Introducing the Research Resource Identification Initiative at PLOS Biology & PLOS Genetics

Reproducibility is one of the holy grails of effective, open biomedical literature. But too often resources (e.g. model organisms, software, antibodies) are not reported with sufficient detail to ensure others can replicate or expand upon the results. Today sees PLOS Biology and PLOS Genetics linking in with an exciting pilot study using the principles set out by a Force11 group, the Research Resource Identification Initiative (#RII). Through the use of unique Resource Identifiers (RRIDs), authors will be able to cite the resources that they use in their manuscripts. This initiative will be completely optional for PLOS authors.  We strongly encourage our PLOS Biology and PLOS Genetics authors to use these RRIDs though wherever possible to identify their model organisms, antibodies or tools; use standard RRIDs that exist in the RRID portal, or create new ones as needed if there isn’t one already. You then simply add your RRIDs to the text of your manuscript; at their first mention (usually the materials and methods section) and we encourage that you add a separate section at the end of the manuscript if you have a longer list of accession numbers. Information can now be found on RRIDs here for PLOS Biology and here for PLOS Genetics

 

How exactly do RRIDs work? The Resource Identification Initiative has three criteria for RRIDs:

  1. Machine readable
  2. Free to generate and access
  3. Consistent across publishers and journals

Right now the feasibility of the system is being tested using three categories of resources – model organisms (mice, zebrafish, and flies), antibodies and tools (i.e. software and databases). Finding or creating the appropriate RRID for your resource couldn’t be easier. A Resource Identification Portal has been created where you can search across different databases, such as The Antibody Registry. Once you have found your resource, you can use a “Cite this” button to be shown the proper citation to insert into your manuscript. For example: Model organism:  “Subjects in this study were Fgf9Eks/Fgf9+ mice (RRID:  MGI:3840442)”.

 

What if my resource doesn’t exist in the database? The Resource Identification Portal allows you to make new entries using the “Add a Resource” option on their homepage. This makes it very easy to generate a new RRID.

 

The Research Identification Initiative so far: This project was an outcome of a meeting held at NIH on June 26th, 2013. A diverse range of journals and publishers are on board with the project – for example Journal of Neuroscience, F1000 Research, Peer J, Nature and Mendeley. By the end of 2014, over 200 papers contained RRIDs. Publications currently reporting RRIDs can be found in Google Scholar or PubMed.

 

If you’re wondering what is the value? Imagine that you’re evaluating what antibody to use, if you can easily track all papers that have used various antibodies previously, you can assess how well the antibody works in others’ hands in different scenarios, and thus be better able to choose which one to use for your study. Or, if you have generated an antibody and made it freely available, you’ll be able to see how frequently it is used by others, and to gain proper recognition via RRID citations for your materials.

 

We hope that this initiative is successful in helping to promote reproducible science. The possible benefits to authors also seem great – including saving time looking for reagents and tools and eventually being able to aggregate and compare findings on a particular animal model.

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This week in PLOS Biology

In this bumper week for PLOS Biology, you can read about bat navigation, transmission of longevity, new neurons for old brains, how yeast anticipate change, a serious downside of illegal drug laws, and how to prioritise conservation efforts.

 

Why Do Bats Fly Differently in Light Versus Dark?

Image credit: Jens Rydell

Image credit: Jens Rydell

Bats are extremely skilful aviators that can manoeuvre accurately using either echolocation or vision. A model of animal flight guidance by Nadav Bar, Yossi Yovel & colleague suggests that bats use estimates of angular velocity and time-integrated sensory information to find their targets, and explains why bats fly straighter in the light than in the dark.

 

Yeast Longevity is Transmissible

Though calorie restriction has long been known to extend lifespan and healthspan in multiple model organisms, the intrinsic mechanisms remain unclear. In a new research paper by Szu-Chieh Mei & Charles Brenner, substances secreted by calorie-restricted yeast are found to induce longer life in other yeast cells, suggesting that intercellular communication is a component of this phenomenon, even in a single-celled organism.

