Why do we love medicines so much?

An evolutionary perspective on the human love of pills, potions and placeboHumans love medicinal drugs; we cannot get enough. Worldwide, the amount of money spent on medicines annually is growing exponentially and is expected to reach around US$1 trillion in 2012. So far, there has been no satisfactory explanation for human ‘pharmophilia'', our powerful tropism to medicines. Most studies that have attempted to provide an explanation have focused on classical supply–demand economics. Here, we suggest a different explanation: pharmophilia evolved as a means to cope with disease and sickness and is mediated through belief-induced neurological and immunological signalling pathways. Given that our love for drugs seems to be hard-wired into our biology, such an assertion has both social and economic repercussions. If public health policies do not take into account our strong pharmophilia, we will continue to overspend on and ‘over-value'' drugs at the expense of non-medicinal treatments and prevention strategies. Human pharmophilia is also a threat to biodiversity; one that has already brought many animal and plant species to the brink of extinction.If public health policies do not take into account our strong pharmophilia, we will continue to overspend on and ‘over-value'' drugs…The World Trade Organization estimates that global spending on pharmaceuticals reached US$427 billion in 2008 and, given an annual growth rate of 5.5%, projects a staggering US$929 billion in 2012. In many countries, expenditure on medicines now accounts for more than 1% of GDP (Hubbard & Love, 2004) and even were the human population to stabilize somewhere around 2050, we would still spend increasing amounts of money on medicines to improve and extend our lives. Today, most of the money spent comes from the 1.3 billion customers in the established market economies (EME), while most of the global population still rely on traditional medicines: 65% of the 6.5 billion humans on Earth depend on folk materia medica. This will change rapidly during the next 40 years. The populations of the EME—the current principal users of expensive pharmaceuticals—will ultimately account for only 11% of the global population by 2050 (UN Population Division, 2008), but the huge population expansion in middle-income countries—of up to 7.8–9 billion people—will massively increase demand for both pharmaceuticals and traditional folk medicine (Sivin, 1987). The ‘bottom billion'' in low-income countries will swell to nearly 2 billion by 2050, but will continue to rely almost entirely on folk medicine.…the huge population expansion in middle-income countries […] will massively increase demand for both pharmaceuticals and traditional folk medicine…This extraordinary expansion has significant implications for national health-care systems, the pharmaceutical industry and billions of patients. Although the EME spend the most on pharmaceuticals in absolute terms—USA, 46.7% of total expenditure; Europe, 24.8%; and Japan, 11.3%—compared with low- to middle-income countries—Sub-Saharan Africa, 1.3%; India, 1.8%—there is a huge difference in terms of out-of-pocket expenditure on medicines. Sub-Saharan Africa and India are leading the way with 65% and 81%, respectively, compared with a maximum of 40% in some EME countries (Davis, 1997).Rightly or wrongly, public health policies have focused on economic factors with little regard for the social, biological and cultural causes of pharmophilia—a phenomenon that has had a considerable impact beyond public health systems on both global biodiversity and traditional medicine. Intelligent public health policies and new policy frameworks that encompass traditional medicines, biodiversity and public health therefore need a better understanding of what drives our consumption of medicines. In this regard, our evolutionary past could provide an explanation to help understand our pharmophilia, as it combines an evolutionary perspective of health with the placebo effect and its underlying biology.The earliest evidence that our ancient ancestors actively sought to improve their health dates to the Middle Palaeolithic period, some 60,000 years ago, and is based on pollen found at a Neanderthal burial site, suggesting the use of medicinal plants (Solecki & Shanidar, 1975; Lietava, 1992). We do not know whether this behaviour extends further into the past, but the finding indicates that our ancient forbears probably used natural remedies to treat injuries and disease.In addition to the historical evidence of the use of medicinal plants, we have growing molecular and clinical knowledge of the placebo effect, which is key for explaining human pharmophilia. The word placebo actually comes from a mis-translation of the Bible by St Jerome, an Illyrian priest (Fig 1) who incorrectly translated the ninth line of Psalm 116, which should be “I will walk”, into “I will please”—placebo in Latin. The first use of placebo as a ‘dummy intervention'' has been credited to the efforts of progressive Catholics in the sixteenth century attempting to discredit right-wing exorcisms (Kaptchuk et al, 2009). The modern confusion and controversy about the placebo effect in modern medicine results from the use of the term ‘placebo'' to refer to an inert dummy medicine, whereas the placebo effect itself is now widely recognized as a real biological mechanism.Health-seeking behaviour is still found across the animal kingdom and ranges from hard-wired, genetically determined behaviours to learned strategiesOpen in a separate windowFigure 1St Jerome writing. Circa 1604 (oil on canvas), Michelangelo Merisi da Caravaggio (1571–1610). Galleria Borghese, Rome, Italy / Bridgeman, Berlin.Notwithstanding the confusion, cultural anthropology has recognized the positive effects of placebo for more than 70 years. It was first described by the anthropologist Melville Herskovits (1948), and latter codified into a seminal article, The Powerful Placebo, by Henry Beecher (1955). Further research by anthropologists and molecular biologists revealed a unique neuroimmunological signalling and regulatory pathway, which is activated by a belief in the healing power of treatment and depends on the interaction of the patient, the medicine man and the medicine—nearly all of which include verbal communication. As Ankrah Twumasi described the Ashanti traditional system, “the positive psychological value of the medicine man as a medicine, which makes it possible for the patient to believe that he has established rapport with the “god” that controls him and contributes to his feeling of health has long been recognized” (Twumasi, 1987).From a neurocognitive and psychophysiological stimulation perspective, the placebo effect is poorly understood. There have also been numerous claims about the efficiency of the placebo effect that have fallen foul of methodological issues and/or have wildly overestimated its potency (Hrobjartsson, 2002). However, recent evidence shows that placebo does produce changes in brain activity similar to agents that act directly on neurological pathways—such as fluoxetine to treat depression—and subsequent immunological pathways (Mayberg et al, 2002). The placebo effect thus seems to operate both by classical conditioning and through thought-induced mechanisms (Lieberman et al, 2004) in cortical areas that generate and maintain cognitive experience through dopaminergic reward pathways. Indeed, pharmacological and psychostimulation are both able to yield similar neuroimmune changes (Fig 2; Faria et al, 2008). This evidence from the neurological and cognitive sciences provides a plausible mechanism for our tropism towards medicines. Irrespective of the real potency of any ingested medicines, a sufficient ‘thought-induced'' belief in their efficiency activates pathways that, in turn, generate a demonstrable biological effect.…evidence from field and laboratory studies demonstrate that human tropism towards medicines is not a recent social phenomenon, but has old evolutionary rootsOpen in a separate windowFigure 2Neurobiology and immunobiology of the placebo effect. Adapted from Pacheco-Lopez et al (2006).From a systems perspective, the placebo effect is a highly flexible neuroimmunological system. Multiple integrating pathways coalesce into a common ‘mission-critical'' system—in this case the neuroimmunological axis, an evolutionarily conserved pathway that is essential for the functioning of the organism—that can be fired up in response to a noxious insult. This biological system fits with the anthropologists'' view that, “the value of medicines seems to be based on a perception of them as having an inherent power to heal” (van der Geest & Whyte, 1989).Indeed, if we look at the placebo effect from an evolutionary perspective, its evolution and impact on our species makes even more sense. First, humans did not evolve in the presence of highly efficient medicines—most were developed only within the past few decades. Second, our ancestors obviously ingested pharmacological agents, mostly from plants, which are much less potent than today''s drugs, but might still have had a mild effect. Finally, we know from a systems perspective that diversity builds resilience. Therefore, we suggest that evolution would have favoured a web of diverse signalling pathways, such as the neuroimmunological axis, to increase resilience and adaptability and help us to heal ourselves.Put another way, as Gustavo Pacheco-Lopez and colleagues eloquently summarize in their extensive review of the neurobiology of immunomodulatory placebo effects: “Placebo effects can, therefore, benefit end organ functioning and the overall health of the individual through the healing power of belief, positive expectations and conditioning processes” (Pacheco-Lopez et al, 2006). But how then has the placebo effect arisen? Or put another way, what is the ultimate causation of this proximate mechanism? (Tinbergen, 1972).To address this question we need to look at evidence from comparative biology to ascertain the evolutionary origins of pharmophilia. In fact, our species is not the only one that uses proto-medicines. Health-seeking behaviour is still found across the animal kingdom and ranges from hard-wired, genetically determined behaviours to learned strategies. At one end of the spectrum, eusocial organisms, such as wood ants, incorporate conifer resin into their nests, which inhibits the growth of a wide range of pathogenic organisms. Medicinal strategies such as geophagy—the consumption of soil and charcoal to detoxify poisonous substances (Struhsaker et al, 1997)—also appear in a wide range of species, from parrots and new-world monkeys to apes such as gorillas and humans. Some of these behaviours might actually be feeding strategies to eat plants with high levels of phenols, which would otherwise be poisonous, or they might be learned strategies to cope with gastric problems after the accidental ingestion of a toxin. Either way, geophagy has been observed across a broad range of taxa, including species that we do not usually consider highly ‘intelligent''. Indeed, there is now good experimental evidence that sheep actively medicate themselves with tannins to control parasites (Lisonbee et al, 2009). The point is that proto-medicine-seeking behaviour appears in two species—sheep and man—that shared a common ancestor around 100 million years ago.The supposed schism between prevention and treatment might simply be a reflection of our deep-seated pharmophiliaHowever, it is species with higher intelligence that provide the most compelling evidence for the evolutionary roots of pharmophilia. Over the past two decades, Michael Huffman and colleagues have investigated the use of plants with medicinal properties by other species, in particular non-human primates. Through field studies and the observation of captive primates, they found that bonobos and chimpanzees—our closest living relatives with whom we shared a common ancestor around 6–7 million years ago—use herbaceous leaves such as Desmodium gangeticum for their phytochemical properties, or rough hispid leaves as a mechanical device by which to rid themselves of parasitic infections such as the worm Oesophagostomum stephanostomum (Huffman & Hirata, 2004; Fowler et al, 2007; Dupain et al, 2002). A recent field study of bonobos in Wamba, Congo, observed febrile, clearly sick adults eating an unidentified species of Manniophyton, known locally as Lukosa (Fig 3); it is a plant that is used in many traditional medicines to control fever.Open in a separate windowFigure 3Bonobo (Pan paniscus) in the wild. The inset shows Manniophyton fulvum.These learned medicinal behaviours are not unique to higher primates. In South Africa, sick Knysa elephants seek out and eat specific types of medicinal mushroom known for their immunostimulatory effects. The fact that these bracket tree fungi are extremely bitter and are not part of the elephants'' normal diet suggests strongly that this is medicine-seeking behaviour (Patterson, 2004). Together, this evidence from field and laboratory studies demonstrates that human tropism towards medicines is not a recent social phenomenon, but has old evolutionary roots.Pharmophilia has profound implications for public policy. In fact, the understanding that the placebo effect probably developed from proto-medicine-seeking behaviour millions of years ago among a range of animal species provides a novel framework to understand why medicines are globally ‘over-valued''. So far, the medicalization of health has been seen almost exclusively as an issue of supply—that is, the promotion of medicines and the medicalization of disease by society and the pharmaceutical industry. Yet, ‘value'' is a complex multidimensional concept that incorporates sociocultural, political and economic parameters. From an evolutionary and psychological perspective, pharmophilia is therefore likely to contribute substantially to increased expenditures across most therapeutic categories of pharmaceutical products.Public health policy and the economic analysis of pharmaceuticals has largely explained our use of medicines to treat illness in terms of rational factors, such as medical needs, patterns of care, access to technology, marketing forces, pricing and costs. However, neither of the two standard views of rational behaviour—‘consistent choice'' or ‘self-interest maximization''—has been able to provide an adequate representation of rationality or of the actual situation, according to the Indian economist Amartya Sen (Sen, 2009). Perhaps the answer lies in pharmophilia, which operates through both the supply and demand side of medicines and creates the uncertainty that current rational behaviour models find so difficult to predict.The ongoing demand for TM […] is accelerating the loss of biodiversity and pushes many plant and animal species close to extinctionIf we include pharmophilia into the analysis, neither the consumer nor the supplier acts rationally—both are driven by our evolutionary desire to seek medicines. If this is really the case, unregulated supply and demand will continue to feed on each other to create an ever-increasing spiral of consumption and costs.Current public policy approaches should take pharmophilia into account. Regulation is therefore the only efficient method of controlling the use of medicines by attempting to reduce demand; perhaps by controlling direct-to-consumer advertising and accepting that people will not act rationally within the context of health and medication. The assumption that a rational, logical argument can lead to a down-valuation of medicines is, according to this view, wrong. The supposed schism between prevention and treatment might simply be a reflection of our deep-seated pharmophilia. As such, extensive public debate about the need to shift public health policies from treatment to prevention will change little.Pharmaceutical public policy should turn this view around and regard the placebo effect as an ally of the medicalization of health. As Peter Davis, a medical sociologist at the University of Auckland in New Zealand, has argued, the use of medicines is a “visible expression of concern”; it is the ‘total drug effect'' that helps to increase the well-being of the patient (Davis, 1997). Although this seems initially to be a rather weak argument, closer inspection reveals that interaction with a doctor and the giving and receiving of medicines clearly does increase well-being. The unfettered popularity of complementary and alternative medicine (CAM)—or rather integrative medicine, as it is now called—is a case in point. While orthodox medicine has been constantly rallying against CAM, all evidence suggests that this has been a Canute-like reaction, a tide we cannot hold back. Despite the pronouncements of eminent scientists and many clinical trials, most of which show modest or no effect, the uptake of such practices is increasing. Cultural arguments that this is filling a holistic lacunae might be partly true, but it does not explain why so many patients believe in the benefits of CAM. The concept of pharmophilia would comfortably explain this apparent mismatch between CAM and patients'' beliefs.However, in both cases—pharmaceuticals and CAM—the problem is not so much the concept as the cost and the potential for harm, both of which need to be managed from a public policy perspective. Surveys in developing and middle-income countries by the World Health Organization and Health Action International have shown that 90% of the population in these countries purchase drugs through out-of-pocket payments, which makes medicines the biggest family expenditure after food (Cameron et al, 2009). The mantra of prevention, public health, non-pharmaceutical interventions, and the doctrine of ‘global public good''—that is, health policy responding to the objectively greatest need—might be intellectually satisfying, but it clearly does not reflect reality and the future trajectory of the continuing ‘pharmaceuticalization'' of disease in these countries (Smith & Mackellar, 2007).The great gap between prevention and cure is not simply a matter of history but a fundamental aspect of our evolution. Public policy cannot expect a rational choice based on utility when our evolved psychologies have such a strong tropism for medicines (Sen, 2009). Recognition of this sheds new light on the issue of how we promote medicines and in particular how we regulate or accept direct-to-consumer advertising, one of the most contentious battlegrounds in market economies. By ‘over-valuing'' medicines, unconstrained public policies in favour of drugs and medicines will have two effects: first, they will further drive up expenditure beyond rational-use limits; second, they will under-value the contribution towards health and disease management of prevention and non-medicinal modalities, such as surgery. The nature of human pharmophilia suggests that continued stringent controls on advertising and more thoughtful rational approaches to cost-effectiveness analyses need to come from public policy as they are unlikely to arise through market forces.Pharmaceuticals represent one end of the spectrum in terms of human medicines. However, the most abundant usage of medicines by far, now and in the future, is traditional medicine (TM). This pharmacopoeia of folk medicine, as well as organized TM systems such as Ayurvedic and Chinese medicine, contains hundreds of thousands of plants, animal, mineral and other substances (Alves & Rosa, 2007). TM dominates health care outside high-income countries and has an increasing role in complementary and/or integrative systems in developed countries (Fig 4). The World Bank estimates that the ratio of those trained in Western medicine to TM practitioners in various African countries is between 1:1,639 in urban South Africa to 1:50,000 in Malawi and Mozambique (Cunningham, 1993). Higher resolution studies, for example in South Africa, estimate that about 5.6% of the national health budget is spent on TM; much more, however, comes from out-of-pocket payments.…any public policies to address the health situation in both affluent and developing countries can only be successful if they take into account the human factorOpen in a separate windowFigure 4The South African medical plants industry. Adapted from Mander et al (2007). GMP, good manufacturing process.It is not only the cost that is at issue here. The ongoing demand for TM, a product of both population growth and increasing per capita purchasing power, coupled with a loss of habitats through climate change, over-usage, deforestation and other factors, is accelerating the loss of biodiversity and pushes many plant and animal species close to extinction. For example, some 200 animal and 550 plant species are actively traded in KwaZulu-Natal (South Africa); 60% of these are now reported as scarce (Mander et al, 2007). Population increases in Asia and Africa with unconstrained demand for TM coupled to non-sustainable habitat loss is a massive threat to biodiversity. The focus of the Convention on International Trade in Endangered Species and other bodies on critical species represents only the tip of the iceberg and public policy has only recently realized the extent of the problem. While problems such as deforestation and habitat loss have attracted public notice and led to public policies to alleviate these, the issue of how to provide sustainable TM for populations in much of Africa and Asia has received scant attention. Integrating TM into public health systems with policy approaches centred on conservation is a huge challenge, in particular because TM remains a totally unregulated arena. However, it is essential that countries that are dependent on TM as a source of health care urgently address the problem. It is only within these nations that effective measures can be taken.More generally, though, any public policies to address the health situation in both affluent and developing countries can only be successful if they take into account the human factor. Our pharmophilia is a deeply engrained behaviour and an important aspect of our health and well-being. It needs to be better understood and incorporated into global health policy frameworks.? Open in a separate windowIsabel BehnckeOpen in a separate windowRichard SullivanOpen in a separate windowArnie Purushotham     

