How to use this Page

Can Peer Review ever be as important as publication? This year's Peer Review Week focuses on the recognition of reviewers. Peer Review Week 2016 is an international initiative that celebrates the essential and often undervalued activity of academic peer review.

The post Publish and be cited! Impact Factors, Open Access, and the plight of peer review appeared first on OUPblog.

The 2016 World Malaria Report estimates that there were approximately 215 million cases of malaria and 438,000 deaths in 2015. The majority of deaths occur in sub-Saharan Africa and among young children, and malaria remains endemic in around 100 countries with over three billion people at risk. Over the past 15 years there have been major gains in reducing the global burden of malaria

The post The quest for a malaria vaccine continues appeared first on OUPblog.

The eradication of infectious diseases in the 20th century is arguably one of the most important achievements in modern medicine. The treatment of such illnesses as tuberculosis, leprosy, syphilis, cholera, pertussis, or diphtheria with antibiotics have reduced suffering, increased hygiene, enormously improved lifestyle, and skyrocketed life expectancy around the globe – particularly in developed countries.

The post Towards a global approach to combat antibiotic resistance appeared first on OUPblog.

The serendipitous discovery of Penicillin by Alexander Fleming in 1929 positively transformed modern medicine. Fleming’s decision to spend his summer holiday in East Anglia and his casual approach to laboratory housekeeping was an auspicious combination. After his return to the laboratory he observed that an uncovered culture plate of Staphyloccocus bacteria had been contaminated.

The post The antimicrobial resistance crisis: is there a global solution? appeared first on OUPblog.

It was a simple request: “Try and put the fun back into microbiology”. I was about to write a new practical course for first year students, and apparently there had been complaints that microbiology is just another form of cookbook chemistry. Discussions showed that they liked the idea of doing their own experiments without a pre-determined outcome. Of course, with living microorganisms, safety must be a major concern, and some control was needed to prevent hazardous surprises, but “fun” and safety are not mutually exclusive.

The post Is the history of science still relevant? appeared first on OUPblog.

Microbiology should be part of everyone’s educational experience. European students deserve to know something about the influence of microscopic forms of life on their existence, as it is at least as important as the study of the Roman Empire or the Second World War. Knowledge of viruses should be as prominent in American high school curricula as the origin of the Declaration of Independence. This limited geographic compass reflects the fact that the science of microbiology is a triumph of Western civilization, but the educational significance of the field is a global concern. We cannot understand life without an elementary comprehension of microorganisms.

Appreciation of the microbial world might begin by looking at pond water and pinches of wet soil with a microscope. Precocious children could be encouraged in this fashion at a very early age. Deeper inquiry with science teachers would build a foundation of knowledge for teenagers, before the end of their formal education or the pursuit of a university degree in the humanities.

Earth has always been dominated by microorganisms. Most genetic diversity exists in the form of microbes and if animals and plants were extinguished by cosmic bombardment, biology would reboot from reservoirs of this bounty. The numbers of microbes are staggering. Tens of millions of bacteria live in a crumb of soil. A drop of seawater contains 500,000 bacteria and tens of millions of viruses. The air is filled with microscopic fungal spores, and a hundred trillion bacteria swarm inside the human gut. Every macroscopic organism and every inanimate surface is coated with microbes. They grow around volcanoes and hydrothermal vents. They live in blocks of sea ice, in the deepest oceans, and thrive in ancient sediment on the seafloor. Microbes act as decomposers, recycling the substance of dead organisms. Others are primary producers, turning carbon dioxide into sugars using sunlight or by tapping chemical energy from hydrogen sulfide, ferrous iron, ammonia, and methane.

Bacterial infections are caused by decomposers that survive in living tissues. Airborne bacteria cause diphtheria, pertussis, tuberculosis, and meningitis. Airborne viruses cause influenza, measles, mumps, rubella, chickenpox, and the common cold. Hemorrhagic fevers caused by Ebola viruses are spread by direct contact with infected patients. Diseases transmitted by animal bites include bacterial plague, as the presumed cause of the Black Death, which killed 200 million people in the 14^th century. Typhus spread by lice decimated populations of prisoners in concentration camps and refugees during the Second World War. Malaria, carried by mosquitos, massacres half a million people every year.