 

Adult Neurogenesis: Are Humans like Rodents?

This new essay by Aurélie Ernst & Jonas Frisén discusses recent work on the birth of new neurons in the human adult brain, examining how it compares to that in other mammals. Although the rates of production of new neurons are the same, humans lack neurogenesis in the olfactory bulb, but show neurogenesis in the striatum. The authors explore the evolutionary changes that may have led to these differences and speculate about the function of adult neurogenesis in humans (particularly striatal neurogenesis), addressing the possibility of taking advantage of neurogenesis for therapeutic purposes (especially in disorders that can affect the striatum, such as Huntington’s disease, Parkinson’s, and stroke).

 

Strategies for Anticipating Change

Image credit: Flickr user Reza

Image credit: Flickr user Reza

Free-living microbes have a challenging existence, entirely beholden to the vagaries of their environment. However, two studies on the unicellular yeast Saccharomyces cerevisiae show that it is sometimes beneficial to anticipate change, and evolution can capitalise on this. Both studies – one by Jue Wang, Michael Springer and colleagues, and one by Ophelia Venturelli, Hana El-Samad and colleagues – look at the way in which yeast cope when faced with a mixture of sugars (imagine rotting fruit lying on the grass in an orchard), one of which is preferred over the other. The yeast consume the preferred sugar (glucose, say), but at some point must decide to make the costly switch to being able to metabolise the less preferred nutrient (galactose). The first paper shows that yeast turn on genes needed for galactose hours before the glucose runs out, but the degree of anticipation varies between wild strains, with each strategy subject to distinct trade-offs. The second paper shows that even within a population of genetically identical yeast, a subset of individuals gambles on change by activating genes pre-emptively.

 

Illegal Drugs Laws: Blocking Research for 50 Years  

Victor

Image credit: Flickr user Victor

Did you know that heroine is a Schedule 2 drug, whereas cannabis is a Schedule 1 drug in the UK? In a passionate new Perspective, David Nutt describes how the laws on illegal drugs have stifled research and development of treatments for brain disorders for more than 50 years. Research on ‘illegal’ drugs before they were made illegal clearly showed therapeutic potential that has never been able to be realised. Here, the author makes concrete suggestions on how to clear these obstacles to research.

 

Conservation Priorities: Restoration? Protection? Both?

Roberto Verzo

Image credit: Flickr user Roberto Verzo

When it comes to habitat conservation, surely prevention is better than cure; we should protect forests as national parks rather than plant new trees, shouldn’t we? A new research article by Hugh Possingham, Michael Bode & Carissa Klein uses a modelling approach to address the question of when we should prioritise protection and restoration strategies. For their two case studies, they found that sometimes restoration is more cost-effective than habitat protection – dependent on the relative costs of the two actions, the rate of habitat loss and the time lag between restored habitat being as useful as intact habitat for securing species and ecosystem services.

 

 

Category: Biology, Climate, Debate, Ecology, Environment, Evolution, Microbiology, Neuroscience, PLOS Biology, Policy, Research | Leave a comment

This Week in PLOS Biology

In PLOS Biology this week, you can read about the the next 10 years of microbiome research, low-cost antimicrobial screening as an educational tool, and a potential new diabetes drug.

 

Transmission and Control of Ebola Virus Disease

Following on from last week’s modelling paper on Ebola in Liberia, you can read a Primer by Gerardo Chowell & Hiroshi Nishiura, which gives more information on the challenges of characterising this disease, and sets the research article in context.

 

Where next for microbiome research?

Image credit: Flickr user Filip Goč

Image credit: Flickr user Filip Goč

The last decade has seen a staggering transformation in our knowledge of microbial communities. In this unique Perspective article, Matt Waldor draws together seven short pieces in which diverse authors speculate as to what the next ten years might hold in store. Topics covered include food, agriculture and the microbiome, synthetic biology, and microbiome evolution.