Tackling animal diseases to protect human health

Veterinary research is gaining in importance not only because of the economic impact of animal diseases, but also because animals are a fertile reservoir of zoonoses; pathogens that could jump the species barrier and infect humans.In 1761, King Louis XV of France proposed that a veterinary school should be founded in Lyon. He had been troubled by the ongoing scourge of cattle disease and inspired by the Italian physician Giovanni Maria Lancisi, who recommended that medical education should include a specialization in animal health. The year 2011 marked the 250th anniversary of that event and was declared ‘World Veterinary Year'' (Vet2011) to celebrate the birth of the veterinary profession and veterinary science. The motto adopted was “Vet for health. Vet for food. Vet for the planet!”, evoking the key role that veterinarians play in protecting both animal and human health, and in enhancing food security. “The emergence of health risks associated with globalization and climate change creates an ever greater need for risk managers at international, regional and national levels. Among these, veterinarians already play and will continue to play a leading role […] for instance performing disease surveillance and providing a first level of alert, so that biological disasters, natural or deliberate and regardless of whether they threaten animals, humans or both, can be stopped at their source in animals,” said Bernard Vallat, Director General of the World Organization for Animal Health (OIE), at the Vet2011 opening ceremony in Versailles, France, on 24 January 2011 (www.oie.int).In the same year, on June 28, delegates from the member countries of the United Nations'' Food and Agriculture Organization (FAO) officially announced the eradication of ‘rinderpest''—a German word for ‘cattle plague''—a highly contagious and deadly virus affecting cattle, buffalo and related species such as African zebu cattle. The mortality rate for rinderpest can reach up to 100% in susceptible herds, and recurring pandemics and outbreaks caused devastating losses to societies dependent on cattle (Fig 1). A severe outbreak of rinderpest in Belgium, in 1920, that originated from imported animals, was the impetus for international cooperation in controlling animal diseases, eventually leading to the establishment of the OIE in 1924.Open in a separate windowFigure 1Animal remains. Dead oxen, some partly buried, thought to have died from rinderpest, circa 1900, South Africa. Photo by Reinhold Thiele/Thiele/Getty Images. Reproduced with permission.After a long series of country-based eradication initiatives that relied on a mixture of quarantine, slaughter and vaccine mass inoculation, the FAO formed the Global Rinderpest Eradication Programme in 1994 to co-ordinate international efforts and to provide technical guidance and financial support, in close co-ordination with the OIE and other institutional partners and donors. The last known case of rinderpest occurred in Kenya in 2001, after which a prolonged phase of surveillance operations started. “This successful eradication shows that actions against animal diseases do not come within concepts of agricultural or merchant good but within the concept of Global Public Good because by alleviating poverty, contributing to public health and food security, and improving market access as well as animal welfare, they benefit all people and generations in the world,” Vallat said in a press release announcing the eradication declaration [1].The year 2011 […]was declared ‘World Veterinary Year'' (Vet2011) to celebrate the birth of the veterinary profession and veterinary science“Rinderpest is the first animal disease to be eradicated by mankind and the second disease in general after smallpox. We must also focus our attention on measures to be taken to ensure that this result is sustainable and benefits future generations. To do this, a post-eradication strategy should be put in place to prevent any recurrence of the disease”, remarked FAO Director-General Jacques Diouf in the press release [1]. “In the final stages of eradication, the virus was entrenched in pastoral areas of the Greater Horn of Africa, a region with weak governance, poor security, and little infrastructure that presented profound challenges to conventional control methods. Although the eradication process was a development activity rather than scientific research, its success owed much to several seminal research efforts in vaccine development and epidemiology and showed what scientific decision-making and management could accomplish with limited resources,” noted Jeffrey Mariner from the Tufts Cummings School of Veterinary Medicine in North Grafton (Massachusetts, USA) and colleagues, in a paper published in Science, which reviewed this remarkable achievement [2]. “The keys to success were the development of a thermostable vaccine and the application of participatory epidemiological techniques that allowed veterinary personnel to interact at a grassroots level with cattle herders to more effectively target control measures”.Potentially dangerous rinderpest virus samples are kept in several laboratories across the world, but not all of those laboratories are considered to work under a regime of sufficient biosecurity. To address this, immediately after rinderpest was stamped out, FAO and OIE member countries agreed to destroy the remaining virus stocks or to safely store them in a limited number of high containment laboratories, banning any research that used the live virus, unless approved by the two organizations. This recommendation came from an external committee composed of seven independent experts, convened by the FAO and OIE, which advised the use of measures similar to those used during the post-eradication period for smallpox; the virus, which might still prove useful for research or vaccine development, should be kept in a limited number of labs—two in the case of smallpox—under the tightest security measures, whilst all other stocks should be destroyed [3]. Monitoring and surveillance for rinderpest virus outbreaks will continue until 2020, and experts are already considering which disease should be the focus of eradication efforts next (Sidebar A).