Contrary to the impression left by this list of infections, relatively few microbes are harmful and we depend on a lifelong cargo of single-celled organisms and viruses. The bacteria in our guts are essential for digesting the plant part of our diet and other bacteria and yeasts are normal occupants of healthy skin. The tightness of our relationship with microbes is illustrated by the finding that human DNA contains 100,000 fragments of genes that came from viruses. We are surprisingly microbial.

Missing the opportunity to learn something about microbiology is a mistake. The uninformed are likely to be left with a distorted view of biology in which they miscast themselves as the most important organisms. For example, “Sarah” is a significant manifestation of life from Sarah’s perspective, but her body is not the individual organism that she imagines, and nor, despite her talents, is she a major player in the ecology of the planet. Her interactions with microbes will include a healthy relationship with bacteria in her gut, bouts of influenza and other viral illnesses, and death in old age from an antibiotic-resistant infection. Sarah’s microbiology will continue after death with her decomposition by fungi. In happier times she will become an expert on Milton’s poetry, and delight students by reciting Lycidas through her tears, but she will never know a thing about microbiology. This is a pity. Learning about viruses that bloom in seawater and fungi that sustain rainforests would not have stopped her from falling in love with Milton.

Even brief consideration of microorganisms can be inspiring. A simple magnifying lens transforms the surface of rotting fruit into a hedgerow of glittering stalks topped with jet-black fungal spores. Microscopes take us deeper, to the slow revolution of the bright green globe of the alga Volvox as its beats its way through a drop of pond water. A greater number of microbes are quite dull things to look at and their appreciation requires greater imagination. Considering that our bodies are huge ecosystems supported by trillions of bacteria is a good place to start, and then we might realize that we fade from view against the grander galaxy of life on Earth. The science of microbiology is a marvel for our time.

Featured image credit: BglII-DNA complex By Gwilliams10. Public domain via Wikimedia Commons

The post Discovering microbiology appeared first on OUPblog.

        

Related Stories

• Looking for Tutankhamun
• Druids and nature
• Population ecologists scale up

 

By Nicholas P. Money

The small picture is the big picture and biologists keep missing it. The diversity and functioning of animals and plants has been the meat and potatoes of most natural historians since Aristotle, and we continue to neglect the vast microbial majority. Before the invention of the microscope in the seventeenth century we had no idea that life existed in any form but the immediately observable. This delusion was swept away by Robert Hooke, Anton van Leeuwenhoek, and other pioneers of optics who found that tiny forms of life looked a lot like the cells that comprise our own tissues. We were, they showed, constructed from the same essence as the writhing animalcules of ponds and spoiled food. And yet this revelation was somehow folded into the continuing obsession with human specialness, allowing Carolus Linnaeus to catalogue plants and big animals and ignore the lilliputian majority. When microbiological inquiry was restimulated by Louis Pasteur in the nineteenth century, it became the science of germs and infectious disease. The point was not to glory in the diversity of microorganisms but exterminate them. In any case, as before, most of life was disregarded.

Things are changing very swiftly now. Molecular fishing expeditions in which raw biological information is examined using metagenomic methods have discovered an abundance of cryptic life forms. This research has made it clear that we are a very long way, centuries perhaps, from comprehending biodiversity properly.

Revelation of the human microbiome, the teeming trillions of bacteria and archaea in our guts that affect every aspect of our wellbeing, is the best publicized part of the inquiry. We are walking ecosystems, farmed by our microbes and dependent upon their metabolic virtuosity. There is much more besides, including the fact that a single cup of seawater contains 100 million cells, which are in turn preyed upon by billions of viruses; that a pinch of soil teems with incomprehensibly rich populations of cells; and that 50 megatons of fungal spores are released into our air supply every year. Even the pond in my Ohio garden is filled with unknowable riches: the most powerful techniques illuminate the genetic identity of only one in one billion of the cells in its shallow water.