 

Learning through Antimicrobials

Eucalyptus trees supply one of the antimicrobials tested (Image credit: Eug, Wikimedia Commons.)

Eucalyptus trees supply one of the antimicrobials tested (Image credit: Eug, Wikimedia Commons.)

Antibiotic resistance is a major worldwide public health issue. Increasing antibiotic resistance and the decline in new ones being approved motivates the search for novel antimicrobial agents, especially from natural sources. A new community page by Karishma Kaushik, Vernita Gordon & colleagues describes their hands-on experimental module aimed at young scientists from developing countries. They learn cutting-edge science in physical, chemical and biological systems that can be used to help the search for new antimicrobial agents (including those from plants like eucalyptus – pictured).

 

Targeting Diabetes: A Selective Epac2 Agonist

Two cAMP analogues (Image credit: Holger Rehmann)

Two cAMP analogues (Image credit: Holger Rehmann)

cAMP is a small molecule produced by cells that activates proteins involved in a wide range of biological processes, including olfaction, regulation of gene expression, insulin secretion, and many others. A new research article by Frank Schwede, Holger Rehmann & colleagues focuses on insulin secretion by the β-cells of the pancreas. They designed a cAMP analogue that specifically only activates Epac2, one of the cAMP-responsive proteins in the signalling cascade. That such selective targeting is therefore possible may open up new options for treatment of diabetes.

 

 

 

Category: Bioinformatics, Biology, Cell signalling, Computational biology, Education, Evolution, Microbiology, PLOS Biology, Research | Leave a comment

This week in PLOS Biology

In PLOS Biology this week you can read about modelling Ebola containment measures, a conceptual framework for IPBES, and new insights into how the injectisome works.

 

Fighting Ebola in Liberia

14712446017_fbcd9d9547_o

Image credit: NIAID, Flickr

In 2014, a major epidemic of human Ebola virus emerged in West Africa. There are still key questions about the path to containment – the relative importance of transmission under medical care versus community-acquired infection, how much hospital capacity must increase and which interventions will be most effective? In a new paper published this week, John Drake, Andrew Park and colleagues use a novel modelling approach to attempt to assess the impact of health care interventions on the current Ebola epidemic in Liberia. Their model is multi-branching and incorporates the impacts of changes in behaviour on potential transmission scenarios. Projections based on up-to-date data suggest that 85% hospitalisation rates have the potential to end the outbreak by June 2015. Also read this blog post about how we expedited publication of this article, and (update Jan 21st) – we just published a great Primer by Gerardo Chowell and Hiroshi Nishiura that sets this study in context.

 

Nature’s Benefits to People – A Conceptual Framework for IPBES

The Intergovernmental Platform on Biodiversity & Ecosystem Services (IPBES) came about in April 2012, as a unified group for reviewing, assessing and synthesizing knowledge gathered on biodiversity and ecosystem services. In a new Community Page this week, Sandra Diáz, Anne Larigauderie & colleagues set out the conceptual framework for IPBES – a simplified model of the interactions between nature and people.

 

A Dynamic Role for the Injectisome’s C-Ring

Credit: doi:10.1371/journal.pbio.1002039

Credit: doi:10.1371/journal.pbio.1002039

The type III secretion system, also known as the injectisome, is a key virulence factor in many gram-negative bacteria, responsible for the injection of bacterial proteins directly into host cells. It shares many attributes with its evolutionary cousin, the bacteria flagellum. However, the function of the injectisome’s cytosolic C-ring, whose flagellar counterpart determines switching of rotational direction, has remained enigmatic. New research by Andreas Diepold, Judith Armitage & colleagues used fluorescently tagged protein subunits to allow them to analyse its behaviour, revealing that the cytosolic C-ring structure has a dynamic relationship to the rest of the complex — suggestive of a role in regulating the secretion of effectors by the injectisome.