Sidebar A | Peste des petits ruminants: next in line for eradication?

Now that rinderpest has been stamped out, many experts believe peste des petits ruminants (PPR) is the next disease amenable to global eradication [11]. Also known as ‘goat plague'' or ‘ovine rinderpest'', PPR is a highly contagious viral disease of goats and sheep characterized by fever, painful sores in the mouth, tongue and feet, diarrhoea, pneumonia and death, especially in young animals. It is caused by a virus of the genus Morbillivirus that is related to rinderpest, measles and canine distemper. The disease has spread across Africa between the equator and the Sahara—with outbreaks in Morocco and Tunisia in 2008—through the Arabian Peninsula, the Middle East, south-west Asia, China and the Indian subcontinent, extending its range alarmingly during the past decade. PPR might cause serious production losses in the developing world—with a significant number of people relying on sheep and goats for their sustenance—and poses a major challenge to international livestock trade. “If one is looking to control the disease to the point of eradication, there are three basic questions: should we do it, can we do it and what is the best way to do it?” said Michael Baron, a leading expert in PPR control at the Pirbright Institute, formerly known as the Institute for Animal Health (Pirbright, UK). The question of whether we should eradicate PPR needs no discussion, Baron maintains, as there would be a large benefit to millions of people if the disease were gone. “Can we is a bit harder, but the example of rinderpest assures us that we can, since the viruses in question share the same properties, and all the main tools are in place,” Baron explained. These tools include a safe and reliable vaccine that stops all known PPR strains, together with simple and effective diagnostic tests. Moreover, the virus is spread by close contact only, has a short infectious period and there is no carrier or persistent state, all of which make its eradication possible. Finally, the virus seems to be primarily restricted to livestock, although some research on wildlife is needed to be sure that they cannot act as reservoirs of infection. “How should we is the bit that still needs work. Rinderpest was quite well studied before eradication was proposed—it had been known of for hundreds of years, whereas PPR has only been known about since 1942—and we need to know more about when we should vaccinate, how often, how much surveillance needs to be done, and how to adapt our control programmes to the fact that sheep and/or goats are simply so much more mobile, and people will insist on moving them around illegally,” Baron said. “We could throw a lot of money at the problem, but it might not get solved any faster than if we think about it and plan the campaign, and conduct some smaller scale pilot studies.”Peste des petits ruminants in the field. This photo, by the Indian photographer Somenath Mukhopadhyay, won the ‘Vets in your daily life'' photo contest in 2011, organized by the European Commission and the World Organization for Animal Health (OIE). “I accompanied this village veterinarian on his rounds when I came across this engaging image of him taking the temperature of a goat affected by peste des petits ruminants. On this third visit to the household, the goat was in recovery phase thanks to the medication it had been given. The photo to me is the ultimate portrayal of what a vet means to us,” commented Mukhopadhyay. Credit: CE/OIE. Reproduced with permission.In addition to fighting animal diseases, another front where veterinarians are deployed and where research is more active is the transmission of diseases from animals to humans; in fact, this is an area of growing concern. Some 60% of human epidemics are caused by animal pathogens found in the wild or in domestic animals. Among such ‘zoonoses''—diseases or infections that are naturally transmissible from vertebrate animals to humans—some can be considered as re-emerging diseases. Brucellosis, which is caused primarily by the bacterial pathogens Brucella melitensis and B. abortus, and which affects several farm animals including sheep, goats and cattle, is such a case. Brucellosis is characterized by the constant changing of the disease, with new foci emerging or re-emerging, as humans are infected through contact with diseased animals or by consuming unpasteurized dairy products. Although infections with Brucella are no longer fatal, they still represent a serious public health problem. 500,000 new human cases are reported each year worldwide with significant economic impact from both the loss of labour and the loss of animal production [4]. As such, research into brucellosis is active in several directions, such as the development of vaccines, vaccine delivery strategies, diagnostic testing for brucellosis in animals, mechanisms of intracellular survival of this persistent bacterial colonizer and research into how it circumvents the immune system [5].Various factors influence the re-emergence of zoonoses or the emergence of new pathogens from animal reservoirs. “To support the growing human population, we have an increasing demand for nutritional support, resulting in intensive agricultural practices, sometimes involving enormous numbers of animals, or multiple species farmed within the same region. These practices can facilitate infection to cross species barriers,” wrote Sally Cutler, from the University of East London (London, UK), and colleagues in a review on the topic [6]. The situation is made worse by the ever-increasing transnational transportation of animals and their products, the progressive encroachment of humans into natural habitats with direct exposure to new zoonotic pathogens, and climate changes that might influence the evolution of pathogens and their vectors. These and other elements represent a complex, multifactorial set of changing circumstances that have an impact on the dynamics of zoonoses [6].“Rinderpest is the first animal disease to be eradicated by mankind and the second disease in general after smallpox”Zoonoses with a wildlife reservoir are increasingly recognized as a significant problem. “I think that this is a vitally important topic, as repeated studies have demonstrated that wildlife, collectively, are the major source of new and emerging diseases—and have been so for many years,” commented James Wood from the University of Cambridge in the UK. “Some of the most important human diseases have arisen from animals, including measles, which is derived from the recently eradicated rinderpest virus of cattle, whooping cough, which is derived from a common animal pathogen that causes diseases like kennel cough in domestic dogs, and smallpox, which was most closely related to a similar virus of camels. Examination of the list of the most feared and fatal human pathogens reveals that a significant number have arisen from bats; why this may be the case is the subject of active research in a number of major labs,” Wood explained. Wood and colleagues have proposed a new holistic and interdisciplinary investigation of zoonotic disease emergence and its drivers, by using the spillover of bat pathogens, including Ebola, Marburg, SARS coronavirus, Hendra, Nipah and several rabies and rabies-related viruses as a case study [7].“One of the key missing pieces of knowledge relates to how some of these infections, in particular those other than the immunodeficiency type viruses, transfer from wildlife to humans—and how human livelihood related activities and poverty impact on this risk,” Wood explained. “This is an area of active research for an international consortium named Dynamic Drivers of Disease in Africa [www.driversofdisease.org], considering henipaviruses from bats in Ghana, Rift Valley fever in Kenya, Lassa fever in Sierra Leone and Trypanosomiasis in Zimbabwe and Zambia. Interdisciplinary work in this consortium aims to unpick at least part of that particular puzzle”.Clearly, a better understanding of the complex interactions between ecological, evolutionary, biochemical and sociological mechanisms that enable animal pathogens to cross the species barrier would greatly expand our ability to predict future epidemics of zoonotic infectious diseases. Several approaches have studied the adaptation of pathogens to new hosts—where they have to face a new genetic and immunological environment—and the evolutionary dynamics of this process. These include cross-species infections of heterologous animals, heterologous cell lines and even the expression of single genes from one species in cell lines derived from a second species [8].New threats are looming on the horizon. A research team led by Joanne Devlin at the University of Melbourne, Australia, showed that different vaccine viruses used simultaneously to control laryngotracheitis—an acute respiratory disease occurring in chickens that is caused by a herpesvirus—have recombined to produce new infectious viruses (Fig 2) with significantly increased virulence or replication [9]. “The findings from our research show that we need to consider the risk of recombination when we use live viral vaccines, even for those viruses where the risk of vaccine recombination has traditionally been thought to be very low, such as herpesviruses,” Devlin said. “In Australia, the relevant regulatory body, the Australian Pesticides and Veterinary Medicines Authority (APVMA), is already considering measures to reduce the risk of recombination between different strains of vaccine viruses, including changes to product labels to prevent different strains of the same virus vaccine being used in the same population of animals. This will prevent recombination occurring between the vaccines. It is likely that similar measures will need to be considered elsewhere too.” Notwithstanding the alarming finding that the combined animal vaccines could create new, more dangerous viruses, the risk for human health is low. “Multiple strains of the same live vaccine (with different attenuating changes in their genomes) are required to be present in the one population in order for vaccine–vaccine recombination to occur and for this to generate more virulent viruses,” Devlin explained. “The use of multiple vaccine strains of the same virus in the one population is a feature of veterinary medicine, rather than human medicine.”Open in a separate windowFigure 2Veterinary vaccines might recombine to produce new virus strains. Different vaccine viruses, of European (left) and Australian (right) origin, used simultaneously to control laryngotracheitis infection in chickens, were found to have recombined to produce new infectious viruses [9]. Credit: Australian Science Media Centre. Reproduced with permission.Ultimately, given the increasingly close and frequent contact between humans and animals, both domesticated and wild, veterinarians are important in identifying and combating new potential theats to human health. However, to better understand and eventually defeat diseases at the animal and human interface, an unprecedented level of interdisciplinary collaboration is going to be needed [10].     