Most biologists continue to be concerned with animals and plants, the thinnest slivers of biological splendor, and students are taught this macrobiology—with the occasional nod toward the other things that constitute almost all of life. Practical problems abound from this nepotism. Ecologists study things muscled and things leafed and conservationists worry most about animals, arguing for expensive stamp-collecting exercises to register the big bits of creation before they go extinct. This is a predicament of considerable importance to humanity. Consider: A single kind of photosynthetic bacterium absorbs 20 billion tons of carbon per year, making this minuscule cell a stronger refrigerant than all of the tropical rainforests.

Surveying our planet for its evolutionary resources, the perceptive extraterrestrial would report that Earth is swarming with viral and bacterial genes. The visitor might comment, in passing, that a few of these genes have been strung together into large assemblies capable of running around or branching toward the sunlight. It is time for us to embrace this kind of objectivity and recognize that the macrobiological bias that drives our exploration and teaching of biology is no more sensible than attempting to evaluate all of English Literature by reading nothing but a Harry Potter book. The science of biology would benefit from a philosophical reboot.

Nicholas P. Money is Professor of Botany and Western Program Director at Miami University in Oxford, Ohio. He is the author of more than 70 peer-reviewed papers on fungal biology and has authored several books. His new book is The Amoeba in the Room: Lives of the Microbes.

Subscribe to the OUPblog via email or RSS.
Subscribe to only earth, environmental, and life sciences articles on the OUPblog via email or RSS.
Image Credit: Scanning electron micrograph of amoeba, computer-coloured mauve. By David Gregory & Debbie Marshall, CC-BY-NC-ND 4.0, via Wellcome Images.

The post The amoeba in the room appeared first on OUPblog.

        

Related Stories

• Earth Day, 44 years on
• Global responsibility, differentiation, and an environmental rule of law?
• New sodium intake research and the response of health organizations

 

By Timothy D. McHugh

Tuberculosis (TB) is a disease of poverty and social exclusion with a global impact. It is these underlying truths that are captured in the theme of World TB Day 2014 ‘Reach the three million: a TB test, treatment and cure for all’. Of the nine million cases of tuberculosis each year, one-third does not have access to the necessary TB services to treat them and prevent dissemination of the disease in their communities. The StopTB Partnership is calling for ‘a global effort to find, treat and cure the three million’ and thus eliminate TB as a public health problem. So is the scientific community making sufficient progress to realise this target?

Early diagnosis is a cornerstone of management of the individual and we know that as the disease progresses and the bacterial load and severity of disease increase, the likelihood of a poor outcome is exacerbated. It is important to distinguish between diagnosis of tuberculosis and detection, which is confirmation of the presence of mycobacteria. Diagnosis for the three million (and many more) is largely dependent on the clinical expertise of the healthcare worker, with minimal input from technology. Whereas detection requires input from microbiological services and the principal tool in this area is sputum smear microscopy. A sputum sample with no evidence of acid fast bacilli is the accepted predictor of low risk of transmission, and so early application is critical in the management pathway. With improvements such as the auramine stain and LED fluorescent microscopy, the smear remains a cost effective component of TB screening programmes. The emergence of multi-drug resistant tuberculosis has accentuated the need for prompt confirmation of drug susceptibility and this is where molecular tools have potential impact. The WHO supported roll out of GeneXpert in resource poor settings is going ahead and we are seeing change in practice, but it is too soon to determine the public health impact of this innovation. The challenge for microbiology is not to get drawn into a ‘one size fits all’ solution. In many settings, the low technology, low cost and rapid screening of smears serves to break the chain of transmission of drug sensitive tuberculosis. Whereas, in areas of high endemicity of drug resistant TB, such as South Africa, an equally fast indication of drug resistance is essential.

