not that much different, at one level. GM crops are crops that have had a gene introduced into them. Sometimes from a related species, sometimes even from the same species, but with the gene expressed in a different part of the tissue. These GM crops have been subjected to molecular modification. How they differ from conventionally bred crops is really a moot point. I think conventionally bred crops really have taken quite distantly related species and interbred them and come up with quite amazing changes in phenotype – in the way that the crop looks. If you look at simple crops like maize or wheat, you can see the way in which conventional breeding has hugely modified the agricultural potential of these crops. So in a way, GM is adding things around the edges but using modern molecular approaches.

What are the potential benefits associated with growing GM crops?

It turns out that if you can introduce genes from distant or even related species, you can do wonderful things in terms of reducing the environmental footprint or reducing disease resistance. Those are just two benefits. In the first case – environmental footprint – this involves reduced fertilizer application. Fertilizers account for about 50 percent of the carbon footprint of agriculture. In the second case, crop diseases involve heavy duty spraying of agrochemicals. If you can reduce the application of those through genetic modification, you’ve got a win-win situation. And I’d point to a third area in which we can get gains, which is healthier foods. We can actually think about biofortification, which is the enrichment of the food we eat through trace minerals or micronutrients which we all need in the food that we eat.

Could you provide an example of the health benefits of GM crops?

Yes one from my own lab actually. It turns out that between a quarter and a third of the world’s population is defective in its zinc uptake. We all need zinc because 10 percent of our proteins require zinc as a binding agent. The reason many of the world’s population are defective in zinc intake is because the endosperm of cereal grains – that is the bit we eat in white rice or in milled wheat – doesn’t contain very much. So we’ve actually taken a GM approach in which we’ve managed to engineer an enhanced zinc content of endosperm of rice and wheat and other cereals, and that will potentially lead to health benefits. We’ve not yet done nutritional studies, but those are the potential gains.

Field of canola - genetically modified plant of the mustard family - in Binalong, New South Wales, Australia. Image source: Flickr, Jan Smith

Where are GM crops currently being cultivated and consumed?

GM crops are currently cultivated in around 28 countries worldwide, over a hectarage of about 170 million hectares. The principle countries for cultivation and consumption are the US and South American countries – Argentina and Brazil. You can, in a way, split the planting of GM crops into two fundamental categories: those that are cultivated for their food value (such as GM maize and GM soya) and those that are cultivated for other products, principally among those is cotton. So there will be few people in the western world who are not wearing a GM product, if they’re wearing something made of cotton.

Do you think enough research has been done to show whether GM crops cause environmental or health related problems?

There is no doubt in my mind about the answer to that question. Many, many studies have been performed, meta-analyses have been conducted on those studies – including by the EU, incidentally – and there is no substantive evidence whatsover of any health or environmental detriment of GM crops. That’s not to say that if you produce a new breed or a new line of germplasm in a crop, there might not be detrimental effects. But those can happen via conventional breeding too, and that’s why we do need regulation. But we don’t need regulation specifically on the basis of the technology on which the breeding has been done.

Just as an example; it’s known that some trillions of meals have been eaten in the US, in probably what is the world’s most litigious country, and nobody has ever brought a claim to court that has successfully argued that GM has ruined their health. If you have been to the US, as many other Europeans have been, you will almost certainly have eaten GM food, and I’m sure you won’t have come back complaining about health effects.

How important is public perception in controlling the direction of crop research and the use of GM crops?

Public perception is incredibly important, and of course the public have a right to know about the types of technologies that are being used to produce food in the country that they live in. And the public have a right to know that the food that they eat is safe. What we need to do is get to a position in which the public are well-informed about the things that GM crops can offer in terms of environmental and health benefits. They need to be appraised of the wider issues, for example the ways in which the economics of food production works. I think in many cases the discussion about GM gets inextricably mixed with arguments about the economics of food production and I think there is the need for some clarity in the public perception of how GM is produced, who researches it, and regarding the overall safety and beneficial aspects of producing GM.