Women in cell biology: a seat at the table and a place at the podium

The Women in Cell Biology (WICB) committee of the American Society for Cell Biology (ASCB) was started in the 1970s in response to the documented underrepresentation of women in academia in general and cell biology in particular. By coincidence or causal relationship, I am happy to say that since WICB became a standing ASCB committee, women have been well represented in ASCB''s leadership and as symposium speakers at the annual meeting. However, the need to provide opportunities and information useful to women in developing their careers in cell biology is still vital, given the continuing bias women face in the larger scientific arena. With its emphasis on mentoring, many of WICB''s activities benefit the development of both men and women cell biologists. The WICB “Career Column” in the monthly ASCB Newsletter is a source of accessible wisdom. At the annual ASCB meeting, WICB organizes the career discussion and mentoring roundtables, childcare awards, Mentoring Theater, career-related panel and workshop, and career recognition awards. Finally, the WICB Speaker Referral Service provides a list of outstanding women whom organizers of scientific meetings, scientific review panels, and university symposia/lecture series can reach out to when facing the proverbial dilemma, “I just don''t know any women who are experts.”Although women are approaching parity in earning PhD and MD degrees, studies of their underrepresentation in academia, as principal investigators in funded science and in leadership positions, have led to the conclusion that gender schemas (Valian, 1999 ) work against women and diminish their success. This picture is supported by the National Academy of Sciences’ (NAS) report Beyond Bias and Barriers, which concludes that “Neither our academic institutions nor our nation can afford such underuse of precious human capital in science and engineering” (NAS, 2007 ) A New Yorker cartoon captures the scene at too many scientific gatherings (Figure 1).Open in a separate windowFIGURE 1:“The subject of tonight''s discussion is: Why are there no women on this panel?” Cartoon by David Sipress from The New Yorker Collection, www.cartoonbank.com. Used under Rights Managed License. Copyright holder Conde Nast.The Women in Cell Biology (WICB) committee was started in the early 1970s with notices of ad hoc meetings posted in women''s washrooms during the American Society for Cell Biology (ASCB) annual meeting and a mimeographed newsletter (Williams, 1996a , 1996b ). One goal for WICB''s “founding mothers” was to achieve more equitable representation as participants within ASCB, including more accurate representation of women within the ASCB leadership and as speakers. Consonant with this goal, WICB was delighted to become a standing committee of the ASCB in 1992. In the 30 years prior to this watershed date, only 13% of ASCB presidents were women. Since 1992, 50% of ASCB presidents have been women. I cannot determine whether this is causal, reflective of a third variable, or pure coincidence. But it is remarkable.The number of women leaders and speakers within ASCB suggests that WICB''s initial goal of more accurate representation of women has been largely achieved. However, the goals of helping women cell biologists successfully juggle career and family, find mentors, and achieve gender equity in job placement continue to be challenges. We have developed multiple WICB-sponsored activities throughout the year, and especially at the annual ASCB meeting, to give cell biologists tools with which to meet these challenges.     

Successive and targeted DNA integrations in the Drosophila genome by Bxb1 and phiC31 integrases

At present φC31 is the only phage integrase system available for directionally regulated site-specific DNA integration in the Drosophila genome. Here we report that mycobacteriophage Bxb1 integrase also mediates targeted DNA integration in Drosophila with high specificity and efficiency. By alternately using Bxb1 and φC31, we were able to carry out multiple rounds of successive and targeted DNA integrations in our genomic engineering founder lines for the purpose of generating complex knock-in alleles.THE serine family of phage integrases such as φC31 are highly useful due to their capability of mediating site-specific and unidirectional DNA integration in heterologous systems (Groth and Calos 2004). In the past few years, φC31-mediated site-specific DNA integration has gained wide applications in Drosophila for efficient and targeted transgenesis (Groth et al. 2004; Bateman et al. 2006; Bischof et al. 2007; Markstein et al. 2008; Ni et al. 2008). In particular, we and several other groups have developed approaches that combine φC31-mediated DNA integration with gene targeting for achieving directed and efficient modifications of endogenous genomic loci in Drosophila (Gao et al. 2008; Choi et al. 2009; Huang et al. 2009a,b; Weng et al. 2009). For example, in our genomic engineering approach, a “founder line” is first generated by homologous recombination-based gene targeting that effectively replaces the target gene with a φC31-attP (“attPC”) integration site. The target locus can then be modified into virtually any desirable knock-in alleles through φC31-mediated integration of corresponding DNA constructs into the founder line (Huang et al. 2009a,b). However, DNA integration effectively destroys the original attPC site by converting it into φC31-attR (“attRC”) and φC31-attL (“attLC”) sites (Groth and Calos 2004), preventing further DNA integrations into the target locus. Nonetheless, successive DNA integrations into a target locus can be highly desirable when making sophisticated knock-in alleles that are best done by integrating multiple constructs (Ow 2007). Although it is possible to carry out such successive DNA integrations by adding extra attPC or attBC (i.e., φC31-attB) sites on the integration construct, in practice we found that the φC31 often carried out random and promiscuous recombination among multiple attBC and/or attPC sites in Drosophila (J. Huang and Y. Hong, unpublished data), making the process highly inefficient and unreliable. Thus, an additional phage integrase is necessary for successive DNA integrations in a target locus.Mycobacteriophage Bxb1 integrase (Ghosh et al. 2003; Nkrumah et al. 2006) is a serine integrase that has been shown capable of efficient site-specific integration in heterologous systems, including malaria, plants, and mammalian cells. In addition, characterized Bxb1-attP (“attPX”) and Bxb1-attB (“attBX”) integration sites not only are distinct from attPC and attBC (Ghosh et al. 2003; Nkrumah et al. 2006), but also are small sizes of ∼50 bp, which will leave small footprints before and after integrations. To test whether Bxb1 could mediate DNA integration in Drosophila, we made a transgenic vector pAttPX that carries a 52-bp attPX (“attPX-52”) (Figure 1A) and a removable w+ marker flanked by loxP sites. Through standard P-element transposition process, we obtained five independent host lines, all coincidently carrying the attPX-52 on the third chromosome. Two of them, the attPX-52#1^[w+] and attPX-52#3^[w+] lines, were converted to w^[−] by excising the w+ marker through Cre/loxP recombination (Figure 1B) (Materials and Methods). We then made a test integration construct, pGE-attBX-GFP, which carries the 46-bp attBX site and a UAS-GFP reporter (Figure 1B), and a construct pET11Bxb1polyA for in vitro synthesis of Bxb1 mRNA (Materials and Methods). pGE-attBX-GFP/Bxb1 mRNA mixtures were prepared and injected into the homozygous attPX-52 embryos using the same protocol of φC31-mediated DNA integration (Groth et al. 2004). We obtained 16 candidate lines from attPX-52#1^[w−] and 9 candidate lines from attPX-52#3^[w−] (Open in a separate windowFigure 1 Bxb1-mediated DNA integration in Drosophila. (A) Map of pAttPX (5.984 kb). pAttPX is a P-element-based transforming vector. (B) Bxb1-mediated DNA integration. w+ marker is first excised from the attPX-52^[w+] host line by Cre-mediated recombination between two flanking loxP sites. pGE-attBX-GFP plasmid is then integrated into the attPX-52^[w−] host line via Bxb1-mediated recombination between attPX and attBX. The integration converts attPX to attRX and attLX. 3′P and 5′P, 5′ and 3′ P-element sequences; w+, hsp70::white+ marker with glass multimer reporter (GMR) enhancer (Huang et al. 2008, 2009b); PX, attPX; BX, attBX; RX, attRX; LX, attLX; Amp^R, ampicillin-resistant gene.

Table 1 

Bxb1-mediated DNA integration in attPX-52 host lines and in crb-PX genomic engineering founder lines

Impact of PubMed search filters on the retrieval of evidence by physicians

Background:

Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians.

Methods:

We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries “therapy”) and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles.

Results:

The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were nonrelevant (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p < 0.003) with no substantive change in comprehensiveness (44% of relevant articles found; p = 0.55).

Interpretation:

The use of PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care.Retrieving health literature is a cornerstone of evidence-based practice. With the rapid increase in available evidence, physicians can no longer rely on one or two key journals to stay current. Increasingly, physicians search bibliographic databases, such as PubMed, for research evidence, which is dispersed across hundreds of journals. Each year, physicians perform over 200 million searches in PubMed.^1,2 Physicians face challenges while searching PubMed and often miss relevant articles while retrieving too many nonrelevant articles.^3–6 Clinical decision-making based on evidence from a search may be impaired if relevant articles are missed. Retrieving many nonrelevant articles impedes the efficiency of searching. Improved search strategies are therefore necessary to retrieve a manageable amount of information. The use of PubMed search filters may help solve this problem. Filters are objectively derived, pretested strategies optimized to help users efficiently retrieve articles for a specific purpose.^7,8PubMed provides two types of clinical search filters: methods-based and topic-based. Methods-based filters (known as clinical queries) were designed to retrieve articles on therapy, diagnosis, prognosis and etiology.^9–13 For example, the clinical queries “therapy” filter is optimized to retrieve publications of randomized controlled trials. Methods-based filters can be used for any clinical discipline and are available for general use in PubMed (www.ncbi.nlm.nih.gov/pubmed/clinical). Topic-based filters, in contrast, are designed to retrieve articles within a specific discipline or topic. For example, the recently developed nephrology filters were optimized to retrieve articles with renal content.¹Physicians can use methods- and topic-based filters alone or in combination. For example, Figure 1A shows a search without search filters for studies about the effectiveness of hepatitis B vaccination in patients with chronic kidney disease. Alternatively, this search could be performed with search filters (Figure 1B). Using filters removes the task of generating and including method-specific or topic-specific terms in a search strategy because the filters act as optimized substitutes. For example, applying the nephrology filter eliminates the need to enter renal terms and synonyms in a search query (e.g., chronic kidney disease, end-stage renal disease, chronic renal failure). The nephrology filter, instead, maximizes the retrieval of all renal content (see the nephrology filter strategy in Figure 1B).Open in a separate windowFigure 1:PubMed searches without (A) and with (B) filters. This figure was created from the PubMed clinical queries Web interface; this page currently does not feature a “clinical category” section. When we performed searches with the nephrology filter (B), we removed the term “chronic kidney disease” because the filter acts as an optimized substitute for clinical content terms.In theory, filters should make searching more efficient; however, empiric evidence of this among physicians is lacking. We conducted this study to determine whether the use of methods-based filters and topic-based filters (alone and in combination) improve the efficiency of physician searches in PubMed. The area of renal medicine is an excellent test model because the literature in this field is dispersed across 400 multidisciplinary journals, and many nephrologists search PubMed for information to guide patient care.^14,15     