 

Category: Biology, Disease, Ecology, Environment, Microbiology, Policy, Research | Leave a comment

Publishing to Keep up with Ebola

Image credit: NIAID, Flickr

Ebola viruses (green) emerge from a cell. Image credit: NIAID, Flickr

As you read this, thread-like viruses less than one micron in length are spreading through human populations in West Africa, taking lives, wrecking communities and generally creating havoc in the countries affected. Infection with the Ebola virus results in an appalling death in about half of all cases within a few weeks, and transmission rates are high, cruelly exploiting contact with the dead or dying. The death toll stands at more 8,235, from the initial outbreak in Dec 2013 up to data available on Jan 4th 2015.

Clearly this was no time for hanging around, and when we received a manuscript that described a new model of Ebola virus transmission, with potentially immediate implications for the management of the current Ebola outbreak, we were concerned about the conflict between responsible high-quality publishing and the pressing need to inform the ongoing ground-fight against the virus.

We straightaway asked the authors to deposit their manuscript in a pre-print server so that it would be immediately available to the public while we put it through the peer-review process. The reviewers returned their comments very rapidly, but several expressed concerns about the possibility of delivering a timely publication.

The timeliness problem arose because the manuscript uses real-life data from medical units in Liberia, and generates projections about how the Ebola outbreak will respond to various changes in clinical management and public behaviour (see the images below). Both the data inputs and the projected outputs are extremely time-sensitive, and the normal publication process ran the risk of delivering a paper that had already been rendered obsolete by the march of events on the ground.

After some editorial heart-searching as to whether it was fair to the authors to pursue a further round of revision and review at PLOS Biology, we decided that we would continue to consider the paper but only if we could expedite publication of the most up-to-date version possible.

The obvious way to do this was as a blog post, a trail already blazed by one of our sister journals, PLOS Neglected Tropical Diseases – also with an Ebola-related paper. However, luck was on our side, as that very week saw the introduction of a new production pipeline at PLOS that promised a greater speed to publication of fully typeset, copy-edited and proof-read papers.

Drake et al's projections through June 2015 of the consequences of the status quo (top) versus 85% hospitalisation (bottom). Credit: 10.1371/journal.pbio.1002056

Drake et al’s projections through June 2015 of the consequences of the status quo (top) versus 85% hospitalisation (bottom). Credit: 10.1371/journal.pbio.1002056

The academic editor was happy that if he could check the final updated projections and we could publish with a couple of weeks then a meaningful – and potentially useful – publication was at least in principle possible. The expedited paper has just been published, almost exactly three weeks later (holidays aren’t the best conditions under which to roll out a brand-new production system). One step closer to the day when the printing press can out-run the virus.

Update Jan 21st – we just published a great Primer by Gerardo Chowell and Hiroshi Nishiura that sets this study in context.

 

ResearchBlogging.orgDrake JM, Kaul RB, Alexander LW, O’Regan SM, Kramer AM, Pulliam JT, Ferrari MJ, Park AW. (2015). Ebola Cases and Health System Demand in Liberia. PLoS Biology, 13 (1) : 10.1371/journal.pbio.1002056

 

Chowell G, Nishiura H. (2015). Characterizing the Transmission Dynamics and Control of Ebola Virus Disease. PLoS Biology, 13 (1) : 10.1371/journal.pbio.1002057

 

Category: Biology, Computational biology, Disease, Infectious disease, Open access, PLOS Biology, Publishing | 3 Comments

This week in PLOS Biology

In PLOS Biology this week you can read about the perception and self-regulation of paina computational model of operant learning and improving the computer-friendliness of phenotypic data.

 

Two Parallel Pathways to Pain

 Image credit: 10.1371/journal.pbio.1002036


Image credit: 10.1371/journal.pbio.1002036

Understanding how pain is processed in the brain is a controversial area of neuroscience, because there doesn’t seem to be a single ‘‘pain cortex’’ that directly codes the subjective perception of pain. Although we’ve known for some time that we can self-regulate pain we experience, it is unclear which circuits underpin this. Choong-Wan Woo, Tor Wager & colleagues used fMRI to show that two distinct parallel neural systems independently contribute to our overall experience of pain — separately modulated by noxious input and by cognitive self-regulation. Read more in the accompanying Primer.