Our domestic policy on the cultivation of GM crops is controlled by the European Union. What led to these comparatively stringent regulations?

It was essentially something called the precautionary principle. First if we think about the way we live our lives in terms of risk and precaution. For example; just over a hundred years ago, ‘modern motor cars’ went around with a red flag in front of them to warn people that a mechanised vehicle was coming. These days, we accept that road deaths occur, but we also accept that the car is overall beneficial to society. We therefore accept that there is risk in our lives; we accept that we presume when we go out in the morning that we’re not going to get killed in a road accident.

I believe the sensible attitude to the way we approach our lives, is that we take a view of risk. That’s rather different from the precautionary principle, which says that if there’s any doubt whatsoever, don’t do it. If there were any doubt whatsoever about whether you would survive the day when you got up to go to work in the morning, you might not get out of bed in the morning. My feeling is that there has been an overriding of this concept of the precautionary principle without a secure, scientific evaluation of risk. I do not believe that GM, per se, presents any risk whatsoever. It certainly doesn’t present the kind of risk that traffic accidents do in modern countries.

Are there implications for EU countries, and others, in not developing and growing GM crops?

Yes I think there are implications, and they fall in two areas. One of which is in terms of the development of research and the commercialisation of research. We have to accept that food production is an industry and many of those involved in that industry are decamping from northwest Europe, which is a rather small area of the globe that has quite a stringent and precautionary attitude to GM crops, because those companies feel that they wont be able to develop their products in northwest Europe. But there is a wider aspect also and that relates to the global need for sustainable food production.

I think we have tremendous expertise here in northwest Europe, and particularly in the UK, in the methods and approaches to developing crops that can be advantageously used in sustainable intensification. Not to capitalise on that expertise because sometimes – not always, but sometimes – that expertise relies on GM is wasting a huge opportunity in which many scientists in the UK would willingly give their expertise to help solve problems that are defined in developing countries in terms of malnutrition and even starvation.

I think there is a commercial aspect but I think more importantly there’s a huge ethical and ‘public good’ aspect, which we’re wasting in taking seriously this precautionary principle about GM.

GM corn varieties. Image source: Keith Weller, US Department of Agriculture

Does the perception of GM crops vary in different countries?

Yes, it certainly does. Even where I’m speaking from in Norwich [UK] it varies. When I speak with farmers, I think they are pretty well universally in agreement that they would love this technology. When I go to events in the centre of town, many local residents, particularly the allotment community, are quite against GM crops and think that organic agriculture might solve world food problems, which if you look into the literature it demonstrably cannot. Nationally, in the UK there is not tremendous support for these technologies. I was invited over ten years ago to Argentina to take part in a public debate on GM and in fact there really was not any opposition – among a wide ranging audience – to the notion that GM would help poor farmers as well as rich farmers, as well as the economy generally, and human health. If you go to Argentina or Brazil or the US, GM is not an issue. There’s widespread public acceptance I’d say.

What do you think needs to happen to move the public discussion on GM crops forward and can scientists help?

Scientists can help by presenting evidence objectively and impartially. That’s our job. Our job is not to talk about economic benefits. We can talk about health benefits or we can talk about risk or we can talk about climatic impact and those sorts of things. But there needs to be a wider ranging discussion. To that extent, I think it’s been helpful that the UK Government has come out to really nail its colours to the mast, in talking about the lost opportunities by not producing GM and talking about the potential benefits that we can have for taking a GM route in the UK.

Listen to excerpts of this Q&A alongside the views of four other leading plant scientists on how to address the impending food crises in the Biome podcast, as part of the Genome Biology special issue on plant genomics.