Blurring lines

The research activities of direct-to-consumer genetic testing companies raise questions about consumers as research subjectsThe recent rise of companies that offer genetic testing directly to consumers, bypassing the traditional face-to-face consultation with a health-care professional, has created a steady stream of debate over the actual and potential value of these services (Hogarth et al, 2008). Despite the debates, however, the reality remains that these services are being offered and have genuine consequences for consumers. As opposed to the issues that have regularly been discussed regarding direct-to-consumer (DTC) genetic testing, the fact that these companies use consumers'' data to perform research has been given relatively little attention. This omission is misconceived as this practice—within the wider realm of DTC genetic testing services—raises its own questions and concerns. In particular, it is blurring the line between consumers and research subjects, which threatens to undermine the public trust and confidence in genetic research that the scientific community has been trying to build over the past decades.Even when a company is relatively transparent about its research activities, one might still be concerned by a lack of consumer awareness of these activitiesWith this in mind, we analysed the websites—including informed consent forms and privacy policies—of five companies that offer DTC full genome testing: 23andMe, deCODE, Navigenics, Gene Essence—the genetic testing service offered by the company BioMarker Pharmaceuticals—and SeqWright. Two questions guided our study: Are consumers aware that the data generated by the company to fulfil the terms of their service will later be used for research? Even if this is the case, is the process of consent provided by companies ethically acceptable from the point of view of academic research?As there are no empirical data available to answer the first question, we turned to the websites of the companies to understand how explicitly they present their research activities. At the time of the study—from July 2009 to January 2010—23andMe, deCODE and Navigenics candidly revealed on their websites that they conduct research using consumer data (Sidebar A). By contrast, SeqWright and Gene Essence provided what we identified as indirect and even ambiguous information about their research activities. For example, in a SeqWright online order form, the company notes: “Please volunteer any diseases from which you currently suffer (this can help us advance medical research by enabling us [sic] discover new SNP [single nucleotide polymorphism]/Disease associations)”. The information in Gene Essence''s privacy policy was similarly vague (http://geneessence.com/our-labs/privacy-policy.html), stating that “electing to provide Optional Profile Information may enable the Company to advance the science of genetics and provide you with an even better understanding of who you are genetically”.

Sidebar A | Information provided by direct-to-consumer genetic testing companies^*

23andMe“You understand that your genetic and other contributed personal information will be stored in 23andMe research databases, and authorized personnel of 23andMe will conduct research using said databases.” (https://www.23andme.com/about/consent; accessed 29 January 2010)deCODE“Information that you provide about yourself under the security of your account and privacy of your chosen username may be used by deCODEme only to gather statistical aggregate information about the users of the deCODEme website. Such analysis may include information that we would like to be able to report back to you and other users of deCODEme, such as in counting the number of users grouped by gender or age, or associating genetic variants with any of the self-reported user attributes. In any such analyses and in presenting any such statistical information, deCODE will ensure that user identities are not exposed.” (http://www.decodeme.com/faq; accessed 29 January 2010)Navigenics“Navigenics is continuously improving the quality of our service, and we strive to contribute to scientific and medical research. To that end, we might de-link Your Genetic Data and Your Phenotype Information and combine it with other members'' information so that we can perform research to: […] Discover or validate associations between certain genetic variations and certain health conditions or traits, as well as other insights regarding human health.” (http://www.navigenics.com/visitor/what_we_offer/our_policies/informed_consent/health_compass; accessed 29 January 2010)^*See main text for information from SeqWright and Gene Essence.If, as appears to be the case, these statements are the only declarations offered by these two companies alluding to their presumed research activities, it is virtually impossible for consumers to understand that their data will be used for research purposes. Moreover, despite the fact that the three other companies do state that they conduct research using consumer genotypes, even their declarations still give cause for concern. For instance, both Navigenics and deCODE ‘tuck away'' most of the information in their terms of service agreements, privacy policies, or in the informed consent sections of their websites. This is worrisome, as most consumers do not even read and/or understand the ‘legalese'' or ‘small print'' when signing online forms (ICO, 2008).…many studies show that participants who have agreed to have their tissue used for one type of research do not necessarily automatically agree to take part in other studies…Even when a company is relatively transparent about its research activities, one might still be concerned by a lack of consumer awareness of these activities. Between July and September 2009, 23andMe offered a new service called the “23andMe research edition”, which was prominently displayed on the company website. This version of their service, which was part of what the company calls the “23andMe research revolution”, was offered for US$99—one-quarter of the price of their traditional personal genome scan—and it offered less information to consumers than the “traditional” service. For instance, the abridged research edition neither offered information about carrier status, pharmacogenomic information and ancestry, nor could the customer browse or download the raw genomic data (https://www.23andme.com/researchrevolution/compare).At a glance, it seemed that 23andMe were marketing the “research edition” as a more affordable option, owing to the fact that the consumers were being given less information and because its name implied that the data would be used for research. Granted, the company did not explicitly express this last assumption, but the term “research edition” could have easily led consumers to this conclusion. However, what is particularly troubling about the two options—“research edition” and “traditional”, presented as distinct products—is that the consent forms for both services were identical. The issue is therefore whether, by calling one option “research edition”, 23andMe made it less clear to individuals purchasing the “traditional” service that their data would also be used for research purposes.Even were we assured that consumers are at least aware of the research being conducted, we must still ask whether the companies are obtaining adequate consent compared with that required from volunteers for similar research studies? To answer this question, we considered official guidelines covering consent, public views on the topic and information gleaned from the websites of DTC genetic testing companies.Concerning public opinion, many studies show that participants who have agreed to have their tissue used for one type of research do not necessarily automatically agree to take part in other studies (Goodson & Vernon, 2004; Schwartz et al, 2001). Furthermore, in a survey of more than 1,000 patients, 72% considered it important to be notified when leftover blood taken for clinical use was to be used for research (Hull et al, 2008). Most of those patients who wanted to be notified would require the researchers to get permission for other research (Hull et al, 2008).…requesting additional information could still be understood by consumers as an additional service that they purchased and not an explicit invitation to take part in researchAlthough some of the companies in our study do mention the diseases that they might study, they are not specific and do not describe the scope of the research that will be done. Indeed, beyond the initial customer signature required to complete the purchase of the genetic testing service, it is not always clear whether the companies would ever contact consumers to obtain explicit consent for internally conducted research. That said, if they were to send out surveys or questionnaires to request supplementary phenotype information, and consumers were to fill out and return those forms, the companies might consider this as consent to research. We would argue, however, that this blurs the line between individuals as consumers and as research participants: requesting additional information could still be understood by consumers as an additional service that they purchased and not an explicit invitation to take part in research.The issue of the identifiability of genomic data is inextricably related to the issue of consent as “[p]romises of anonymity and privacy are important to a small but significant proportion of potential participants” (Andrews, 2009). In the study performed by Hull and colleagues, 23% of participants differentiated between scenarios where samples and data were stored anonymously or with identifiers (Hull et al, 2008). The issue of anonymity is particularly important under the US Common Rule definition of ‘human subject'' research (HHS, 2009). It dictates that research conducted using samples from people that cannot be identified is not considered human subject research and as such does not require consent. Although this rule applies only to federally funded research, it might become pertinent if companies collaborate with publicly funded institutions, such as universities. More generally, regulations such as the Common Rule and the US Food and Drug Administration''s regulations for the protection of human subjects highlight the importance of the protection of individuals in research. Research activities conducted by companies selling DTC genetic tests should therefore be similarly transparent and accountable to a regulatory body.On the basis of the information from the websites of the companies we surveyed, it is not unambiguously clear whether the data used in their research is anonymized or not. That said, 23andMe claims it will keep consumers informed of future advancements in science and might ask them for additional phenotype information, suggesting that it maintains the link between genotype data and the personal information of its customers. As such, research conducted by 23andMe could be considered to involve human subjects. Thus, if 23andMe were to comply voluntarily with the Common Rule, they would have to obtain adequate informed consent.Even in cases in which data or samples are anonymized, studies show that people do care about what happens to their sample (Hull et al, 2008; Schwartz et al, 2001). Furthermore, it is becoming more and more apparent that there are intrinsic limits to the degree of protection that can be achieved through sample and data de-identification and anonymization in genomic research (Homer et al, 2008; Lin et al, 2004; McGuire & Gibbs, 2006; P3G Consortium et al, 2009). This further weakens the adequacy of companies obtaining broad-sense consent from consumers who, most probably, are not even aware that research is being conducted.The European Society of Human Genetics (ESHG) has recently issued a statement on DTC genetic testing for health-related purposes, which states that “[t]he ESHG is concerned with the inadequate consent process through which customers are enrolled in such research. If samples or data are to be used in any research, this should be clear to consumers, and a separate and unambiguous consent procedure should take place” (ESHG, 2010). Another document was recently drafted by the UK Human Genetics Commission (HGC), entitled ‘Common Framework of Principles for Direct-to-Consumers Genetic Testing Services'' (HGC, 2009). The principles were written with the intention of promoting high standards and consistency in the DTC genetic testing market and to protect the interests of consumers and their families. Although this document is not finalized and the principles themselves cannot control or regulate the market in any tangible way, this framework, along with the ESHG statement, constitute the most up-to-date and exhaustive documents addressing DTC genetic testing activities.On the basis of the information from the websites of the companies we surveyed, it is not unambiguously clear whether the data used in their research is anonymized or not…companies should be completely transparent with the public about whether people purchasing their tests are consumers or research subjects or bothPrinciple 4.5 states: “If a test provider intends to use a consumer''s biological samples and/or associated personal or genetic data for research purposes, the consumer should be informed whether the research has been approved by a research ethics committee or other competent authority, whether the biological sample and data will be transferred to or kept in a biobank or database, and about measures to ensure the security of the sample. The consumer should be informed of any risks or potential benefits associated with participating in the research.” Principle 5.6 of the HGC''s draft states that a “[s]eparate informed consent should be requested by the test provider before biological samples are used for any secondary purposes, e.g research, or before any third party is permitted access to biological samples. Consumers'' biological samples and personal and genetic data should only be used for research that has been approved by a research ethics committee (REC) or other relevant competent authority.”None of the companies we surveyed reveal on their websites whether internal research protocols have been approved by a REC or by an independent “competent authority”. Furthermore, no such independent body exists that deals specifically with the research activities of commercial companies selling DTC genetic tests. Additionally, if a company did claim to have internal ethical oversight, it would be questionable whether such a committee would really have any power to veto or change the company''s research activities.Moreover, while all five companies do state what will happen to the DNA sample—in most cases, unless asked otherwise by the consumer, the DNA sample will be destroyed shortly after testing—not enough is revealed about what will happen to the data. Some companies say where data is kept and comment on the security of the website, but as mentioned previously, companies are not clear about whether data will be anonymized. Traditionally, a great deal of focus has been placed on the fate and storage of biological samples, but genome-wide testing of hundreds of thousands of individuals for thousands or even millions of SNPs generates a lot of data. This information is not equivalent, of course, to a full genome sequence, but it can fuel numerous genomic studies in the immediate and medium-term future. As such, additional issues above and beyond basic informed consent also become a concern. For instance, what will happen to the data if a company goes bankrupt or is sold? Will the participants be sent new consent forms if the nature of the company or the research project changes drastically?The activities of companies offering DTC genetic testing have not only blurred the lines between medical services and consumer products, but also between these two activities and research. As a consequence, the appropriate treatment and autonomy of individuals who purchase DTC genetic testing services could be undermined. Paramount to this issue is the fact that companies should be completely transparent with the public about whether people purchasing their tests are consumers or research subjects or both. Although an individual who reads through the websites of such companies might be considered a simple ‘browser'' of the website, once the terms and conditions are signed—irrespective of an actual reading or comprehension—the curious consumer becomes a client and a research subject.…consumers who become research participants should be treated with the same respect and under the same norms as those involved in biobank researchCompanies using consumer samples and data to conduct research are in essence creating databases of information that can be mined and studied in the same way as biobanks and databases generated by academic institutions. As such, consumers who become research participants should be treated with the same respect and under the same norms as those involved in biobank research. As stated by the Organization for Economic Co-operation and Development, research should “respect the participants and be conducted in a manner that upholds human dignity, fundamental freedoms and human rights and be carried out by responsible researchers” (OECD, 2009). On the basis of our analysis of the websites of five companies offering DTC full genome testing, there is little evidence that the participation of ‘consumers'' in research is fully informed.The analysis of company websites was conducted in 2009 and early 2010. The information offered to consumers by the companies mentioned in this Outlook might have changed following the study''s completion or the article''s publication.? Open in a separate windowHeidi C. HowardOpen in a separate windowPascal BorryOpen in a separate windowBartha Maria Knoppers     