 

How Animals Select Actions with Rewarding Outcomes

A key component of survival is learning to associate rewarding outcomes with specific actions, such as searching for food. Actions are represented in the cortex, and rewarding outcomes activate neurons that release dopamine. These signals are then sent to the striatum— the input station for a collection of brain structures called the basal ganglia, which play an important role in action selection. A new paper by Kevin Gurney, Mark Humphries & Peter Redgrave uses a computational model that shows how the brain’s internal signal for outcome changes the strength of neuronal connections, leading to the selection of rewarded actions and the suppression of unrewarded ones. Read more in the accompanying Synopsis.

 

Computing Phenotype

Image credit: doi:10.1371/journal.pbio.1002033.g001

Image credit:
doi:10.1371/journal.
pbio.1002033.g001

 

Phenotypic data (i.e. observable traits such as anatomy and behaviour) represent much of what we know about life and drive much of life science research. A new Perspective by Andrew Deans & colleagues argues that the current form in which phenotypic data are recorded inhibits their productive use. Their article asks us to imagine a future in which we could compute across phenotype data as easily as genomic data, calls for efforts to realize this vision, and discusses the potential benefits.

 

 

 

Category: Bioinformatics, Biology, Computational biology, Neuroscience, PLOS Biology, Systems biology | Leave a comment

Media response: forecasting diseases using Wikipedia

“It’s a perfect mix of exciting science, modern everyday technology, and public health.” Dr Marcel Salathé

Many of us use Wikipedia solely as an online encyclopedia but we need to think bigger – there’s a huge amount to be learnt from the way people interact with sites like this. A recent PLOS Computational Biology article explores this idea in a way that has caught the public’s imagination.

According to recently published research, analysing page views of Wikipedia articles could make it possible to monitor and forecast diseases around the globe.

Analysing page views of Wikipedia articles could make it possible to monitor and forecast diseases around the globe.  Image Credit: Stephen Ritchie / Flickr

Analysing page views of Wikipedia articles could make it possible to monitor and forecast diseases around the globe.
Image Credit: Stephen Ritchie / Flickr

Dr Sara Del Valle and her team from Los Alamos National Laboratory successfully monitored influenza outbreaks in the United States, Poland, Japan and Thailand, dengue fever in Brazil and Thailand, and tuberculosis in China and Thailand.

The team was able to forecast all but one of these outbreaks (tuberculosis in China) at least 28 days in advance. The results suggest that people start searching for disease-related information on Wikipedia before they seek medical attention. However, the way the Wikipedia data is currently released limits their ability to geo-locate the disease-related information.

The paper outlined several shortcomings in regards to transparency, openness, and reproducibility that need to be overcome before an operational, global disease monitoring and forecasting system can be built. Del Valle said, “We are currently working with the Wikimedia Foundation, the operators of Wikipedia, to develop a public, geo-located form of the access logs which preserves reader and editor privacy.”

 

In the media:

Since the paper’s publication in November 2014 the article has gained much media attention. The paper was notably reported around the world, in outlets such as The Washington Post, Le Monde, BBC, Los Angeles Times, Agerpres, Süddeutsche.de, The Atlantic,  and Popular Mechanics. The team further participated in a Reddit “Ask Me Anything” (AMA) which received over 2944 “upvotes”, 483 comments, and landed on the front page.

The crux of public interest is channelled through social media. Looking at the stats alone the article has been tweeted over 130 times, mentioned on Facebook over 180 times, had a BuzzFeed article and the paper has since received its first Wikipedia citation.

Simply put, within one month the article has gained over 19,000 views. We therefore asked authors and editor for their thoughts about the high volume of public interest surrounding this paper.