Mario Caccamo, Acting Director, The Genome Analysis Centre, UK

The world population is growing at an immense rate and is predicted to reach nine billion by 2050. Despite this, the land area over which crops can be grown will remain relatively constant, highlighting the need to significantly increase crop yields. Due to the importance of plant genomics in solving the impending food crisis, Genome Biology felt the time was ripe to dedicate a special issue to the topic, with an Editorial by Mario Caccamo providing an excellent overview of plant genomics research.

Plant growth and development are strongly influenced by environmental conditions, and with global warming affecting climate, it will be critical to understand how crops respond to environmental signals. In a recent study published in Genome Biology, Mario Pezotti and colleagues address this relationship in the fruit crop grapevine whose berries are susceptible to environmental changes, thereby affecting the quality of wine produced. They show that different seasonal climates have a much greater effect on berry gene expression and metabolism than different vineyard environments. For more discussion of this research, check out the Biome research synopsis and this accompanying podcast.

Another moreish crop, this time close to the hearts of many chocoholics, is the cacao tree. David Kuhn and colleagues describe the sequencing of a cacao cultivar, and use this to identify genes regulating pod color and quality, in their highly accessed Genome Biology research article. It is hoped that these results will aid cacao breeding programs, as discussed in the accompanying Biome research synopsis and this special edition podcast.

Whilst chocolate and wine are often reserved as treats, a more staple crop is that of bread wheat – one of the most economically important food crops across the world, yet one still lacking a complete genome sequence. In another Genome Biology special issue study, Catherine Feuillet and colleagues describe the construction of a physical map of wheat chromosome 1BL. It is hoped that applying the same methods to other wheat chromosomes will lead to a complete bread wheat genome sequence, as Feuillet discusses in this accompanying podcast.

Finally, GM crops first hit the headlines 30 years ago, but what exactly are GM crops and why have they been undergoing something of a renaissance of late? Dale Sanders tackles these and other questions in this special edition podcast. If you’re interested in reading more about the debate on GM crops, then check out our Q&A piece with Sanders.

* Please note that at the time of recording, Catherine Feuillet was located at INRA, France.
^§ Please note that the speakers discuss their own personal views and are not wishing to represent the viewpoints of their institutes.

The collection was initiated by Kuan-Teh Jeang (Teh), Founding Editor-in-Chief of Retrovirology, who sadly passed away earlier this year. Teh leaves behind a great legacy to the retroviral research community not only through his research, with discoveries into the mechanism of HIV transcription and replication, but also through his leadership of Retrovirology and his determination to advance retroviral research.

HIV thirty years on - A cross-journal collection

The ‘HIV thirty years on’ collection includes two articles published in BMC Biology from authors noted for their significant contributions to HIV research. Robin Weiss, whose 1984 Nature paper showed that the cell surface CD4 molecule on T cells acts as a receptor for HIV, gives his perspective on progress made in the last 30 years, focusing on the gymnastics of HIV entry into cells, and how this can be blocked by antibodies or drugs. Andrew McMichael describes in an interview how he was drawn into work on HIV in the 1980s and has been pursuing a T cell vaccine ever since. McMichael explains why there is still hope that with the right vaccine design it will be possible to induce T cell responses capable of suppressing the virus much more effectively than those acquired during natural infection.

Several reviews from Retrovirology provide in depth looks at advances in various aspects of retroviral research. Natasja de Groot and Ronald Bontrop consider the evidence for past epidemics of HIV-1/SIV like retroviruses in chimpanzee populations, and their potential relevance to today’s HIV pandemic. The interaction between host cells and HIV is key to understanding the infection mechanisms of the virus and how to overcome them. Eveline Santos da Silva and colleagues focus on the viral envelope cytoplasmic tail; looking at its structure, function and interaction with host cellular components. Viral cells are notorious for being able to exploit host cells for their own ends and HIV is no exception. Marie Larsson and colleagues look at T cell inhibition during HIV infection, while Carine Van Lint and colleagues review HIV latency in human cells and potential therapeutics to target this stage of infection.