Photo by WHO/Jean Cheung

Diagnosis leads to treatment. TB is curable but treatment regimens are long, toxic and complex to deliver. Following the stakeholders meeting in Cape Town in 2000 there has been a major effort to open up the drug development pipeline. There are two aspects to this, firstly new agents and secondly clinical trials. There is a new enthusiasm for exploring new compounds with action against TB and the publication of the whole genome of Mycobacterium tuberculosis allowed the interrogation of its biochemistry, opening the door for medicinal chemists to contribute their expertise. The development of MDRTB has led us to reconsider compounds previously excluded as too toxic or too difficult to administer; these drugs, such as PAS and thioridazene, are now being re-visited or forming the basis of fresh iterations of chemical screening programmes. After 30 years of no new drugs for TB treatment, two phase 3 trials (RIFAQUIN and OFLATUB) were reported in 2013 and a third (REMoxTB) is expected to report shortly. These studies have shaken things up. They each have potential to make improvements in TB treatment. However, it could be argued that their real benefit lies in the development of a network of facilities capable of undertaking TB clinical trials, as exemplified by the Global Alliance for TB Drug Development and the EDCTP funded PanACEA consortium, and their contribution to the active debate about how to efficiently deliver clinical trials that have a real impact on individuals and populations. We are now looking outside the world of TB and to, for example, cancer trial methodology for innovations such as the multi-arm multi-stage (MAMS) approach. A significant challenge here is to convert the results of studies undertaken, with the aim of full regulatory approval, into the rather more complex environment of programmatic delivery.

The host-pathogen interaction for M. tuberculosis is manifest in the pathology of tuberculosis and has proven to be a fruitful area of immunological research. This, together with the (variable) success of BCG vaccination, has led us to the reasonable expectation of a vaccine for control of tuberculosis. There has been much innovation in this area and new studies are in the pipeline. The quest for immunological markers of disease continues. Useful diagnostic tools for latency have been developed in the shape of IGRA tests (Tuberculosis: Diagnosis and Treatment), but, more importantly, recent advances lead us to the idea that we may be able to define a host response signature to tuberculosis. If successful, this approach may allow us to select those patients for whom a shorter course of therapy is adequate. From the UK MRC studies it was clear that as many as 80% of patients would be cured with a four-month regimen; the difficulty was that they could not be identified in advance or during treatment. A host response biomarker may well enable us to address this issue.

M. tuberculosis is a fascinating organism with many features of its biology that are distinct from other bacteria. For this reason the TB research community has become rather insular, not necessarily drawing on the experience from the wider bacteriology community. This was further exacerbated by the apparent fall in incidence of TB through the 1960s and 70s. Complacency is the term that comes to mind. Despite the commitment of groups such as those led by Mitchison and Grossett, there has been very little innovation in detection and diagnosis, and no new drug introduced to first line treatment after the 1960s. The declaration by WHO of TB as a global health emergency alerted us to the need for new ideas and new tools to meet this challenge. Twenty years down the line, we have rolled out new diagnostics and a new drugs pipeline that flows with the first phase 3 trials reporting shortly. Similarly, innovation in vaccine design and application moves forward and importantly our understanding of operational and behavioural aspects of controlling TB increases. However, we must not become complacent again. M. tuberculosis is not just an academic challenge and as long as the three million exist, we need to focus all our knowledge to achieve a TB test, treatment and cure for all.

Timothy D. McHugh is Professor of Medical Microbiology at the Centre for Clinical Microbiology, University College London. This is an adapted version of Professor McHugh’s commentary for the Transactions of the Royal Society of Tropical Medicine and Hygiene.

The Transactions of the Royal Society of Tropical Medicine and Hygiene publishes authoritative and impactful original, peer-reviewed articles and reviews on all aspects of tropical medicine.

Subscribe to the OUPblog via email or RSS.
Subscribe to only health and medicine articles on the OUPblog via email or RSS.
Image credit: From the TB in Brazil series by WHO/Jean Cheung. Via the Stop TB Partnership.

The post World TB Day 2014: Reach the three million appeared first on OUPblog.

        

Related Stories

• Will caloric restriction help you live longer?
• Fluoridation of drinking water supplies: tapping into the debate
• What Coke’s cocaine problem can tell us about Coca-Cola Capitalism