 

The authors told us:

“We were very surprised by the level of public interest in our work,” said Nicholas Generous, lead author of the article. “While we thought the topic was interesting enough that a few outlets would pick it up, we didn’t expect anything like what actually happened. Having the opportunity to directly interact with the public on a topic they were genuinely interested in was extremely rewarding.”

Sara Del Valle and her team Image Credit: Sara Del Valle

Sara Del Valle and her team
Image Credit: Sara Del Valle

 

Sara Del Valle: “We were overwhelmed by the media response to our paper. We are thrilled that the public can connect with what we are doing and hope to continue bringing new ideas that can transform public health. Engaging the public in scientific endeavors is what really makes our work exciting.”

 

The editor told us:

The editor, Dr Marcel Salathé from the Center for Infectious Disease Dynamics at Penn State University, says the paper is part of a new, rapidly growing field called Digital Epidemiology.

“With the unprecedented growth of global access to the internet, we are only at the beginning of what will be a major shift in epidemiology.

“I’m excited that PLOS Computational Biology takes a leading role in publishing research in this area. Open Access will play a key part to rapidly establish standards and best practices, as well as to foster a public debate around the ethical challenges facing the field. As such, I’m both thrilled and not very surprised at the same time to see that the paper has attracted so much media attention. It’s a perfect mix of exciting science, modern everyday technology, and public health.”

Category: Biology, Computational biology, Data, Disease, Infectious disease, Open access, PLOS Computational Biology | Tagged , , | 2 Comments

This week in PLOS Biology

In PLOS Biology this week you can read about wolves in Yellowstone National Park, regulation of hair growth, how proteins evolve new RNA-binding functions and the regulation of heat-shock response by histone demethylation.

 

Yellowstone Wolves and their Effects on Natural Systems

Image credit: Daniel Stahler/National Park Service (NPS) journal.pbio.1002025.g001

Image credit: Daniel Stahler/National Park Service (NPS) journal.pbio.1002025.g001

Wolves were re-introduced to Yellowstone National Park in 1995 and 1996 after a 70-year absence. Since then, wolves have had effects on Yellowstone that ripple across the entire structure of the food web that defines biodiversity in the Northern Rockies ecosystem. In a new essay, Andy Dobson discusses the different ecological interpretations of the effects wolves have had on the ecosystem. He argues that ecology in general needs more ecosystem-level studies of species interactions, which ultimately drive levels of biodiversity. A new generation of scientists who can grapple with the vast complexities of these questions is needed.

 

Hair Growth is Regulated by Macrophages

doi:10.1371/journal.pbio.1002002.g004

doi:10.1371/journal.pbio.1002002.g004

The cyclic life of hair follicles consists of recurring phases of growth, decay, and rest. Using a mouse model, Donatello Castellana, Ralk Paus & Mirna Perez-Moreno report that macrophages in the skin signal to skin stem cells via Wnt ligands in the resting phase of the follicle life cycle. This tale of niche cells modulating stem cell behaviour could be relevant for the development of technologies with potential applications in regeneration, aging, and cancer.

 

From tRNA Loading to mRNA Splicing Via Promiscuity

Image credit: doi:10.1371/journal.pbio.1002028.g003

Image credit: doi:10.1371/journal.pbio.1002028.g003

New research by Lilian Lamech, Anna Mallam & Alan Lambowitz addresses the broad question of how proteins evolve new RNA-binding functions. Specifically, the way in which a fungal mitochondrial tyrosyl-tRNA synthetase (mtTyrRS) has evolved to promote the splicing of group I introns. Using small-angle X-ray scattering (SAXS) and biochemical assays, the study supports the theory of pre-adaptive or constructive neutral evolution, and identify a previously unappreciated role for non-specific interactions in the evolution of RNA-binding proteins and other multi-subunit protein and ribonucleoprotein complexes.