Science and rock

An innovative partnership between a research institute and a music festival is helping to connect scientists and young people in Portugal. It is also bringing in money to fund research.Science, more than ever, ought to be seen as a socio-cultural activity. It is a collective enterprise involving scientists and the public, aimed at understanding the world and contributing to a better standard of living, either by having an impact on technological developments or health-related issues. Yet, the perception of science and scientists among the public is not always positive. New scientific and technological developments can sometimes be greeted with disinterest, scepticism or even fear, due largely to misinformation, political agendas and a lack of understanding of science in the public sphere. As such, there is a clear need to improve scientific education at all levels, both in schools and universities, as well as among the general public.Informal environments can be important in promoting public engagement with science-related issues. Schools cannot act alone, and evidence shows that non-school settings, which are often overlooked, can strongly stimulate and contribute to science learning [1,2]. Informal environments have two main benefits: the first is the awareness, motivation and excitement that learners experience when discovering science in an informal setting; the second is that people are more comfortable and able to interact more easily with science without feeling overwhelmed.Although tacit and not always as scientifically accurate as more formal education, science learning within informal environments can still have a positive influence on the academic success of students, as well as on the likelihood that they will ultimately consider a science-related career. Such experiences can also promote informed engagement in civic science-related issues such us environmental concerns, policies and fundraising.Importantly, learning science within these environments should be developed through partnerships between scientific institutions, local communities, funding bodies, government agencies and volunteers, all of which need to understand the overall value of science to society to engage with the project [3].Music festivals offer important advantages as informal venues for learning about science because they are interactive. This makes it possible for participants to engage emotionally and cognitively, and encourages them to extend their science learning over time. Importantly, festivals offer access to members of the public who would be unlikely to attend events such as science fairs or science cafés. The UK group Guerilla Science (http://guerillascience.co.uk), for example, has demonstrated the positive impact that these kinds of unexpected encounter with science and art can have on the public perception of science.…non-school settings, which are often overlooked, can strongly stimulate and contribute to science learningIn recent years, commercial brands have begun to see the potential of music festivals as a valuable channel to reach young people. However, rather than using traditional advertising, brands allow consumers to engage with them through different experiences in what is called ‘experimental marketing'' [4,5]. What is not so common, however, is that event organizers give scientists the opportunity to engage young people in the same way.To address this deficit and raise the profile of science at music festivals, António Coutinho, the Director of the Instituto Gulbenkian de Ciência (IGC), and Álvaro Covões, the Director of Everything is New, which organizes the popular Optimus Alive Oeiras music and art festival in Portugal, announced a new partnership between the two organizations in May 2008. In a press conference, the Directors explained the impact that they hoped bringing science to music festivals might have on the public understanding of science, while music journalists were surprised to find themselves interviewing scientists about their daily lives and research. Importantly, the Directors announced that the partnership would include a financial component, such that revenue from the festival would be used to fund fellowships at the IGC.Four years later and the partnership is still going strong. In 2011, the Coldplay concert at Optimus Alive Oeiras was sold out and fans were treated to all their favourite songs. What they were not expecting was that they would also interact with scientists from the IGC. Despite the proximity of the IGC to the festival venue, this was probably the first time that many of them had even thought about the institute, what it does and who works there.At the IGC stand, close to the main stage, science and music mix in unexpected ways. Different science-related activities are used to engage visitors. Revellersqueue to speak with scientists (Fig 1), extract DNA from strawberries by using everyday reagents, make flavoured ice-cream frozen in liquid nitrogen and find out how our genes determine eye colour, the alignment of little fingers, ear shape and the ability to roll your tongue. Visitors can take home a microcentrifuge tube containing strawberry DNA and, hopefully, a desire to know more about science and scientists. There are also ‘sci-arts'' installations and photo exhibitions about the research projects and young scientists sponsored through the partnership.Open in a separate windowFigure 1The Instituto Gulbenkian de Ciência booth at Optimus Alive Oieras in 2009. Festival-goers queue to meet scientists and conduct miniature science experiments, introducing them to science in an informal and enjoyable learning environment. Photo courtesy of Instituto Gulbenkian de Ciência.The highlight of the activities at the festival, however, is probably the ‘speed-dating'' with scientists (Fig 2). This event takes the form of a five-minute conversation between a festival-goer and a scientist in a relaxed and entertaining space. The conversations serve to break down stereotypes of scientists, encourage interest in careers in science and involve the public in scientific research. The questions asked are often insightful, surprising and thoughtful: “will we have a vaccine against cancer?”; “what degree should I take to be a scientist?”; “does a scientist also listen to music?” or even “is it safe to eat genetically modified food?” The IGC researchers who take part range from PhD students and postdocs to group leaders. They all have different backgrounds including biology, physics, bioinformatics, medicine and chemistry. The topics of conversation range from the latest work on genetics or cancer to more general questions about what motivates scientists, the day-to-day life of researchers and how research fits in with a private life. Conversations frequently last more than the allotted five minutes and the visitors have the opportunity to speak with at least three scientists from the IGC.Open in a separate windowFigure 2Speed-dating with scientists. Members of the public get five minutes to sit and talk with an Instituto Gulbenkian de Ciência scientist about life as a researcher, science and the latest research. Conversations often go on for more than five minutes and the interactions are rewarding for all participants. Photo courtesy of Instituto Gulbenkian de Ciência.The feedback from festival-goers is excellent. The opinions offered in the surveys of visitors are overwhelmingly positive: “I loved the enthusiasm of the scientists. Keep going like that. I also want to be a scientist,” wrote one respondent. “Very interesting initiative. I''m not from the natural sciences area but it was great to meet with scientists that open the doors of their research to us. Knowledge is never too much,” commented another. “This initiative was a success and we hope it happens again.” The surveys also reveal that visitors to the IGC space in the last four years—around 600 people each year—are mostly teenagers and young adults: 29% are between 13 and 19 years old, and 51% are between 20 and 29 years old. Only 15% of the visitors are between 30 and 39 years old, 4.5% are over 40 years old, and only 0.5% are under 13 years old.Web-based platforms have also been used successfully to disseminate the activities and results of the initiative. On the music festival website and its Facebook page, which are visited by thousands of people each day, a section on science is highlighted describing the partnership and the activities at the IGC space. Additionally, a Facebook page was created by the IGC, which allows the winners of the fellowships to interact with the general public (www.facebook.com/BolsasOptimusAliveOeirasIGC). On YouTube, three videos of the IGC presence at the festival, prepared by the IGC, are also available (http://www.youtube.com/user/IGCiencia).This feedback and interaction is particularly pleasing, as teenagers are a notoriously difficult audience for science engagement. If we aim to increase the number of people pursuing scientific careers, we must find new ways to attract this age group to science-related issues. According to the European Commission, Europe will need one million more researchers by 2020 than it has at present, and it is urgent that we find new ways to attract young people to careers in science [6]. A study of American teenagers shows that a lack of contact with scientists in their daily lives, and a lack of understanding of what scientists do, discourages young people from pursuing careers in scientific areas. As such, contact with motivated scientists could change these attitudes toward science and scientific careers [7].Having scientists present alongside pop stars is also a good way of showing that scientists spend their free time similarly to other people, by attending social and entertaining activities. Hopefully, this juxtaposition breaks down barriers and engages teenagers from multiple backgrounds with a broad range of interests and musical tastes. Young adults, another age group present at music festivals, are also an extremely important audience for science communication. Although they might have finished their formal education, their interest and engagement in scientific issues is still extremely important to society.Scientists gain important experiences and skills from working at the festival. For the last four years, around 70 scientists per year, mainly from the IGC, have volunteered for the IGC space at the festival (Fig 3). Science communication skills are fundamental to scientific career progress and personal fulfilment. A survey carried out by the European Molecular Biology Organization (EMBO; Heidelberg, Germany) found that senior life scientists believe that PhD and other postgraduate training programmes should give more attention to scientific communication, both public and peer-to-peer, and that these transferrable skills should be developed early and regularly updated [8,9]. Another survey by People Science & Policy (PSP), commissioned by the Royal Society, Research Councils UK and the Wellcome Trust, showed that although lack of time is a constraint, scientists want to engage more with the public, especially with policy-makers, students and industry, and that it is important that scientific institutions and other organizations find ways to facilitate public engagement by scientists [10]. As one volunteer expressed: “I have to acknowledge Everything is New and the IGC for this prestigious opportunity, as this is a new challenge for me and is a way of bringing science closer to the general public.”Open in a separate windowFigure 3The Instituto Gulbenkian de Ciência volunteers at Optimus Alive Oieras in 2009. Photo courtesy of Instituto Gulbenkian de Ciência.In addition to the value of engaging the public with science, the partnership has important financial benefits for the IGC. Fundraising is a key aspect of the partnership, which highlights the importance of private funding for biomedical research in Portugal. Everything is New, the festival promoter, supports two research fellowships per year for graduates in areas such as biodiversity, genetics and evolution. Since 2009, Optimus Alive Oeiras–IGC Research Fellowships have given young science graduates the opportunity to pursue research in areas that interest them (Sidebar A). Each fellowship is for a 12-month period and is carried out partly at the IGC and partly at a foreign institute (