Therapeutics are also tackled: Ravindra Gupta, David Van de Vijver and colleagues discuss the drugs that are waiting in the wings to help alleviate the HIV burden. In a review by Torben Schiffner, Quentin Sattentau, and  Lucy Dorrell the considerable impetus given to vaccine research by the finding that a few broadly neutralizing antibodies do arise during natural infection with HIV is highlighted. Schiffner and colleagues explain how this has re-ignited efforts to develop a prophylactic vaccine, with a number of promising and innovative approaches being used.

With the development of antiretroviral therapy, patients infected with HIV are living longer, with much improved quality of life, and BMC Medicine‘s contributions to the collection address how the advances in understanding HIV are being translated into daily clinical practice. A significant but unswered question is when to start therapy: Ricardo Franco and Michael Saag argue for starting therapy as soon as possible to reduce viral loads and prevent transmission, while Jens Lundgren and colleagues recommend a more cautious approach, recommending that therapy should be deferred until immunodeficiency develops to avoid unnecessary side effects.

In addition to appropriate timing of therapy, early diagnosis of HIV and its comorbidities is essential for effective treatment. In a video Q&A, Stephen Lawn discusses a new diagnostic test for HIV-associated tuberculosis (TB), and describes how it could save lives in resource-limited settings by improving rapid detection.

More of the latest research into HIV will be addressed at this year’s Frontiers in Retrovirology conference, run in conjunction with Retrovirology and marking the tenth anniversary of the journal.

The complete list of series articles:

HIV thirty years on

Pacific Biosciences single-molecule real-time (SMRT) technology has not gained a favourable reputation to date. Rich Roberts argues another look at the technology is needed. Image source: PacificBiosciences

By enabling the parallel sequencing of DNA, the introduction of next-generation sequencing technologies has been instrumental in driving down the costs involved in genomic studies. The technologies were genuinely game-changing, but the switch to high throughput assays introduced several limitations: biased error patterns and short read lengths.

In theory, single-molecule sequencing, in which DNA molecules are sequenced without amplification steps, was to offer a route to achieve high-throughput sequencing without these limitations; however, the first wave of single-molecule sequencing instruments floundered: Helicos Biosciences went bankrupt, ‘Project Starlight’ from Life Technologies was put on hiatus, and Pacific Biosciences’ single-molecule real-time (SMRT) platform quickly earned itself a reputation for unreliable, error-prone performance.

As the previously rapid climb in cost efficiency brought about by next-generation sequencing plateaus, the failure of single-molecule sequencing to deliver might leave some genomics aficionados despondent about the prospects for their field. But a recent Correspondence article in Genome Biology saw Nobel laureate Richard Roberts, together with Cold Spring Harbor’s Mike Schatz and Mauricio Carneiro of the Broad Institute, argue that the latest iteration of Pacific Biosciences’ SMRT platform is a powerful tool, whose value should be reassessed by a skeptical community.

In this Q&A, Roberts tells us why he thinks there’s a need for re-evaluation, and what sparked his interest in genomics in the first place.

How does SMRT sequencing differ from other existing next-generation sequencing technologies, and what benefits does it bring?

SMRT sequencing is a single molecule technique that can generate long reads (10-15Kb), is highly accurate and can distinguish methylated bases from the normal A,C,G,T.

This latter property is unique as no other method can do that for N6-methyladenine or N4-methylcytosine without additional chemistry being involved. This methylation information is both useful and intriguing. It can be used to determine methyltransferase recognition sequences and hence often the companion restriction enzyme specificity and contains important functional information that the methyltransferase is active. In addition it offers the possibility of looking at the epigenetic potential of bacteria. The significance of the long reads is also very important because it means that for small genomes the complete sequence can be obtained without the need for expensive and time-consuming gap closing methods that other Next-Gen technologies require. Instead of trying to do a 100,000 piece jigsaw puzzle the problem of sequence assembly is reduced to a 1,000 piece jigsaw puzzle – a considerable improvement.