 

Recruiting Histone Demethylase to Target Genes

The methylation state of the histone subunits of nucleosomes regulates gene transcription, but the delicate balance of counteracting methyl-transferases and demethylases is crucial for establishment and maintenance of appropriate methylation. This paper by Mo-bin Cheng, Yan Zhang, Ye Zhang, Yu-fei Shen & colleagues reports how specific phosphorylation of the histone demethylase KDM3A by the kinase MSK1 allows it to be  recruited to promoters by Stat1 in response to heat shock, permitting the coordinated expression of many genes in human cells.

 

Category: Biology, Cell biology, Cell signalling, Developmental biology, Ecology, Epigenetics, Evolution, Molecular biology, PLOS Biology, Regeneration, Research | 1 Comment

Deep Ancestry: A source of inspiration by Michael Harris

The second of our Deep Reads blog series follows the PLOS Genetics Deep Reads article, “Strands in the History of Molecular Genetics”, published yesterday. Deep Ancestry: A source of inspiration” was written by Michael Harris, a PhD student at the University of Cambridge. His current research is focused on the use of optogenetics in cell signalling. When not in the lab he can be found cooking, trekking and keeping up on his science books.

I’ve wanted to be a scientist since I was 8 years old. Being somewhat dyslexic, I used to struggle a lot with reading, but it was always the science books that engaged me: Are We Hardwired: the Role of Genes in Human Behavior (William R. Clark); Endless Forms Most Beautiful: The New Science of Evo Devo (Sean B. Carroll); Stiff: The Curious Lives of Human Cadavers (Mary Roach); the list goes on. I couldn’t get enough of them! There is, however, one book that stands out above the rest in my mind as driving me toward becoming a geneticist, Deep Ancestry: Inside the Genographic Project by Spencer Wells. I was 17 when I read it, and the experience influenced my decision to undertake a degree in Genetics with Japanese Language & Linguistics at the University of Manchester.

In this book, Wells describes how DNA can be used to track patterns of human migration. He explains how, through the use of parsimony, small changes in sequence between distinct groups of peoples can be compared to generate a kind of family tree, and model past migrations and human history.  This book also introduces basic population genetics and molecular biology concepts in an engaging and relevant context (even if some of the claims are now a little outdated).  I can attest to how much reading this book helped me during the first year of my undergraduate degree!

pic1

Xunantunich, Belize – taking in the view after completing the field course.
Image credit: Michael Harris

Despite outlining how small mutations in the genome can be used to elucidate when distinct human populations diverged from one another, Wells emphasises that the goal of the Genographic Project is not to highlight the differences between people, but to illustrate that we are all linked together by our ancestry. He des this by telling the stories of five key people that he met during the course of his research, and explaining how the sequencing of their DNA helped provide important evidence for a particular course of human migrations joining us all together.

Researchers from the Genographic team travelled the world collecting DNA samples from indigenous populations at far flung places across the globe. As a nerdy British teenager growing up in Japan and a devoted member of my school’s Biology Club, I could scarcely imagine more exciting research! Travelling the world, interacting with all sorts of amazing cultures, and ultimately helping solve one of mankind’s greatest philosophical musings: where do we come from? I was sold! I wanted so badly to be those researchers, out scouring the globe, piecing together the puzzle of our past. And to an extent I’ve lived this dream.

In 2010, I was selected to work on a field course in conservation genetics in Belize. Not quite human population genetics, but I wasn’t going to turn down this opportunity! And while I was up to my chest in a rainforest pond at two in the morning gathering data, I just had to think to myself with a smile, “Well, this is what you wanted…” To me this is the embodiment of science; it’s about discovery and adventure, and that constant desire for knowledge and understanding, something that I think Deep Ancestry captures beautifully. Wells enthusiastically recounts stories of accomplishments in the Genographic Project and conveys the true spirit of scientific research. This is something that I continue to strive for, whether I’m in the field studying 100-year-old mahogany trees or at the microscope watching fluorescent proteins being tracked through the cytoplasm of a cell. I can’t help but feel a constant sense of awe and wonder at the natural world in everything that I do.