Listening to public concerns about human life extension

The public view of life-extension technologies is more nuanced than expected and researchers must engage in discussions if they hope to promote awareness and acceptanceThere is increasing research and commercial interest in the development of novel interventions that might be able to extend human life expectancy by decelerating the ageing process. In this context, there is unabated interest in the life-extending effects of caloric restriction in mammals, and there are great hopes for drugs that could slow human ageing by mimicking its effects (Fontana et al, 2010). The multinational pharmaceutical company GlaxoSmithKline, for example, acquired Sirtris Pharmaceuticals in 2008, ostensibly for their portfolio of drugs targeting ‘diseases of ageing''. More recently, the immunosuppressant drug rapamycin has been shown to extend maximum lifespan in mice (Harrison et al, 2009). Such findings have stoked the kind of enthusiasm that has become common in media reports of life-extension and anti-ageing research, with claims that rapamycin might be “the cure for all that ails” (Hasty, 2009), or that it is an “anti-aging drug [that] could be used today” (Blagosklonny, 2007).Given the academic, commercial and media interest in prolonging human lifespan—a centuries-old dream of humanity—it is interesting to gauge what the public thinks about the possibility of living longer, healthier lives, and to ask whether they would be willing to buy and use drugs that slow the ageing process. Surveys that have addressed these questions, have given some rather surprising results, contrary to the expectations of many researchers in the field. They have also highlighted that although human life extension (HLE) and ageing are topics with enormous implications for society and individuals, scientists have not communicated efficiently with the public about their research and its possible applications.Given the academic, commercial and media interest in prolonging human lifespan […] it is interesting to gauge what the public thinks about the possibility of living longer, healthier lives…Proponents and opponents of HLE often assume that public attitudes towards ageing interventions will be strongly for or against, but until now, there has been little empirical evidence with which to test these assumptions (Lucke & Hall, 2005). We recently surveyed members of the public in Australia and found a variety of opinions, including some ambivalence towards the development and use of drugs that could slow ageing and increase lifespan. Our findings suggest that many members of the public anticipate both positive and negative outcomes from this work (Partridge 2009a, b, 2010; Underwood et al, 2009).In a community survey of public attitudes towards HLE we found that around two-thirds of a sample of 605 Australian adults supported research with the potential to increase the maximum human lifespan by slowing ageing (Partridge et al, 2010). However, only one-third expressed an interest in using an anti-ageing pill if it were developed. Half of the respondents were not interested in personally using such a pill and around one in ten were undecided.Some proponents of HLE anticipate their research being impeded by strong public antipathy (Miller, 2002, 2009). Richard Miller has claimed that opposition to the development of anti-ageing interventions often exists because of an “irrational public predisposition” to think that increased lifespans will only lead to elongation of infirmity. He has called this “gerontologiphobia”—a shared feeling among laypeople that while research to cure age-related diseases such as dementia is laudable, research that aims to intervene in ageing is a “public menace” (Miller, 2002).We found broad support for the amelioration of age-related diseases and for technologies that might preserve quality of life, but scepticism about a major promise of HLE—that it will delay the onset of age-related diseases and extend an individual''s healthy lifespan. From the people we interviewed, the most commonly cited potential negative personal outcome of HLE was that it would extend the number of years a person spent with chronic illnesses and poor quality of life (Partridge et al, 2009a). Although some members of the public envisioned more years spent in good health, almost 40% of participants were concerned that a drug to slow ageing would do more harm than good to them personally; another 13% were unsure about the benefits and costs (Partridge et al, 2010).…it might be that advocates of HLE have failed to persuade the public on this issueIt would be unwise to label such concerns as irrational, when it might be that advocates of HLE have failed to persuade the public on this issue. Have HLE researchers explained what they have discovered about ageing and what it means? Perhaps the public see the claims that have been made about HLE as ‘too good to be true‘.Results of surveys of biogerontologists suggest that they are either unaware or dismissive of public concerns about HLE. They often ignore them, dismiss them as “far-fetched”, or feel no responsibility “to respond” (Settersten Jr et al, 2008). Given this attitude, it is perhaps not surprising that the public are sceptical of their claims.Scientists are not always clear about the outcomes of their work, biogerontologists included. Although the life-extending effects of interventions in animal models are invoked as arguments for supporting anti-ageing research, it is not certain that these interventions will also extend healthy lifespans in humans. Miller (2009) reassuringly claims that the available evidence consistently suggests that quality of life is maintained in laboratory animals with extended lifespans, but he acknowledges that the evidence is “sparse” and urges more research on the topic (Miller, 2009). In the light of such ambiguity, researchers need to respond to public concerns in ways that reflect the available evidence and the potential of their work, without becoming apostles for technologies that have not yet been developed. An anti-ageing drug that extends lifespan without maintaining quality of life is clearly undesirable, but the public needs to be persuaded that such an outcome can be avoided.The public is also concerned about the possible adverse side effects of anti-ageing drugs. Many people were bemused when they discovered that members of the Caloric Restriction Society experienced a loss of libido and loss of muscle mass as a result of adhering to a low-calorie diet to extend their longevity—for many people, such side effects would not be worth the promise of some extra years of life. Adverse side effects are acknowledged as a considerable potential challenge to the development of an effective life-extending drug in humans (Fontana et al, 2010). If researchers do not discuss these possible effects, then a curious public might draw their own conclusions.Adverse side effects are acknowledged as a considerable potential challenge to the development of an effective life-extending drug in humansSome HLE advocates seem eager to tout potential anti-ageing drugs as being free from adverse side effects. For example, Blagosklonny (2007) has argued that rapamycin could be used to prevent age-related diseases in humans because it is “a non-toxic, well tolerated drug that is suitable for everyday oral administration” with its major “side-effects” being anti-tumour, bone-protecting, and mimicking caloric restriction effects. By contrast, Kaeberlein & Kennedy (2009) have advised the public against using the drug because of its immunosuppressive effects.Aubrey de Grey has called for scientists to provide more optimistic timescales for HLE on several occasions. He claims that public opposition to interventions in ageing is based on “extraordinarily transparently flawed opinions” that HLE would be unethical and unsustainable (de Grey, 2004). In his view, public opposition is driven by scepticism about whether HLE will be possible, and that concerns about extending infirmity, injustice or social harms are simply excuses to justify people''s belief that ageing is ‘not so bad'' (de Grey, 2007). He argues that this “pro-ageing trance” can only be broken by persuading the public that HLE technologies are just around the corner.Contrary to de Grey''s expectations of public pessimism, 75% of our survey participants thought that HLE technologies were likely to be developed in the near future. Furthermore, concerns about the personal, social and ethical implications of ageing interventions and HLE were not confined to those who believed that HLE is not feasible (Partridge et al, 2010).Juengst et al (2003) have rightly pointed out that any interventions that slow ageing and substantially increase human longevity might generate more social, economic, political, legal, ethical and public health issues than any other technological advance in biomedicine. Our survey supports this idea; the major ethical concerns raised by members of the public reflect the many and diverse issues that are discussed in the bioethics literature (Partridge et al, 2009b; Partridge & Hall, 2007).When pressed, even enthusiasts admit that a drastic extension of human life might be a mixed blessing. A recent review by researchers at the US National Institute on Aging pointed to several economic and social challenges that arise from longevity extension (Sierra et al, 2009). Perry (2004) suggests that the ability to slow ageing will cause “profound changes” and a “firestorm of controversy”. Even de Grey (2005) concedes that the development of an effective way to slow ageing will cause “mayhem” and “absolute pandemonium”. If even the advocates of anti-ageing and HLE anticipate widespread societal disruption, the public is right to express concerns about the prospect of these things becoming reality. It is accordingly unfair to dismiss public concerns about the social and ethical implications as “irrational”, “inane” or “breathtakingly stupid” (de Grey, 2004).The breadth of the possible implications of HLE reinforces the need for more discussion about the funding of such research and management of its outcomes ( Juengst et al, 2003). Biogerontologists need to take public concerns more seriously if they hope to foster support for their work. If there are misperceptions about the likely outcomes of intervention in ageing, then biogerontologists need to better explain their research to the public and discuss how their concerns will be addressed. It is not enough to hope that a breakthrough in human ageing research will automatically assuage public concerns about the effects of HLE on quality of life, overpopulation, economic sustainability, the environment and inequities in access to such technologies. The trajectories of other controversial research areas—such as human embryonic stem cell research and assisted reproductive technologies (Deech & Smajdor, 2007)—have shown that “listening to public concerns on research and responding appropriately” is a more effective way of fostering support than arrogant dismissal of public concerns (Anon, 2009).Biogerontologists need to take public concerns more seriously if they hope to foster support for their work? Open in a separate windowBrad PartridgeOpen in a separate windowJayne LuckeOpen in a separate windowWayne Hall     