What instigated you to write a commentary specifically on Pacific Biosciences’ SMRT sequencing technology?

There has been a misconception in the scientific research community that the method is very inaccurate.  In fact it is the most highly accurate of all of the Next-Gen sequencing technologies available.  This is because the errors, while high on a single read, are completely random and disappear statistically as more reads are made. A recent paper has shown that human polymorphisms can be found with greater accuracy using this technology.

Given that Pacific Biosciences’ SMRT sequencing has been subject to negative rumors, how did you come to realise that this technology is actually a valuable and accurate tool? 

My original principle interest was in the methylation patterns as it seemed to offer the possibility of determining the recognition specificities of restriction modification systems in an extremely facile way. This turned out to be true and has yielded a plethora of new and interesting results. Along the way it became clear that this technology had much greater promise than the early scurrilous rumours suggested. A major reason that the community has not appreciated this is that very few of them have tried it. The original rumors put them off from buying the machines.

Of all the different benefits of SMRT sequencing, which do you think will be the most persuasive in getting people to adopt it?

I suspect that the accuracy of the sequence and the ability to easily close small genomes will be an important selling point. At present GenBank is littered with shotgun sequences that for the most part are close to worthless because they tell you very little about the organism from which they came.  This is because you never know what is missing – it could be the gene you are most interested in!

In contrast a complete genome sequence is invaluable as it tells you the full genetic potential of the organism.  All we need to do now is to improve our bioinformatics so that we can properly interpret that DNA sequence. Unfortunately, we are not spending enough money doing the functional analysis of the sequences we are obtaining and our biological research agenda is suffering because of it. Just at the moment we should be greatly increasing our efforts to gain functional insights into the millions of genes we are discovering by sequencing and for which we either have no idea of what they do, or many of our predictions are simply wrong.  But the only way we will know if they are wrong is by critically testing selected subsets of them.  I don’t see anything like enough funding to do this.  It is very short-sighted of NIH and the biological community not to demand more functional annotation of the genomes we are sequencing.

Should nanopore sequencing become a commercially viable reality, do you think SMRT sequencing will become redundant or can these two technologies co-exist?  

It depends what you mean by nanopore sequencing. I haven’t heard of anything that I believe in so far.  Where is the data showing that it works? Despite the claim by Oxford Nanopore that they can read methylated bases, they never answered my emails offering to test those claims critically.

Current next-generation sequencing software is designed for short reads. With the longer sequence reads of SMRT sequencing, are we going to have to revisit old software solutions that were developed for long reads generated by Sanger sequencing?

It is always a good idea to revisit software. In the case of 10 Kb reads the earlier software should be up to the task as it has become easier.  However, with methylated base data also available some other improved approaches should be possible. I helped write the original assembly programs back in the 1970s, but have not given much thought to the problem since then as we were just interested in what would now be considered short sequences (Adenovirus-2 was just 36 Kb long).  The sequences needing assembly today are megabases or gigabases long and more challenging.  I am having too much fun exploring bacterial epigenetics!

You have forged an extensive career in biochemistry and molecular biology. What led to your interest in genomics?

As an organic chemist in the late 1960s I became fascinated by the chemical problems posed by molecular biology. It was clear that DNA sequencing was going to become of crucial importance. After doing a post-doc spent sequencing some tRNAs I moved to Cold Spring Harbor Laboratory with the idea of developing new methods to sequence DNA.  I thought the newly-discovered restriction enzymes would be key in generating small DNA molecules (not available naturally) with which to develop methods. Instead I got seduced by the restriction enzymes and their companion methyltransferases and these have now been the main focus of my research for 40 years. They are fascinating and have led me into areas I would never have suspected.  They are a paradigm of biology and exhibit most of the traits that make biology such a fascinating subject. I can’t imagine leaving them behind just yet. For one thing they led me into bioinformatics, which is now also a great love of my life.

During the course of your career you have made several notable contributions that have significantly furthered biological research. Which contribution are you most proud of or consider the most important?