Wells also gives a good account of the multidisciplinary nature of research. It is by collaborating with linguists, climatologists, historians, archeologists and many others that he and his team are able to build a more accurate picture of the patterns of human migration. This is something else that I’ve also tried to incorporate into my scientific career. Though I’ve not lost my passion for genetics, I have now begun a PhD at Cambridge University in Immunology & Infectious Disease; that is, after being a plant scientist, a developmental biologist, a parasitologist, and a pharmacologist. I love genetics and I also love science as a whole, with all of its overlap and interconnectedness.

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The Eagle, Cambridge – getting more ‘inspiration’ at the pub made famous by Watson and Crick.
Image credit: Michael Harris

Deep Ancestry by Spencer Wells, though the most influential for me, is just one book among many that has helped shape me into the scientist that I am today. There is no doubt in my mind that reading about great scientists from the past (or present) can help inspire the current generation of researchers. As the Confucian saying goes: “No matter how busy you may think you are, you must find time for reading, or surrender yourself to self-chosen ignorance.”

 

Category: Blog, Books, Community, Ecology, Evolution, Genetics, Genomics, PLOS Genetics | Tagged , , , , , | Leave a comment

This week in PLOS Biology

In PLOS Biology this week you can read about life without microbes, host-parasite coevolution, the temporal precision of distinguishing odours and how viruses package their genomes.

 

Life in a World without Microbes

Credit: Hieronymus Bosch

Credit: Hieronymus Bosch

According to Louis Pasteur, “Life would not long remain possible in the absence of microbes.” Or would it? In a new Perspective, Jack Gilbert and Josh Neufeld explore the challenges of a microbe-free existence. In doing so they hope to promote discussion about the value of microbial services supporting life on this planet. They explore the human gut microbiome, the scenario of a world without Bacteria and Archaea, and conclude with the implications of a world without all microbes, including microbial eukaryotes and viruses.

 

Parasitism Drives the Evolution of Complexity

It is obvious to any observer that evolution often proceeds towards increasing complexity. But when and why is greater complexity favoured? One hypothesis is that antagonistic coevolution between hosts and parasites drives this process by promoting evolutionary ‘arms races.’ As it would be incredibly difficult to examine this kind of evolution using conventional experiments, instead Luis Zaman, Charles Ofria & colleagues used the digital evolution of self-replicating computer programs in a scenario where hosts and parasites compete for processing power; their results show that coevolution promotes complexity and evolvability. Note that PLOS Biology featured a paper using a related digital evolution approach back in May

 

Smellyvision – Mice Perceive Odours with a Resolution of 13 Milliseconds

Different odours evoke different spatial patterns of activity in the odour-processing regions of the brain. For example, the timing of neuronal activity in a brain region called the olfactory bulb, relative to when an animal sniffs, conveys important information about odours. In a study published this week in PLOS Biology, Michelle Rebello, Justus Verhagen and collaborators provide evidence that the mammalian olfactory system is capable of very high rates of transmission of transient information. Using an innovative optogenetics approach, they found that mice can precisely discriminate virtual “odour movies” associated with patterns of neuronal activity that differed by as little as 13 ms. Read more in the synopsis.

 

Viral DNA-Packing Machine in the Corner

Credit: 10.1371/journal.pbio.1002024

Credit: 10.1371/journal.pbio.1002024

Chuan Hong, Wah Chiu & colleagues have used cryo-electronmicroscopy and modelling to tease apart how PRD1, a dsDNA membrane-containing virus, packages its genome. They characterise a unique vertex of this icosahedral virus, identifying the structure and function of a complex of proteins that forms a DNA-packaging motor and a transmembrane conduit which together serve to fill the viral particle with its genome. Check out the following stunning movies:

 

Movie S1: http://youtu.be/6daQvMfUnAw

Movie S2: http://youtu.be/g554Q0kCYzI

Movie S3: http://youtu.be/WhzvuL9lgTw

 

Category: Biology, Computational biology, Evolution, Microbiology, Molecular biology, Neuroscience, Policy, Research, Resources | Leave a comment