Minding the gaps: metabolomics mends functional genomics

Two recent studies in PNAS and Nat Chem Biol highlight the power of modern mass-spectrometry techniques for enzyme discovery applied to microbiology. In so doing, they have uncovered new potential targets for the treatment of tuberculosis.Proc Natl Acad Sci USA (2013) 110 28, 11320–11325 doi: 10.1073/pnas.1221597110Nat Chem Biol (2013). doi:10.1038/nchembio.1355. Advance online publication 29 September 2013Many have come to regard metabolism as a well-understood housekeeping activity of all cells, functionally compartmentalized away from other biological processes. However, growing reports of unexpected links between a diverse range of disease states and specific metabolic enzymes or pathways have begun to challenge this view. In doing so, such discoveries have exposed more glaring, and neglected, deficiencies in our understanding of cellular metabolism, triggering a broad resurgence of interest in metabolism.“Metabolomics […] offers a global window into the biochemical state of a cell or organism…”Metabolomics is the newest of the systems-level disciplines and seeks to reveal the physiological state of a given cell or organism through the global and unbiased study of its small-molecule metabolites [1]. Metabolites are the final products of enzymes and enzyme networks, the substrates and products of which often cannot be deduced from genetic information and the levels of which reflect the integrated product of the genome, proteome and environment [2]. Metabolomics thus offers a global window into the biochemical state of a cell or organism, made experimentally possible by the unprecedented discriminatory power and sensitivity of modern mass-spectrometry-based technologies (Fig 1). Two recent reports from the Carvalho and Neyrolles groups, published recently in Proceedings of the National Academy of Science USA and Nature Chemical Biology [3,4], exemplify the rapidly growing impact of metabolomics-based approaches on tuberculosis research.Open in a separate windowFigure 1Modern mass spectrometry illuminates bacterial metabolism. A comparison of activity-based metabolomic profiling with classic metabolic tracing. See the text for details.Within the field of infectious diseases, the deficiencies in our understanding of microbial metabolism have emerged most prominently in the area of tuberculosis research. Despite the development of the first chemotherapies more than 50 years ago, tuberculosis remains the leading bacterial cause of death worldwide, due in part to a failure to keep pace with the emergence of drug resistance [5]. The causes of this shortfall are multifactorial. However, a key contributing factor is our incomplete understanding of the metabolic properties of Mycobacterium tuberculosis (Mtb), its aetiological agent. Unlike most bacterial pathogens, Mtb infects humans as its only known host and reservoir, within whom it resides largely isolated from other microbes. Mtb has thus evolved its metabolism to serve interdependent physiological and pathogenic roles. Yet, more than a century after Koch''s initial discovery of Mtb and 15 years after the first publication of its genome sequence, knowledge of Mtb''s metabolic network remains surprisingly incomplete [6,7,8].“…tuberculosis remains the leading bacterial cause of death worldwide…”As for almost all sequenced microbial genomes, homology-based in silico approaches have failed to suggest a function for nearly 40% of Mtb genes that, presumably, include a significant number of orphan enzyme activities for which no gene has been ascribed [8]. Such approaches have further neglected the impact of evolutionary selection and its ability to dissociate sequence conservation from biochemical activity and physiological function, in order to help optimize the fitness of a given organism within its specific niche. For Mtb, such genes and enzymes represent an especially promising and biologically selective, but untapped, source of potential drug targets.In the study from the Carvalho group, successful application of a recently developed metabolomics assay—known as activity-based metabolomic profiling (ABMP)—allowed the authors to reassign a putatively annotated nucleotide phosphatase (Rv1692) as a D,L-glycerol 3-phosphate phosphatase [3,9]. ABMP was specifically developed to identify enzymatic activities for genes of unknown function by leveraging the analytical discriminatory power of liquid-chromatography-coupled high-resolution mass spectrometry (LC-MS) to analyse the impact of a recombinant enzyme and potential co-factors on a highly concentrated, small-molecule extract derived from the homologous organism (Fig 1). By monitoring for the matched time and enzyme-dependent depletion and accumulation of putative substrates and products, this assay enables the discovery of catalytic activities—rather than simple binding—by using the cellular metabolome as arguably the most physiological chemical library of potential substrates that can be tested, in a label and synthesis-free manner. Moreover, candidate activities assigned by this method can be confirmed by using independent biochemical approaches—such as reconstitution with purified components—and genetic techniques—such as wild-type and genetic knockout, knockdown or overexpression strains. In reassigning Rv1692 as a glycerol phosphate phosphatase, rather than a nucleotide phosphatase, Carvalho and colleagues demonstrate the potential of ABMP to overcome the biochemical challenge of assigning substrate specificity to a member of a large enzyme superfamily—in this case, the haloacid dehydrogenase superfamily. But, perhaps more significantly, they also direct new biological attention to the largely neglected area of Mtb membrane homeostasis, in which Rv1692 might play an important role in glycerophospholipid recycling and catabolism.“…knowledge of Mtb''s metabolic network remains surprisingly incomplete”Neyrolles and colleagues make use of the same metabolomics platform to perform metabolite-tracing studies by using stable-isotope-labelled precursors, which led them to reassign a putatively annotated asparagine transporter (AnsP1) as an aspartate transporter. AnsP1 bears 55% sequence identity and 70% similarity to an orthologue in Salmonella that belongs to the amino acid transporter family 2.A.3.1, whereas aspartate transporters are typically members of the dicarboxylate amino acid:cation symporter family 2.A.23 [4]. This study demonstrates the ability of metabolomic platforms to not only characterize the activity of a given protein within its natural physiological milieu, but also revive classical experimental methods by using modern technologies. The availability of stable (non-radioactive) isotopically labelled precursors has now made it possible to resolve their specific metabolic fates. In this case, such an approach revealed that Mtb can use aspartate as both a carbon and nitrogen source, after its uptake through AnsP1. Looking beyond the specific biochemical assignment of AnsP1 as an aspartate—rather than asparagine—transporter, this study illustrates the potential impact of such discoveries on downstream paths of investigation. In this case, the remarkable application of high-resolution dynamic secondary ion mass spectroscopy to provide the first direct biochemical images of the nutritional environment of the Mtb-infected phagosome.New technologies are often developed in the context of specific needs. However, their impact is usually not realized until extended beyond such contexts, sometimes resulting in major paradigm shifts. The above examples highlight just two emerging possibilities of how metabolomics technologies can be extended beyond the context of global comparisons and provide unique biological insights. To the extent that the analytical power of these platforms can be adapted to other functional approaches, metabolomics promises to pay handsome biochemical and physiological dividends.     

Bit by bit: the Darwinian basis of life

All known examples of life belong to the same biology, but there is increasing enthusiasm among astronomers, astrobiologists, and synthetic biologists that other forms of life may soon be discovered or synthesized. This enthusiasm should be tempered by the fact that the probability for life to originate is not known. As a guiding principle in parsing potential examples of alternative life, one should ask: How many heritable “bits” of information are involved, and where did they come from? A genetic system that contains more bits than the number that were required to initiate its operation might reasonably be considered a new form of life.Thanks to a combination of ground- and space-based astronomical observations, the number of confirmed extrasolar planets will soon exceed 1,000. An increasing number of these will be said to lie within the “habitable zone” and even be pronounced as “Earth-like.” Within a decade there will be observational data regarding the atmospheric composition of some of those planets, and just maybe those data will indicate something funny going on—something well outside the state of chemical equilibrium—on a potentially hospitable planet. Perhaps our astronomy colleagues should be forgiven for their enthusiasm in declaring that humanity is on the brink of discovering alien life.But haven''t we heard this before? Didn''t President Clinton announce in 1996 that a Martian meteorite recovered in Antarctica [1] “speaks of the possibility of life” on Mars? (No, it turned out to be mineralic artifacts.) Wasn''t some “alien” arsenic-based life discovered recently in Mono Lake, California [2]? (No, it''s a familiar proteobacterium struggling to survive in a toxic environment.) Didn''t Craig Venter and his colleagues recently create a synthetic bacterial cell [3], “the first self-replicating species we''ve had on the planet whose parent is a computer”? (No, its parent is Mycoplasma mycoides and its genome was dutifully reconstructed through DNA synthesis and PCR amplification.)Why are we so confused (or so lonely) that we have such trouble distinguishing life from non-life and distinguishing our biology from another? A key limitation is that we know of only one life form, causing us to regard life from that singular perspective (Figure 1). We see life as cellular, with a nucleic acid genome that is translated to a protein machinery. Life self-reproduces, transmits heritable information to its progeny, and undergoes Darwinian evolution based on natural selection. Life captures high-energy starting materials and converts them to lower-energy products to drive metabolic processes. Life exists on at least one temperate, rocky planet, where it has persisted for about four billion years. There are likely to be tens of thousands of “habitable” planets within a thousand light years of Earth, and more than a billion such planets in our galaxy, so surely (say the astronomers) we are not alone.Open in a separate windowFigure 1Phylogenetic tree of life based on small-subunit ribosomal RNA sequences, showing representative species from each of the three kingdoms (compiled by Pace [11]).The root of the tree is indicated by a horizontal line. The locations on the tree of Halomonas sp. (GFAJ-1) [2] and Mycoplasma mycoides (JCVI-syn1.0) [3] are indicated by black circles adjacent to Escherichia and Bacillus, respectively.     

Figure text extraction in biomedical literature

Background

Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (http://figuresearch.askHERMES.org) to allow bioscientists to access figures efficiently. Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures.

Methodology

We first evaluated an off-the-shelf Optical Character Recognition (OCR) tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT) to improve the performance of the OCR tool for figure text extraction through the use of three innovative components: image preprocessing, character recognition, and text correction. We first developed image preprocessing to enhance image quality and to improve text localization. Then we adapted the off-the-shelf OCR tool on the improved text localization for character recognition. Finally, we developed and evaluated a novel text correction framework by taking advantage of figure-specific lexicons.

Results/Conclusions

The evaluation on 382 figures (9,643 figure texts in total) randomly selected from PubMed Central full-text articles shows that FigTExT performed with 84% precision, 98% recall, and 90% F1-score for text localization and with 62.5% precision, 51.0% recall and 56.2% F1-score for figure text extraction. When limiting figure texts to those judged by domain experts to be important content, FigTExT performed with 87.3% precision, 68.8% recall, and 77% F1-score. FigTExT significantly improved the performance of the off-the-shelf OCR tool we used, which on its own performed with 36.6% precision, 19.3% recall, and 25.3% F1-score for text extraction. In addition, our results show that FigTExT can extract texts that do not appear in figure captions or other associated text, further suggesting the potential utility of FigTExT for improving figure search.Open in a separate windowFigure 9Additional reasons for OCR errors.(A) High image complexity. (B) Thick stroke. (C) Low image contrast. (D) Small font size. (E) Non-standard font type.