Obviously the discovery of split genes and RNA splicing was an amazing outcome of research into Adenovirus transcription. But I feel that the role I played in discovering so many of the early restriction enzymes and pushing their commercialization has had a profound impact on biological research and enabled the whole biotechnology industry to take off. Because we were very generous in giving away samples of the first restriction enzymes to anyone who wanted them I made a lot of friends who have remained so throughout my scientific life. That has been extremely rewarding!

Readers interested in the application of SMRT sequencing to human genomics might be interested in this presentation by Mount Sinai’s Eric Schadt, previously of Pacific Biosciences.

To join the debate about the virtues (and vices) of this technology, please look out for Genome Biology’s Twitter chat – more information from the BioMed Central blog.

The outbreak of HCV infection in Valencia that led to the court case was exceptionally large and complex, and the phylogenetic evidence would not have been sufficient by itself to identify the source. The issues raised by the use of phylogenetic inference in court are discussed more generally in an accompanying commentary by Anne-Mieke Vandamme, who two years ago convened a working group of the world’s leading experts on this subject, and Oliver Pybus, who uses phylogenetic analyses in his own work on the molecular epidemiology and epidemic history of HIV and HCV.

Convictions obtained through DNA fingerprinting, where samples from the same person are identical, are now commonplace, but  Vandamme and Pybus point out that sequence-based phylogenetic analysis of highly mutable viruses such as HIV and Hepatitis C virus is much less straightforward. These methods have become increasingly sophisticated, and in addition to proving invaluable in reconstructing the likely evolutionary history of viral epidemics, they are starting to be used more frequently in forensic settings. Tracing the source of the infection through a phylogenetic analysis, however, presents challenges of interpretation that are formidable, because HCV (like HIV) evolves within a single infected individual. This challenge is particularly compounded when, as in the Valencian case,  the outbreak occurred over a considerable length of time.

Phylogenetic analyses reconstruct the most likely path of evolution leading to the diversity of viral sequences present at any one time, allowing an estimation of the evolutionary distance between the viruses carried by any two individuals, and the probability that they derive from a common source. In some cases, when the sequences found in one individual nest within a greater diversity of sequences found in a putative source, they provide evidence for the direction of transmission from one individual to another. But as Vandamme and Pybus point out, it is always possible that sequences present in infected individuals have come from some source that hasn’t been sampled. A further complication arises from the fact that HCV replicates in the liver, so samples taken from blood (as in the Valencian case) may not reflect all of the sequences present in the individual. This could explain why the phylogenetic tree constructed by Gonzalez-Candelas and colleagues did not in fact point to the anaesthetist as the source of the outbreak (though he was clearly a part of it). Strong evidence from other sources however clearly pointed to the anaesthetist as the source; and indeed, Vandamme and Pybus emphasize that it is generally the case that sequence-based viral phylogenies are used only to support evidence of other kinds in convictions.

The sequence-based analysis did however clearly indicate that 47 patients, who on the basis of their medical history could have been infected with HCV-1a by the anesthetist, in fact carried sequence variants indicating they were far more likely to have been infected from an alternative local source.

Not surprisingly then, some experts argue that viral phylogenies should only be used to rule putative sources of infection out (or cast serious doubt upon them), not to assign culpability.

As so often with structural studies, homologous proteins from various species have been recruited to build a picture of the structural basis of the E1 mechanism, and the details of E1 structural acrobatics have been worked out by Brenda Schulman and colleagues from St. Jude Children’s Research Hospital, USA and by Christopher Lima and colleagues from Sloan-Kettering Institute, USA through a collage of pictures largely derived from two different E1s juggling with two different ubiquitin-related small proteins (SUMO and NEDD8). These are described, with exemplary schematic diagrams, in a recent review in BMC Biology by Sonja Lorenz and colleagues Aaron Cantor, Michael Rape and John Kuriyan from the University of California, Berkeley, USA, who also discuss the structural flexibility required for transfer to the target by E3 enzymes, and the exploitation of this flexibility in the regulation of ubiquitin signalling.

Cartoon representations of E1 ubiquitin enzyme in the adenylation state. Image source: Lorenz et al, BMC Biology, 2013, 11:65

The minutiae of structure and mechanism, however, no matter how elegant, do not always lend themselves to lively and engaging prose, and in response to the comment of a referee to this effect, Lorenz and colleagues have summarized the macromolecular juggling sequence as the E1 passes its substrate from one catalytic site to the next in a video – with the careful disclaimer that the transitions between the different states captured by the crystal structures are of course hypothetical. The domains light up in color as each comes into play, and the whole thing is set to the score of ‘The juggler’ by Ernst Toch, modified and performed on the piano by first author Sonja Lorenz, and culminating in a triumphant chord as the E2 enzyme docks into its binding site at the end of the sequence.

Home garden in Mutugama, Sri Lanka. Image source: Wikimedia Commons, freelk

“Fundamentally, home gardening provides a supplemental source of foodstuff for the family. But their importance goes beyond that. In many developing countries, home gardening becomes a survival strategy when food security is threatened by limited food availability and access. At other times, it is a resilience strategy to mitigate risk and vulnerability due to different natural and man-made stresses.”

Home gardens comprise small areas of land close to the homestead, where a family can grow subsistence produce. These gardens can incorporate a diverse range of agricultural practices. Commonly, gardens are used for growing fruit, vegetables, plantation crops, spices, herbs and medicinal plants as well as rearing livestock, which not only provide a vital source of protein but also additional income.

“The significance of home gardens is grossly undervalued and their full potential is yet to be unravelled”
Dilrukshi Galhena, Michigan State University

Home gardens represent an environmentally friendly and sustainable agricultural practice, which is effective at improving food security and economic stability. Galhena remarks that “There are a number of programs supporting home gardening in many countries. The majority of these efforts prioritize developing countries with acute hunger and malnourishment problems. The Food and Agriculture Organization (FAO) of the United Nations and Helen Keller International (HKI) have made remarkable strides in successfully implementing home garden projects.”

However, it still remains important to ensure that future policies and interventions encourage the most efficient and effective use of home gardens, while preserving natural resources and processes (ecosystem services).

“It is an important challenge to keep up the involvement and enthusiasm for home gardening. To overcome resource limitations, programs on home gardening should call for strategies to facilitate training in best practices and to integrate low-input approaches that will improve the productivity of home gardens. Creating awareness of the benefits of home gardening, stimulating entrepreneurship and facilitating market links are indispensable to the sustainability and promotion of home gardens,” asserts Galhena.

“Home gardening can add to the process of building peaceful societies by helping to mitigate issues such as hunger and poverty that often lead to conflict.”
Dilrukshi Galhena, Michigan State University

The authors identify post-conflict situations as circumstances where home gardens may play a particularly critical role in ensuring food and nutritional security. They specifically focus on Sri Lanka, a country where home gardens have been used extensively for centuries and that has recently seen an end to a 30 year civil war. “Our visit to Sri Lanka, specially the civil war-affected areas in the North inspired us to investigate the issues related to food security and livelihoods,” says Galhena. “Home gardens have helped war-affected people in Sri Lanka improve their food situation and at the same time engage in an employment activity to support their own families and the local community.”

However, due to a lack of research documenting this situation, Galhena and colleagues conclude by  recommending further investigation in order to base policy on solid evidence. “One of the biggest knowledge gaps we identified is the lack of literature capturing and sharing the experiences of home gardening in post-conflict scenarios,” adds Galhena. “We still need to do a lot of work and gather empirical evidence from countries like Sri Lanka. Documenting and quantifying the impact of home gardens in post-conflict situations, will be useful to broaden our knowledge and to assist countries and regions emerging from conflict.”